- A neural substrate of prediction and reward
Institute of Physiology, University of Fribourg, CH 1700 Fribourg, Switzerland
Science 275:1593-9. 1997
..Taken together, these findings can be understood through quantitative theories of adaptive optimizing control...
- GROMACS: fast, flexible, and free
David van der Spoel
Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, S 75124 Uppsala, Sweden
J Comput Chem 26:1701-18. 2005
..It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org...
- Mapping short DNA sequencing reads and calling variants using mapping quality scores
The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
Genome Res 18:1851-8. 2008
..Both read mapping and genotype calling are evaluated on simulated data and real data. MAQ is accurate, efficient, versatile, and user-friendly. It is freely available at http://maq.sourceforge.net...
- Scalable molecular dynamics with NAMD
James C Phillips
Beckman Institute, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
J Comput Chem 26:1781-802. 2005
..NAMD is distributed free of charge with source code at www.ks.uiuc.edu...
- A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
LIRMM, CNRS, 161 rue Ada, 34392, Montpellier Cedex 5, France
Syst Biol 52:696-704. 2003
..This new method is implemented in the PHYML program, which is freely available on our web page: http://www.lirmm.fr/w3ifa/MAAS/...
- Prediction of total genetic value using genome-wide dense marker maps
T H Meuwissen
Research Institute of Animal Science and Health, 8200 AB Lelystad, The Netherlands
Genetics 157:1819-29. 2001
..It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval...
- Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies
Department of Molecular Biology, Max Planck Institut für Infektionsbiologie, Schumann Strasse 21 22, 10117 Berlin, Germany
Genetics 164:1567-87. 2003
..The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu...
- CHARMM: the biomolecular simulation program
B R Brooks
Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
J Comput Chem 30:1545-614. 2009
..This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983...
- The Amber biomolecular simulation programs
David A Case
Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, CA 92037, USA
J Comput Chem 26:1668-88. 2005
- HyPhy: hypothesis testing using phylogenies
Sergei L Kosakovsky Pond
Antiviral Research Center, University of California San Diego San Diego, CA 92103, USA
Bioinformatics 21:676-9. 2005
..AVAILABILITY: http://www.hyphy.org CONTACT: firstname.lastname@example.org SUPPLEMENTARY INFORMATION: HyPhydocumentation and tutorials are available at http://www.hyphy.org...
- Comparison of multiple Amber force fields and development of improved protein backbone parameters
Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794, USA
Proteins 65:712-25. 2006
..It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides and better accord with experimental NMR relaxation data of test protein systems...
- A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
Department of Zoology, University of Cambridge, Cambridge, England
Mol Biol Evol 18:691-9. 2001
- Efficient methods to compute genomic predictions
P M Vanraden
Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 2350, USA
J Dairy Sci 91:4414-23. 2008
..Actual gains may differ because the simulation did not account for linkage disequilibrium in the base population or selection in subsequent generations...
- RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
Department of Computer Science, Technical University of Munich Boltzmannstrasse 3, D 85748 München, Germany
Bioinformatics 21:456-63. 2005
..Due to the combinatorial and computational complexity the size of trees which can be computed on a Biologist's PC workstation within reasonable time is limited to trees containing approximately 100 taxa...
- A new statistical method for haplotype reconstruction from population data
Department of Statistics, University of Oxford
Am J Hum Genet 68:978-89. 2001
..Furthermore, our algorithm performs well in absolute terms, suggesting that reconstructing haplotypes experimentally or by genotyping additional family members may be an inefficient use of resources...
- Population structure and eigenanalysis
Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
PLoS Genet 2:e190. 2006
..This means that we can predict the dataset size needed to detect structure...
- A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
J Comput Chem 24:1999-2012. 2003
..charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed...
- Rare-variant association testing for sequencing data with the sequence kernel association test
Michael C Wu
Department of Biostatistics, The University of North Carolina at Chapel Hill, 27599, USA
Am J Hum Genet 89:82-93. 2011
..We also provide analytic power and sample-size calculations to help design candidate-gene, whole-exome, and whole-genome sequence association studies...
- A whole-cell computational model predicts phenotype from genotype
Jonathan R Karr
Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA
Cell 150:389-401. 2012
..We conclude that comprehensive whole-cell models can be used to facilitate biological discovery...
- Epidemic spreading in scale-free networks
, , Barcelona, Spain
Phys Rev Lett 86:3200-3. 2001
..This new epidemiological framework rationalizes data of computer viruses and could help in the understanding of other spreading phenomena on communication and social networks...
- Community structure in social and biological networks
Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
Proc Natl Acad Sci U S A 99:7821-6. 2002
..We also apply the method to two networks whose community structure is not well known--a collaboration network and a food web--and find that it detects significant and informative community divisions in both cases...
- Detecting recent positive selection in the human genome from haplotype structure
Pardis C Sabeti
Whitehead Institute MIT Center for Genome Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
Nature 419:832-7. 2002
..More generally, the method could be used to scan the entire genome for evidence of recent positive selection...
- ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
Adam A Margolin
Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
BMC Bioinformatics 7:S7. 2006
..This method uses an information theoretic approach to eliminate the majority of indirect interactions inferred by co-expression methods...
- Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
D Allan Drummond
FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
Cell 134:341-52. 2008
- Functional cartography of complex metabolic networks
NICO and Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
Nature 433:895-900. 2005
..Remarkably, we find that metabolites that participate in only a few reactions but that connect different modules are more conserved than hubs whose links are mostly within a single module...
- COPASI--a COmplex PAthway SImulator
Virginia Bioinformatics Institute, Virginia Tech, Washington St 0477, Blacksburg, VA 24061, USA
Bioinformatics 22:3067-74. 2006
..Therefore, there is a big need for software tools that allow access to diverse simulation and modeling methods as well as support for the usage of these methods...
- Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
Alexander D MacKerell
Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA
J Comput Chem 25:1400-15. 2004
..This extension of the potential energy function is anticipated to facilitate improved treatment of biological macromolecules via MM approaches in general...
- Automated phylogenetic detection of recombination using a genetic algorithm
Sergei L Kosakovsky Pond
Department of Pathology, University of California San Diego, USA
Mol Biol Evol 23:1891-901. 2006
..Finally, we demonstrate that prescreening alignments with our method allows one to analyze recombinant sequences for positive selection...
- The structure of haplotype blocks in the human genome
Stacey B Gabriel
Whitehead MIT Center for Genome Research, Cambridge, MA 02139, USA
Science 296:2225-9. 2002
..Our results provide a foundation for the construction of a haplotype map of the human genome, facilitating comprehensive genetic association studies of human disease...
- PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
Todd J Dolinsky
Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St Louis, 700 S Euclid Ave, Campus Box 8036, St Louis, MO 63110, USA
Nucleic Acids Res 35:W522-5. 2007
..These features are available through a new web interface (http://pdb2pqr.sourceforge.net/), which offers users a wide range of options for PDB file conversion, modification and parameterization...
- Efficiency and cost of economical brain functional networks
Brain Mapping Unit, Department of Psychiatry, Addenbrooke s Hospital, University of Cambridge, Cambridge, United Kingdom
PLoS Comput Biol 3:e17. 2007
- PRODRG: a tool for high-throughput crystallography of protein-ligand complexes
Alexander W Schuttelkopf
Division of Biological Chemistry and Molecular Microbiology, Wellcome Trust Biocentre, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Scotland
Acta Crystallogr D Biol Crystallogr 60:1355-63. 2004
..However, tests with distorted starting coordinates show that PRODRG topologies perform better, both in terms of ligand geometry and of crystallographic R factors...
- Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers
Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica and Instituto Nacional de Bioinformatica, Parc Cientific de Barcelona, Barcelona 08028, Spain
Biophys J 92:3817-29. 2007
..The total simulation time used to validate the force field includes near 1 mus of state-of-the-art molecular dynamics simulations in aqueous solution...
- A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Honggerberg, 8093 Zurich, Switzerland
J Comput Chem 25:1656-76. 2004
..The partial charges were then adjusted to reproduce the hydration free enthalpies in water (53A6). Both parameter sets are fully documented, and the differences between these and previous parameter sets are discussed...
- Computational systems biology
Sony Computer Science Laboratories, Inc, Shinagwa, Tokyo, Japan
Nature 420:206-10. 2002
..Computational systems biology addresses questions fundamental to our understanding of life, yet progress here will lead to practical innovations in medicine, drug discovery and engineering...
- Evaluation of methods for detecting recombination from DNA sequences: computer simulations
Department of Zoology, Brigham Young University, Provo, UT 84602, USA
Proc Natl Acad Sci U S A 98:13757-62. 2001
..Results shown here will provide some guidance in the selection of the most appropriate method/s for the analysis of the particular data at hand...
- Protein homology detection by HMM-HMM comparison
Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, D 72076 Tubingen, Germany
Bioinformatics 21:951-60. 2005
..Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction and evolution...
- The human disease network
Kwang Il Goh
Center for Complex Network Research and Department of Physics, University of Notre Dame, Notre Dame, IN 46556, USA
Proc Natl Acad Sci U S A 104:8685-90. 2007
..A selection-based model explains the observed difference between essential and disease genes and also suggests that diseases caused by somatic mutations should not be peripheral, a prediction we confirm for cancer genes...
- The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
Genomatica, Inc, Bioprocessing Division, 5405 Morehouse Drive, Suite 210, San Diego, CA 92121, USA
Metab Eng 5:264-76. 2003
..These methods also provide an efficient and robust method to calculate the range of flux distributions that can be derived from quantitative fermentation data...
- Crystallography & NMR system: A new software suite for macromolecular structure determination
A T Brunger
The Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA, and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
Acta Crystallogr D Biol Crystallogr 54:905-21. 1998
..User-friendly task-oriented input files are available for nearly all aspects of macromolecular structure determination by X-ray crystallography and solution NMR...
- Bayesian inference of phylogeny and its impact on evolutionary biology
J P Huelsenbeck
Department of Biology, University of Rochester, Rochester, NY 14627, USA
Science 294:2310-4. 2001
- Discovering regulatory and signalling circuits in molecular interaction networks
Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA Institute for Systems Biology, Seattle, WA 98103, USA
Bioinformatics 18:S233-40. 2002
..The method we present here combines a rigorous statistical measure for scoring subnetworks with a search algorithm for identifying subnetworks with high score...
- Multiscale mobility networks and the spatial spreading of infectious diseases
Center for Complex Networks and Systems Research, School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA
Proc Natl Acad Sci U S A 106:21484-9. 2009
..The present approach outlines the possibility for the definition of layered computational approaches where different modeling assumptions and granularities can be used consistently in a unifying multiscale framework...
- The MARTINI force field: coarse grained model for biomolecular simulations
Siewert J Marrink
Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
J Phys Chem B 111:7812-24. 2007
..Application to a bilayer/cholesterol system at various concentrations shows the typical cholesterol condensation effect similar to that observed in all atom representations...
- Defining network topologies that can achieve biochemical adaptation
Center for Theoretical Biology, Peking University, Beijing 100871, China
Cell 138:760-73. 2009
..These design rules provide a framework for functionally classifying complex natural networks and a manual for engineering networks. For a video summary of this article, see the PaperFlick file with the Supplemental Data available online...
- Development and current status of the CHARMM force field for nucleic acids
A D MacKerell
Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 N Pine Street, Baltimore, MD 21201, USA
Biopolymers 56:257-65. 2000
..In addition, it is compatible with the CHARMM force fields for proteins and lipids, allowing for simulation studies of heterogeneous systems...
- MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
Nucleic Acids Res 30:3059-66. 2002
..FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy...
- Extension of the bayesian alphabet for genomic selection
Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, IA 50011, USA
BMC Bioinformatics 12:186. 2011
..The methods were compared in terms of inference of the number of QTL and accuracy of genomic estimated breeding values (GEBVs), using simulated scenarios and real data from North American Holstein bulls...
- Neuronal avalanches in neocortical circuits
John M Beggs
Unit of Neural Network Physiology, Laboratory of Systems Neuroscience, National Institute of Mental Health, Bethesda, Maryland 20892 4075, USA
J Neurosci 23:11167-77. 2003
..In the critical state, the network may satisfy the competing demands of information transmission and network stability...
- Oscillations in NF-kappaB signaling control the dynamics of gene expression
D E Nelson
Centre for Cell Imaging, School of Biological Sciences, Bioscience Research Building, Crown Street, Liverpool, L69 7ZB, UK
Science 306:704-8. 2004
..The functional consequences of NF-kappaB signaling may thus depend on number, period, and amplitude of oscillations...
- Bayes empirical bayes inference of amino acid sites under positive selection
Department of Biology, University College London, London, UK
Mol Biol Evol 22:1107-18. 2005
..The results suggest that in small data sets the new BEB method does not generate false positives as did the old NEB approach, while in large data sets it retains the good power of the NEB approach for inferring positively selected sites...
- Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
Alasdair T R Laurie
School of Biochemistry and Microbiology, University of Leeds, UK
Bioinformatics 21:1908-16. 2005
..Energetically favourable probe sites are clustered according to their spatial proximity and clusters are then ranked according to the sum of interaction energies for sites within each cluster...
- Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
Mol Biol Evol 22:2472-9. 2005
..We applied the new tests to reanalyze several real data sets and used computer simulation to examine the performance of the two tests by examining their false-positive rate, power, and robustness...
- Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
Jeffrey J Gray
Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, J 567 Health Sciences, Box 357350, Seattle, WA 98195, USA
J Mol Biol 331:281-99. 2003
- Testing for an unusual distribution of rare variants
Benjamin M Neale
The Center for Human Genetic Research, Massachusetts General Hospital, Boston, United States of America
PLoS Genet 7:e1001322. 2011
..Through simulations and analysis of case/control data, we demonstrate good power relative to existing methods that assess the burden of rare variants in individuals...
- Robust single-particle tracking in live-cell time-lapse sequences
Department of Cell Biology, The Scripps Research Institute, 10550 N Torrey Pines Rd, La Jolla, California 92037, USA
Nat Methods 5:695-702. 2008
..Both applications indicate the requirement for robust and complete tracking of dense particle fields to dissect the mechanisms of receptor organization at the level of the plasma membrane...
- The second wave of synthetic biology: from modules to systems
Priscilla E M Purnick
Department of Electrical Engineering, Princeton University, Princeton, New Jersey 08544, USA
Nat Rev Mol Cell Biol 10:410-22. 2009
..The ability to create such systems will result in innovative approaches to a wide range of applications, such as bioremediation, sustainable energy production and biomedical therapies...
- A protocol for generating a high-quality genome-scale metabolic reconstruction
Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
Nat Protoc 5:93-121. 2010
..Therefore, this protocol provides a helpful manual for all stages of the reconstruction process...
- A high-resolution human contact network for infectious disease transmission
Department of Biology, Stanford University, Stanford, CA 94305 5020, USA
Proc Natl Acad Sci U S A 107:22020-5. 2010
..Immunization strategies based on contact network data were most effective at high vaccination coverage...
- A methodology for performing global uncertainty and sensitivity analysis in systems biology
Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 0620, USA
J Theor Biol 254:178-96. 2008
- The asynchronous state in cortical circuits
Center for Molecular and Behavioral Neuroscience, Rutgers University, Newark, NJ 07102, USA
Science 327:587-90. 2010
..Our results suggest a reexamination of the sources underlying observed correlations and their functional consequences for information processing...
- Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins
Ana Maria Fernandez-Escamilla
Nat Biotechnol 22:1302-6. 2004
..Furthermore, the algorithm opens the door to a fully automated, sequence-based design strategy to improve the aggregation properties of proteins of scientific or industrial interest...
- New approaches to population stratification in genome-wide association studies
Alkes L Price
Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
Nat Rev Genet 11:459-63. 2010
..Here, we review recent progress on methods that correct for stratification while accounting for these additional complexities...
- Systems biology: a brief overview
Sony Computer Science Laboratories, Inc, 3 14 13 Higashi Gotanda, Shinagawa, Tokyo 141 0022, Japan
Science 295:1662-4. 2002
..However, many breakthroughs in experimental devices, advanced software, and analytical methods are required before the achievements of systems biology can live up to their much-touted potential...
- Parameter estimation in biochemical pathways: a comparison of global optimization methods
Carmen G Moles
Process Engineering Group, Instituto de Investigaciones Marinas CSIC, 36208 Vigo, Spain
Genome Res 13:2467-74. 2003
..Although these stochastic methods cannot guarantee global optimality with certainty, their robustness, plus the fact that in inverse problems they have a known lower bound for the cost function, make them the best available candidates...
- Strategies for containing an emerging influenza pandemic in Southeast Asia
Neil M Ferguson
Department of Infectious Disease Epidemiology, Faculty of Medicine, Imperial College London, St Mary s Campus, Norfolk Place, London W2 1PG, UK
Nature 437:209-14. 2005
..Policy effectiveness depends critically on how quickly clinical cases are diagnosed and the speed with which antiviral drugs can be distributed...
- Scale-free networks provide a unifying framework for the emergence of cooperation
F C Santos
GADGET, Apartado 1329, 1009 001 Lisbon, Portugal
Phys Rev Lett 95:098104. 2005
..Such emergence is shown to be inhibited whenever the correlations between individuals are decreased or removed. These results are shown to apply from very large population sizes down to small communities with nearly 100 individuals...
- Context-specific metabolic networks are consistent with experiments
Scott A Becker
Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
PLoS Comput Biol 4:e1000082. 2008
..This work represents progress towards producing constraint-based models of metabolism that are specific to the conditions where the expression profiling data is available...
- Dendroscope: An interactive viewer for large phylogenetic trees
Daniel H Huson
Center for Bioinformatics Tübingen ZBIT, Eberhard Karls Universitat Tubingen, Sand 14, 72076 Tubingen, Germany
BMC Bioinformatics 8:460. 2007
..Moreover, many programs are difficult to install or are not available for all common operating systems...
- Information-based functional brain mapping
Section on Functional Imaging Methods, Laboratory of Brain and Cognition, National Institute of Mental Health, Building 10, Room 1D80B, 10 Center Drive MSC 1148, Bethesda, MD 20892 1148, USA
Proc Natl Acad Sci U S A 103:3863-8. 2006
- A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
Adam M Feist
Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
Mol Syst Biol 3:121. 2007
..The increased scope and computational capability using this new reconstruction is expected to broaden the spectrum of both basic biology and applied systems biology studies of E. coli metabolism...
- Gene regulatory network inference: data integration in dynamic models-a review
Leibniz Institute for Natural Product Research and Infection Biology Hans Knoell Institute, Jena, Germany
Biosystems 96:86-103. 2009
..The review provides an overview of common modelling schemes and learning algorithms and outlines current challenges in GRN modelling...
- Strategies for mitigating an influenza pandemic
Neil M Ferguson
Department of Infectious Disease Epidemiology, Faculty of Medicine, Imperial College London, St Mary s Campus, Norfolk Place, London W2 1PG, UK
Nature 442:448-52. 2006
..Estimates of policy effectiveness will change if the characteristics of a future pandemic strain differ substantially from those seen in past pandemics...
- CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA
J Comput Chem 31:671-90. 2010
..CGenFF thus makes it possible to perform "all-CHARMM" simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems...
- The normalization model of attention
John H Reynolds
Salk Institute for Biological Studies, La Jolla, CA 92037 1099, USA
Neuron 61:168-85. 2009
- Evolution of indirect reciprocity by image scoring
M A Nowak
Department of Zoology, University of Oxford, UK
Nature 393:573-7. 1998
..We propose that the emergence of indirect reciprocity was a decisive step for the evolution of human societies...
- The transmissibility and control of pandemic influenza A (H1N1) virus
Center for Statistics and Quantitative Infectious Diseases, Fred Hutchinson Cancer Research Center and the University of Washington, Seattle, WA 98109, USA
Science 326:729-33. 2009
..If a vaccine were available soon enough, vaccination of children, followed by adults, reaching 70% overall coverage, in addition to high-risk and essential workforce groups, could mitigate a severe epidemic...
- Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis
Yurii S Aulchenko
Department of Epidemiology and Biostatistics, Erasmus MC, 3000 CA Rotterdam, The Netherlands
Genetics 177:577-85. 2007
..However, there is little or no difference in empirical power of MG and the proposed method. In any scenario, GRAMMAR is much faster than MG and enables rapid analysis of hundreds of thousands of markers...
- Stochastic simulation of chemical kinetics
Daniel T Gillespie
Dan T Gillespie Consulting, Castaic, CA 91384, USA
Annu Rev Phys Chem 58:35-55. 2007
- A fast, powerful method for detecting identity by descent
Brian L Browning
Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98105, USA
Am J Hum Genet 88:173-82. 2011
..This is useful for estimation of relationship and for adjusting for relatedness in association studies. FastIBD is incorporated in the freely available Beagle software package...
- Molecular dynamics and protein function
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 102:6679-85. 2005
..We also describe results for the F(1) ATPase molecular motor and the Src family of signaling proteins as examples of applications of simulations to specific biological systems...
- Predicting quantitative traits with regression models for dense molecular markers and pedigree
Gustavo de Los Campos
Department of Animal Sciences, University of Wisconsin, Madison, Wisconsin 53706, USA
Genetics 182:375-85. 2009
..Results indicate that inclusion of markers in the regression further improved the predictive ability of models. An R program that implements the proposed model is freely available...
- NEURON: a tool for neuroscientists
M L Hines
Department of Computer Science, Yale University, New Haven Connecticut 06520-8001, USA
Neuroscientist 7:123-35. 2001
..This article describes two tools that address the problem of how to achieve computational efficiency and accuracy...
- The role of the airline transportation network in the prediction and predictability of global epidemics
School of Informatics and Center for Biocomplexity, Indiana University, Bloomington, IN 47401, USA
Proc Natl Acad Sci U S A 103:2015-20. 2006
..These measures may be used for the analysis of containment policies and epidemic risk assessment...
- Testing the reliability of genetic methods of species identification via simulation
Howard A Ross
Bioinformatics Institute, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand
Syst Biol 57:216-30. 2008
..The requirement for extensive genetic sampling may render these techniques inappropriate in some circumstances...
- Comparing families of dynamic causal models
Will D Penny
Wellcome Trust Centre for Neuroimaging, University College, London, United Kingdom
PLoS Comput Biol 6:e1000709. 2010
..We illustrate the methods using Dynamic Causal Models of brain imaging data...
- Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer
M D Ritchie
Program in Human Genetics, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN 37232, USA
Am J Hum Genet 69:138-47. 2001
..To our knowledge, this is the first report of a four-locus interaction associated with a common complex multifactorial disease...
- Estimating the impact of school closure on influenza transmission from Sentinel data
MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Diseases Epidemiology, Imperial College London, Norfolk Place, London W2 1PG, UK
Nature 452:750-4. 2008
..The impact of school closure would be reduced if it proved difficult to maintain low contact rates among children for a prolonged period...
- MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus
Department of Mathematics, University of Vienna, Vienna, Austria
Bioinformatics 26:2064-5. 2010
..The implementation is designed to be easily extendable and widely deployable. The interface and output format are compatible with ms. Performance is comparable even with selection included...
- BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology VIB, Ghent University, Technologiepark 927, B 9052, Ghent, Belgium
Bioinformatics 21:3448-9. 2005
- Relaxed phylogenetics and dating with confidence
Alexei J Drummond
Department of Zoology, University of Oxford, Oxford, United Kingdom
PLoS Biol 4:e88. 2006
..From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution...
- Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative
Equipe Méthodes et Algorithmes pour la Bioinformatique LIRMM CNRS, Universite Montpellier II, Montpellier 34392, France
Syst Biol 55:539-52. 2006
..The aLRT is implemented within the algorithm used by the recent fast maximum likelihood tree estimation program PHYML (Guindon and Gascuel, 2003)...
- Seasonal transmission potential and activity peaks of the new influenza A(H1N1): a Monte Carlo likelihood analysis based on human mobility
Center for Complex Networks and Systems Research, School of Informatics and Computing, Indiana University, Bloomington, IN, USA
BMC Med 7:45. 2009
- Efficiency and power in genetic association studies
Paul I W de Bakker
Center for Human Genetic Research, Massachusetts General Hospital, 185 Cambridge Street, CPZN 6818, Boston, Massachusetts 02114 2790, USA
Nat Genet 37:1217-23. 2005
..Power is robust to the completeness of the reference panel from which tags are selected. These findings have implications for prioritizing tag SNPs and interpreting association studies...
- Adaptive exponential integrate-and-fire model as an effective description of neuronal activity
Dept d Informatique, Equipe Odyssée, Ecole Normale Superieure, 45 rue d Ulm, 75230 Paris Cedex 05, France
J Neurophysiol 94:3637-42. 2005
..These results are promising because this simple model has enough expressive power to reproduce qualitatively several electrophysiological classes described in vitro...
- Ten simple rules for dynamic causal modeling
K E Stephan
Laboratory for Social and Neural Systems Research, Institute for Empirical Research in Economics, University of Zurich, Zurich, Switzerland
Neuroimage 49:3099-109. 2010
..By providing good practice recommendations for DCM, in the form of ten simple rules, we hope that this article serves as a helpful tutorial for the growing community of DCM users...
- Dynamic causal models of steady-state responses
R J Moran
Wellcome Trust Centre for Neuroimaging, Institute of Neurology, University College London, London, UK
Neuroimage 44:796-811. 2009
..We conclude with an illustrative application to multi-channel local field potential data acquired during a learning experiment in mice...
- Optimality principles in sensorimotor control
Department of Cognitive Science, University of California San Diego, La Jolla, California 92093 0515, USA
Nat Neurosci 7:907-15. 2004
..At the heart of the framework is the relationship between high-level goals, and the real-time sensorimotor control strategies most suitable for accomplishing those goals...
- Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans
Department of Ecology and Evolutionary Biology, 2019 Kraus Natural Science Building, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109 1048, USA
Science 314:1898-903. 2006
..It captures the observed boom-and-bust pattern of viral evolution, with periods of antigenic stasis during which genetic diversity grows, and with episodic contraction of this diversity during cluster transitions...
- Dynamic strength of molecular adhesion bonds
Department of Physics, University of British Columbia, Vancouver, Canada
Biophys J 72:1541-55. 1997
..Balsera, Y. Oono, and K. Schulten. 1997. Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys. J., this issue), we describe how Brownian dynamics can help bridge the gap between molecular dynamics and probe tests...
- A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility
Jason H Moore
Computational Genetics Laboratory, Department of Genetics, Dartmouth Hitchcock Medical Center, One Medical Center Dr, 706 Rubin Bldg, HB7937, Lebanon, NH 03756, USA
J Theor Biol 241:252-61. 2006
..We then apply this strategy to detecting, characterizing, and interpreting epistatic models in a genetic study (n = 500) of atrial fibrillation and show that both classification and model interpretation are significantly improved...