computer simulation

Summary

Summary: Computer-based representation of physical systems and phenomena such as chemical processes.

Top Publications

  1. ncbi A neural substrate of prediction and reward
    W Schultz
    Institute of Physiology, University of Fribourg, CH 1700 Fribourg, Switzerland
    Science 275:1593-9. 1997
  2. ncbi 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
  3. pmc Mapping short DNA sequencing reads and calling variants using mapping quality scores
    Heng Li
    The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
    Genome Res 18:1851-8. 2008
  4. pmc 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
  5. ncbi A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    Stephane Guindon
    LIRMM, CNRS, 161 rue Ada, 34392, Montpellier Cedex 5, France
    Syst Biol 52:696-704. 2003
  6. pmc 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
  7. pmc Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies
    Daniel Falush
    Department of Molecular Biology, Max Planck Institut für Infektionsbiologie, Schumann Strasse 21 22, 10117 Berlin, Germany
    Genetics 164:1567-87. 2003
  8. pmc 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
  9. pmc 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
  10. ncbi 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

Detail Information

Publications310 found, 100 shown here

  1. ncbi A neural substrate of prediction and reward
    W Schultz
    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...
  2. ncbi 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...
  3. pmc Mapping short DNA sequencing reads and calling variants using mapping quality scores
    Heng Li
    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...
  4. pmc 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...
  5. ncbi A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    Stephane Guindon
    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/...
  6. pmc 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...
  7. pmc Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies
    Daniel Falush
    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...
  8. pmc 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...
  9. pmc 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
    ....
  10. ncbi 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: muse@stat.ncsu.edu SUPPLEMENTARY INFORMATION: HyPhydocumentation and tutorials are available at http://www.hyphy.org...
  11. ncbi Comparison of multiple Amber force fields and development of improved protein backbone parameters
    Viktor Hornak
    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...
  12. ncbi A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    S Whelan
    Department of Zoology, University of Cambridge, Cambridge, England
    Mol Biol Evol 18:691-9. 2001
    ....
  13. ncbi 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...
  14. ncbi RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
    A Stamatakis
    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...
  15. pmc A new statistical method for haplotype reconstruction from population data
    M Stephens
    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...
  16. pmc Population structure and eigenanalysis
    Nick Patterson
    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...
  17. ncbi A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    Yong Duan
    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...
  18. pmc 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...
  19. pmc 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...
  20. ncbi Epidemic spreading in scale-free networks
    R Pastor-Satorras
    , , 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...
  21. pmc Community structure in social and biological networks
    M Girvan
    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...
  22. ncbi 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...
  23. pmc 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...
  24. pmc 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
    ....
  25. pmc Functional cartography of complex metabolic networks
    Roger Guimerà
    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...
  26. ncbi COPASI--a COmplex PAthway SImulator
    Stefan Hoops
    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...
  27. ncbi 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...
  28. ncbi 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...
  29. ncbi 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...
  30. pmc 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...
  31. pmc Efficiency and cost of economical brain functional networks
    Sophie Achard
    Brain Mapping Unit, Department of Psychiatry, Addenbrooke s Hospital, University of Cambridge, Cambridge, United Kingdom
    PLoS Comput Biol 3:e17. 2007
    ....
  32. ncbi 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...
  33. pmc Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers
    Alberto Perez
    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...
  34. ncbi A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6
    Chris Oostenbrink
    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...
  35. ncbi Computational systems biology
    Hiroaki Kitano
    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...
  36. pmc Evaluation of methods for detecting recombination from DNA sequences: computer simulations
    D Posada
    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...
  37. ncbi Protein homology detection by HMM-HMM comparison
    Johannes Söding
    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...
  38. pmc 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...
  39. ncbi The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
    R Mahadevan
    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...
  40. ncbi 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...
  41. ncbi 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
    ....
  42. ncbi Discovering regulatory and signalling circuits in molecular interaction networks
    Trey Ideker
    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...
  43. pmc Multiscale mobility networks and the spatial spreading of infectious diseases
    Duygu Balcan
    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...
  44. ncbi 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...
  45. pmc Defining network topologies that can achieve biochemical adaptation
    Wenzhe Ma
    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...
  46. ncbi 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...
  47. pmc MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
    Kazutaka Katoh
    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...
  48. pmc Extension of the bayesian alphabet for genomic selection
    David Habier
    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...
  49. ncbi 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...
  50. ncbi 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...
  51. ncbi Bayes empirical bayes inference of amino acid sites under positive selection
    Ziheng Yang
    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...
  52. ncbi 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...
  53. ncbi Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
    Jianzhi Zhang
    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...
  54. ncbi 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
    ....
  55. pmc 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...
  56. pmc Robust single-particle tracking in live-cell time-lapse sequences
    Khuloud Jaqaman
    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...
  57. ncbi 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...
  58. pmc A protocol for generating a high-quality genome-scale metabolic reconstruction
    Ines Thiele
    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...
  59. pmc A high-resolution human contact network for infectious disease transmission
    Marcel Salathé
    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...
  60. pmc A methodology for performing global uncertainty and sensitivity analysis in systems biology
    Simeone Marino
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 0620, USA
    J Theor Biol 254:178-96. 2008
    ....
  61. pmc The asynchronous state in cortical circuits
    Alfonso Renart
    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...
  62. ncbi 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...
  63. pmc 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...
  64. ncbi Systems biology: a brief overview
    Hiroaki Kitano
    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...
  65. pmc 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...
  66. ncbi 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...
  67. ncbi 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...
  68. pmc 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...
  69. pmc 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...
  70. pmc Information-based functional brain mapping
    Nikolaus Kriegeskorte
    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
    ....
  71. pmc 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...
  72. ncbi Gene regulatory network inference: data integration in dynamic models-a review
    Michael Hecker
    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...
  73. ncbi 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...
  74. pmc CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
    K Vanommeslaeghe
    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...
  75. pmc The normalization model of attention
    John H Reynolds
    Salk Institute for Biological Studies, La Jolla, CA 92037 1099, USA
    Neuron 61:168-85. 2009
    ....
  76. ncbi 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...
  77. pmc The transmissibility and control of pandemic influenza A (H1N1) virus
    Yang Yang
    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...
  78. pmc 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...
  79. ncbi Stochastic simulation of chemical kinetics
    Daniel T Gillespie
    Dan T Gillespie Consulting, Castaic, CA 91384, USA
    Annu Rev Phys Chem 58:35-55. 2007
    ....
  80. pmc 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...
  81. pmc Molecular dynamics and protein function
    M Karplus
    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...
  82. pmc 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...
  83. ncbi 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...
  84. pmc The role of the airline transportation network in the prediction and predictability of global epidemics
    Vittoria Colizza
    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...
  85. ncbi 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...
  86. pmc 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...
  87. pmc 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...
  88. ncbi Estimating the impact of school closure on influenza transmission from Sentinel data
    Simon Cauchemez
    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...
  89. pmc MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus
    Gregory Ewing
    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...
  90. ncbi BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
    Steven Maere
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology VIB, Ghent University, Technologiepark 927, B 9052, Ghent, Belgium
    Bioinformatics 21:3448-9. 2005
    ....
  91. pmc 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...
  92. ncbi Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative
    Maria Anisimova
    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)...
  93. pmc Seasonal transmission potential and activity peaks of the new influenza A(H1N1): a Monte Carlo likelihood analysis based on human mobility
    Duygu Balcan
    Center for Complex Networks and Systems Research, School of Informatics and Computing, Indiana University, Bloomington, IN, USA
    BMC Med 7:45. 2009
    ....
  94. ncbi 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...
  95. ncbi Adaptive exponential integrate-and-fire model as an effective description of neuronal activity
    Romain Brette
    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...
  96. pmc 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...
  97. pmc 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...
  98. pmc Optimality principles in sensorimotor control
    Emanuel Todorov
    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...
  99. ncbi Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans
    Katia Koelle
    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...
  100. pmc Dynamic strength of molecular adhesion bonds
    E Evans
    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...
  101. ncbi 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...

Research Grants67

  1. Systems Biology of Glycosylation
    Sriram Neelamegham; Fiscal Year: 2013
    ..v) Validation in animal models of inflammation, peritonitis and COPD (chronic obstructive pulmonary disease), key hypothesis generated using computer simulation and ex vivo experimentation.
  2. Computer Simulation of Acute Coronary Syndrome Care in the Emergency Department
    DANIEL JOSEPH FRANCE; Fiscal Year: 2010
    ..applicant): The primary objective of this study is to use queuing theory - the study of waiting lines - and computer simulation, to determine how tight coupling between hospitals and emergency departments (ED) affects time-critical ..
  3. Center for Protein Folding Machinery
    Vijay S Pande; Fiscal Year: 2013
    ..from 6 institutions with expertise in chaperone biochemistry, protein folding, electron cryomicrosopy, computer simulation and design. X-ray crystallography, single-molecule imaging and trapping, and clinical research...
  4. NMR Studies of Structures and Dynamics of Proteins
    Arthur G Palmer; Fiscal Year: 2013
    ..a specific aim to develop improved approaches for characterizing protein dynamics by NMR spectroscopy and computer simulation. This research will explicate molecular aspects of catalysis and recognition in these two paradigmatic ..
  5. Non-linear Characterization of the Stretch Reflex Arc and its Neuromodulation
    AMAN BEHAL; Fiscal Year: 2011
    ..Towards achieving our specific aims, the confluence of experimental, analytical, and computer simulation techniques will be exploited...
  6. CRCNS:US French Coll:Computational Imaging of the Aging Cerebral Microvasculature
    Bradley P Sutton; Fiscal Year: 2013
    ..Combined with a computer simulation of vascular trees, the structural characteristics of the microvasculature can be extracted using these ..
  7. Model of Platelet Adhesion and Thrombus Formation
    Michael R King; Fiscal Year: 2013
    ..We propose to develop a multiscale computer simulation that is validated with a unique experimental model in which human platelets can be observed in the ..
  8. SCORE: Principal Differential Analysis with Covariates for Functional Data
    Joan G Staniswalis; Fiscal Year: 2012
    ..b>Computer simulation studies will be executed to verify that the asymptotic theory for the bias and variance of the estimators ..
  9. Knee OA: Setting Priorities for Care, Policy, Research
    Elena Losina; Fiscal Year: 2010
    ..In this application, we propose to build a comprehensive computer simulation model of knee OA to evaluate the health and economic effects of four major developments in OA prevention ..
  10. The Audible Human Project
    Thomas J Royston; Fiscal Year: 2013
    ..In order to achieve this goal, the following specific aims will be undertaken: (1) Develop the AHP computer simulation model to simulate breath sound generation, how specific lung pathologies alter the acoustic environment, ..
  11. MOLECULAR BASIS OF BORRELIA PATHOGENESIS
    Alan G Barbour; Fiscal Year: 2010
    ..and (e) integrate the findings from studies for goals (a) to (d) through mathematical modeling and computer simulation. Specific aim 1: Genetic basisfor antigenic variation...
  12. NTP statistical and computer support
    JANET TEAGUE; Fiscal Year: 2010
    ..research of importance to DIR by investigating properties of alternative statistical procedures by computer simulation and by supplying theoretical and computational support for biomathematical research efforts...
  13. Renal Processing of Albumin
    Oliver Smithies; Fiscal Year: 2010
    ..In 2003, I proposed a gel permeation/diffusion hypothesis and computer simulation postulating that the GBM is the predominant source of the size selectivity of the kidney, because there is ..
  14. Development of Thermoacoustic Tomography Brain Imaging
    Mark A Anastasio; Fiscal Year: 2013
    ....
  15. Statistical Methods for Epigenetic Mediation of Exposure-response Relations
    Duncan C Thomas; Fiscal Year: 2013
    ..The statistical performance of these methods will be studied by computer simulation. We will apply these methods to various subsets of participants in the Children's Health Study (CHS) - ..
  16. Simulation of Proton Translocation in Biomolecules
    Gregory A Voth; Fiscal Year: 2013
    ..In this project the continued development and application of a unique and powerful multiscale computer simulation methodology is described for the study of proton transport in several key classes of proton translocating ..
  17. Computer simulations of populations of mammalian motor units
    CHARLES HECKMAN; Fiscal Year: 2013
    ..To bridge this gap, this proposal seeks to develop a highly realistic and thoroughly validated computer simulation of the set of motor units for a single muscle...
  18. New Electroanalytical Methods for Single-Cell Exocytosis
    Bo Zhang; Fiscal Year: 2013
    ..We will analyze single exocytotic events using an integrated on-chip microelectrode. We will use computer simulation to achieve a deeper understanding of dopamine transport at the electrode/cell interface...
  19. THEORY OF SOLUTE AND WATER TRANSPORT ACROSS EPITHELIA
    Alan M Weinstein; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): The overall objective of this project is mathematical modeling and computer simulation of fluid and electrolyte disorders in kidney tubules...
  20. Improving Robustness of a Tactical Model of Aedes/Dengue Dynamics
    Fred Gould; Fiscal Year: 2013
    ..b>Computer simulation studies have often offered an alternative to direct experimentation in scientific fields ranging from space ..
  21. Using Computer Simulation to Enhance Retention of Motivational Interviewing Skill
    DALE EDWARD OLSEN; Fiscal Year: 2010
    ..The proposed research will produce an innovative new training tool with the potential to increase learning and retention of MI skills among clinicians, thereby benefiting their patients. ..
  22. Computer Simulation of Electron and Proton Transfer
    Arieh Warshel; Fiscal Year: 2013
    ..Aim3 - ET Processes - ET and ET/PT in CcO will be explored. Aim4 - Validations - Crucial validation of the different models will be conducted. 1 ..
  23. Task space control of normal &pathological locomotion
    CHENG YUN KAREN LIU; Fiscal Year: 2013
    ..Based on the analytical results, a further study will create a physics-based computer simulation of pathological amputee gait with corrective joint torques computed from the differences discovered between ..
  24. The Virtual Physiological Rat Project
    Daniel A Beard; Fiscal Year: 2013
    ..b>Computer simulation will be used to integrate disparate data (genomic, anatomic, physiological, etc...
  25. Optimizing HIV Care in Less Developed Countries
    KENNETH ALAN FREEDBERG; Fiscal Year: 2012
    ..funding to develop the "Cost-effectiveness of Preventing AlDS Complications (CEPAC) International" Model, a computer simulation of the natural history, clinical management, outcomes, and costs of HIV disease in South Africa, Cote d&..
  26. COMPUTER SIMULATION THEORY OF GLOBULAR PROTEIN DYNAMICS
    Jeffrey Skolnick; Fiscal Year: 2013
    ..Each Aim is part of a more comprehensive objective to increase our understanding of subcellular processes and biochemical function that will help accelerate drug discovery as well as provide general biochemical insights. ..
  27. Engineered imaging nanoparticle for realtime detection of cancer in the tumor bed
    W David Lee; Fiscal Year: 2011
    ..Based upon mouse and dog tests and using our computer simulation of the imaging agent performance we forecast a peak contrast in humans at 36-48 hours from injection...
  28. Agent-Based Modeling to Reveal Mechanisms of Idiopathic Interstitial Lung Disease
    VIRGINIA ANN FOLCIK NIVAR; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): A computer simulation of lung disease will be created to be a tool for virtual experimentation...
  29. A Dual Resolution Cone Beam CT System for 3-D Breast Imaging
    Chris C Shaw; Fiscal Year: 2010
    ..1), we propose to investigate and demonstrate the feasibility of the dual resolution CBCT technique with computer simulation and bench top imaging experiments...
  30. The Cost-Effectiveness of MRI in Early Rheumatoid Arthritis
    Lisa G Suter; Fiscal Year: 2010
    ..Ronald Scott Braithwaite, an expert in meta-analysis and computer simulation modeling;and Dr. John Concato, a leading expert in research methodology and clinical epidemiology...
  31. Statistical Support for NTP and NIEHS
    JANET TEAGUE; Fiscal Year: 2009
    ..research of importance to DIR by investigating properties of alternative statistical procedures by computer simulation and by supplying theoretical and computational support for biomathematical research efforts. ..
  32. Computer Modeled Multiportal Approaches to the Skull Base
    Kris Moe; Fiscal Year: 2013
    ..Normative data on the approach combinations will be generated and ultimately, these results will serve as a platform for future robotic integration and computer simulation into skull base surgery.
  33. Source-Filter Interaction in Speech
    Ingo R Titze; Fiscal Year: 2013
    ..Recent advances in speech production research, primarily with computer simulation, have shown that the primary sound source in the larynx (glottal airflow) can be highly influenced by ..
  34. National Center for Simulation in Rehabilitation Research
    Scott L Delp; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Computer simulation has revolutionized science and engineering...
  35. Simulation of learning: models and biological validation
    Michel Baudry; Fiscal Year: 2012
    ..It is therefore our goals to develop new technological tools based on mathematical modeling and computer simulation of the molecular processes taking place in realistic biological networks to reach such an understanding...
  36. Clinical impact and cost-effectiveness of pain management in knee OA
    Elena Losina; Fiscal Year: 2013
    ..perform total knee replacement (TKR)? We propose to address these and related questions using a validated computer simulation model of knee OA natural history and treatment outcomes...
  37. COMPUTER SIMULATION OF AMPHIPHILIC AGGREGATES
    Michael Klein; Fiscal Year: 2009
    This competing renewal is requesting continuing support for the Klein group's computer simulation studies on membranes and membrane-bound species, with special emphasis on biophysical problems difficult to tackle with brute force ..
  38. Rewiring the yeast brain: Redundancy and interference in genetic networks
    NICOLAS EMILE BUCHLER; Fiscal Year: 2011
    ..We will use computer simulation and an experimental directed evolution approach in a tractable, model eukaryote (Saccharomyces cerevisiae) ..
  39. Design Studies and Optimization of Phase-Contrast Mammography
    Mark A Anastasio; Fiscal Year: 2013
    ..The images it produces will improve a reader's ability to detect subtle cancer features and it could also dramatically reduce the radiation exposure to the patient. ..
  40. Phase Contrast Cone Beam CT Imaging
    Ruola Ning; Fiscal Year: 2013
    ..The specific aims of this project include: 1) Perform computer simulation to optimize the parameters for the design and construction of the table-top DPC system, 2) Develop phase ..
  41. Effects of individual behavioral responses on benefits of influenza vaccination
    Byung Kwang Yoo; Fiscal Year: 2011
    ..g., dynamic modeling) and statistics (e.g., panel data analysis and computer simulation) as well as to gain more knowledge on child influenza vaccination and vaccine distribution/production ..
  42. Computer Models of Normal and Abnormal Discharge Patterns in Human Motoneurons
    Randall K Powers; Fiscal Year: 2013
    ..The goal of this proposal is to develop a sophisticated computer simulation platform to quantitatively link cellular data from animal preparations to firing pattern data in human ..
  43. Antimicrobial Use and Control of Clostridium difficile transmission and infection
    Michael A Rubin; Fiscal Year: 2013
    ..difficile strain. Methods We will refine and enhance a high-fidelity agent-based computer simulation of nosocomial C. difficile transmission created as part of a previous project...
  44. A New Method for Biomembrane Simulations
    Gregory A Voth; Fiscal Year: 2012
    ..for the description of realistic heterogeneous membranes and membrane bound proteins, with a goal of making computer simulation more directly relevant to the fluid mosaic picture of real biological membranes;(Aim 2) the application of ..
  45. Hydrophobic Effects in Biophysical Systems and Protein-Protein Interactions
    David Chandler; Fiscal Year: 2010
    ..The proposed research aims at using the theoretical methods of computer simulation and statistical mechanics to establish a quantitative understanding of the role of hydrophobic interactions ..
  46. Alcohol Associated Outcomes Among HIV+/- Aging Veterans
    AMY CAROLINE JUSTICE; Fiscal Year: 2010
    ..related biomarkers predict decreased survival, and that even moderate alcohol use shortens survival using computer simulation. We have explored patient and provider attitudes and found that HIV-positive veterans and their physicians ..
  47. A Dual Resolution Cone Beam CT System for 3-D Breast Imaging
    Chris Shaw; Fiscal Year: 2007
    ..1), we propose to investigate and demonstrate the feasibility of the dual resolution CBCT technique with computer simulation and bench top imaging experiments...
  48. THEORY OF BIOMOLECULAR DIFFUSION
    JAMES A MCCAMMON; Fiscal Year: 2013
    ..The broad objectives of the proposed work are to provide new computer simulation tools that will enable the detailed analysis of the role of molecular diffusion in biological processes at ..
  49. Evaluating the Cost Effectiveness of Alternative Sample Designs for Genetic Assoc
    Nathan L Tintle; Fiscal Year: 2011
    ..Research conclusions will be developed mathematically, confirmed via computer simulation and demonstrated on data from actual genetic association studies...
  50. Mathematical modeling and computer simulation of aortic dissection
    BOYCE EUGENE GRIFFITH; Fiscal Year: 2013
    ..Finally, these models will be used to study the surgical and medical management of patients who require or who have undergone partial repair of a Stanford Type A dissection. ..
  51. Integrated Modeling of Cardiac Metabolism and Transport
    Daniel A Beard; Fiscal Year: 2013
    ..Finally, based on the findings from the rat models and human studies, we will use computer simulation to determine if and how changes in energy state can explain cardiac pumping failure in vivo.
  52. ULTRASOUND THERAPY DELIVERY THROUGH INTACT SKULL
    Kullervo Hynynen; Fiscal Year: 2013
    ..We have also developed computer simulation programs, control technology and treatment methods that will improve the delivery of ultrasound energy...
  53. CRCNS: Computational Models of Multisensory Processing
    M Alex Meredith; Fiscal Year: 2010
    ..Second, that biological data will be used in a computer simulation that incorporates (a) an integrate and fire spiking neuron model, b) static and dynamic synaptic plasticity ..
  54. Theoretical and experimental strudy of the population and evolutionary dynamics o
    BRUCE RICHARD LEVIN; Fiscal Year: 2012
    ..To achieve these goals, we will construct and analyze the properties of mathematical and computer simulation models that combine the pharmacodynamics of antibiotics and bacteria and the pharmacokinetics of the ..
  55. Improvements to Respondent-Driven Sampling for the Study of Hidden Populations
    Matthew J Salganik; Fiscal Year: 2011
    ..This research will achieve these specific aims through a combination of mathematical modeling, computer simulation, and the analysis of existing RDS data sets...
  56. DESIGN AND ANALYSIS OF HUMAN GENE MAPPING STUDIES
    MICHAEL LEE BOEHNKE; Fiscal Year: 2013
    ..I describe how my colleagues and I will address these problems through analytic methods, computer simulation, and application to interesting complex disease genetics data, and how we will generalize these solutions ..
  57. Model Portability for Complex Patients
    Jonathan Brown; Fiscal Year: 2009
    DESCRIPTION (provided by applicant): Computer simulation offers a promising technology to combine and make sense of all the disparate data and knowledge that influence, or should influence modern medical care for complex patients...
  58. IDU Peer Recruitment Dynamics and Network Structure in Respondent Driven Sampling
    Jianghong Li; Fiscal Year: 2013
    ..b>Computer simulation will also be used to assess the sensitivity of potential assumption violations.
  59. Modeling of Cardiac Calcium Dynamics;Ryanodine Receptor induced Arrhythmias
    Daisuke Sato; Fiscal Year: 2013
    ..caused at the ryanodine receptor (RyR) level and induce triggered activities at the tissue level, we use computer simulation and mathematical analysis of physiologically detailed models of Ca cycling and the action potential (AP)...
  60. A computer simulation of the Sub-Saharan HIV pandemic that can estimate benefit a
    RONALD SCOTT BRAITHWAITE; Fiscal Year: 2011
    ..To address these priorities, we aim to create a computer simulation of the HIV pandemic that can evaluate the benefit and value of NIAAA-funded interventions in Sub-Saharan ..
  61. Enhancing Mexican Capacity for CVD Policy Research
    Alicia Fernandez; Fiscal Year: 2013
    ..We propose to collaborate with an outstanding team in Mexico to create an integrated new computer simulation model of the Coronary Heart Disease (CHD) Policy Model that will include additional effect modifiers and ..
  62. Telemetric Implantable Intraocular Pressure Sensor Syste
    LAWRENCE WAN; Fiscal Year: 2003
    ..For this project, a computer designed silicon, piezoelectric pressure sensor and computer simulation of the lOP sensor and process will be developed along with a bench-top proof-of-concept prototype and ..
  63. Targeted prostate biopsy using mathematical optimization
    Christos Davatzikos; Fiscal Year: 2007
    ..thoroughly understand the performance of all these random systematic sampling methods has led to several computer simulation studies that utilize whole-mounted histological stained sections from prostatectomy specimens in order to ..
  64. Translation and Dissemination of Simulator for Novice Drivers
    R Allen; Fiscal Year: 2009
    ..to simplify the presentation of multimedia course materials and the DBAT and integrate them with the computer simulation. The software platform can launch various multimedia materials (e.g...
  65. THE OPTIMAL MANAGEMENT OF CEREBRAL ANEURYSMS
    Joseph King; Fiscal Year: 2004
    ..My immediate goal is to develop a decision analytic and cost-effectiveness computer simulation model to evaluate the outcomes of neurosurgical decisions in patients with cerebral aneurysmsal disease...
  66. Computer Simulation of Epstein Barr Virus Infection
    David Thorley Lawson; Fiscal Year: 2009
    ..In the absence of a suitable animal model, we propose to develop a new generation of computer simulation. The application of supercomputing on distributed clusters of processors will allow us to develop an ..
  67. END-STAGE LIVER DISEASE/PREVALENCE & TREATMENT VARIATION
    Cindy Bryce; Fiscal Year: 2004
    ..The applicant will obtain further instruction in computer simulation, geographic information systems, and advanced statistical analysis; in addition, she will receive clinical ..