James Thompson

Summary

Affiliation: University of Washington
Country: USA

Publications

  1. pmc PeakSeeker: a program for interpreting genotypes of mononucleotide repeats
    James M Thompson
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, USA
    BMC Res Notes 2:17. 2009
  2. pmc Genetic algorithm learning as a robust approach to RNA editing site prediction
    James Thompson
    Department of Biological Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
    BMC Bioinformatics 7:145. 2006
  3. pmc Correction: genetic algorithm learning as a robust approach to RNA editing site site prediction
    James Thompson
    Department of Biological Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
    BMC Bioinformatics 7:406. 2006
  4. pmc High-resolution comparative modeling with RosettaCM
    Yifan Song
    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
    Structure 21:1735-42. 2013
  5. pmc Structure prediction for CASP8 with all-atom refinement using Rosetta
    Srivatsan Raman
    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
    Proteins 77:89-99. 2009
  6. pmc Rosetta in CAPRI rounds 13-19
    Sarel J Fleishman
    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
    Proteins 78:3212-8. 2010
  7. pmc Structure-guided forcefield optimization
    Yifan Song
    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
    Proteins 79:1898-909. 2011
  8. pmc Incorporation of evolutionary information into Rosetta comparative modeling
    James Thompson
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Proteins 79:2380-8. 2011
  9. ncbi request reprint Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home
    Rhiju Das
    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
    Proteins 69:118-28. 2007
  10. pmc Crystal structure of a monomeric retroviral protease solved by protein folding game players
    Firas Khatib
    Department of Biochemistry, University of Washington, Seattle, Washington, USA
    Nat Struct Mol Biol 18:1175-7. 2011

Collaborators

Detail Information

Publications12

  1. pmc PeakSeeker: a program for interpreting genotypes of mononucleotide repeats
    James M Thompson
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, USA
    BMC Res Notes 2:17. 2009
    ..A method to interpret the genotypes of mononucleotide repeats would permit the widespread use of those highly informative microsatellites in genetic research...
  2. pmc Genetic algorithm learning as a robust approach to RNA editing site prediction
    James Thompson
    Department of Biological Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
    BMC Bioinformatics 7:145. 2006
    ..We evaluate its potential use on the best data set available for these purposes: C --> U editing sites in plant mitochondrial genomes...
  3. pmc Correction: genetic algorithm learning as a robust approach to RNA editing site site prediction
    James Thompson
    Department of Biological Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
    BMC Bioinformatics 7:406. 2006
    ..The consequences of this error are reflected in changes to our results, although the general conclusions presented in our original publication remain largely unchanged...
  4. pmc High-resolution comparative modeling with RosettaCM
    Yifan Song
    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
    Structure 21:1735-42. 2013
    ..The CASP10 experiment suggests that RosettaCM yields models with more accurate side-chain and backbone conformations than other methods when the sequence identity to the templates is greater than ∼15%...
  5. pmc Structure prediction for CASP8 with all-atom refinement using Rosetta
    Srivatsan Raman
    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
    Proteins 77:89-99. 2009
    ..These improvements over the starting template-based models and refinement tests demonstrate the power of Rosetta structure refinement in improving model accuracy...
  6. pmc Rosetta in CAPRI rounds 13-19
    Sarel J Fleishman
    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
    Proteins 78:3212-8. 2010
    ..Analysis of our failures in the CAPRI challenges suggest that conformational sampling at the termini of exposed beta strands is a particularly pressing area for improvement...
  7. pmc Structure-guided forcefield optimization
    Yifan Song
    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
    Proteins 79:1898-909. 2011
    ..The method can be used generally to integrate different sources of information for forcefield improvement...
  8. pmc Incorporation of evolutionary information into Rosetta comparative modeling
    James Thompson
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Proteins 79:2380-8. 2011
    ....
  9. ncbi request reprint Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home
    Rhiju Das
    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
    Proteins 69:118-28. 2007
    ..These results indicate that refinement with an all-atom energy function, although computationally expensive, is a powerful method for obtaining accurate structure predictions...
  10. pmc Crystal structure of a monomeric retroviral protease solved by protein folding game players
    Firas Khatib
    Department of Biochemistry, University of Washington, Seattle, Washington, USA
    Nat Struct Mol Biol 18:1175-7. 2011
    ..The refined structure provides new insights for the design of antiretroviral drugs...
  11. pmc Epe1 recruits BET family bromodomain protein Bdf2 to establish heterochromatin boundaries
    Jiyong Wang
    Department of Biological Sciences, Columbia University, New York, New York 10027, USA
    Genes Dev 27:1886-902. 2013
    ..They also reveal a previously unappreciated function of H4K16ac in cooperation with H3K9 methylation to regulate heterochromatin spreading...
  12. pmc A classification model for BRCA2 DNA binding domain missense variants based on homology-directed repair activity
    Lucia Guidugli
    Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
    Cancer Res 73:265-75. 2013
    ....