Ian H Holmes

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi Tools for simulating evolution of aligned genomic regions with integrated parameter estimation
    Avinash Varadarajan
    Biophysics Graduate Group, University of California Berkeley, CA 94720 3200, USA
    Genome Biol 9:R147. 2008
  2. ncbi XRate: a fast prototyping, training and annotation tool for phylo-grammars
    Peter S Klosterman
    Department of Bioengineering, University of California, Berkeley CA, USA
    BMC Bioinformatics 7:428. 2006
  3. ncbi A probabilistic model for the evolution of RNA structure
    Ian Holmes
    Department of Bioengineering, University of California, Berkeley 94720 1762, USA
    BMC Bioinformatics 5:166. 2004
  4. ncbi Using evolutionary Expectation Maximization to estimate indel rates
    Ian Holmes
    Department of Statistics, 1 South Parks Road, Oxford OX1 3TG, UK
    Bioinformatics 21:2294-300. 2005
  5. ncbi Accelerated probabilistic inference of RNA structure evolution
    Ian Holmes
    Department of Bioengineering, University of California, Berkeley, CA 94720 1762, USA
    BMC Bioinformatics 6:73. 2005
  6. ncbi Phylocomposer and phylodirector: analysis and visualization of transducer indel models
    Ian Holmes
    Department of Bioengineering, University of California, Berkeley, CA, USA
    Bioinformatics 23:3263-4. 2007
  7. ncbi Evolutionary triplet models of structured RNA
    Robert K Bradley
    Biophysics Graduate Group, University of California, Berkeley, California, United States of America
    PLoS Comput Biol 5:e1000483. 2009
  8. ncbi xREI: a phylo-grammar visualization webserver
    Lars Barquist
    Department of Bioengineering, University of California, Berkeley, USA
    Nucleic Acids Res 36:W65-9. 2008
  9. ncbi JBrowse: a next-generation genome browser
    Mitchell E Skinner
    Department of Bioengineering, University of California at Berkeley, Berkeley, California 94720, USA
    Genome Res 19:1630-8. 2009
  10. ncbi Setting up the JBrowse genome browser
    Mitchell E Skinner
    University of California at Berkeley, Berkeley, California, USA
    Curr Protoc Bioinformatics . 2010

Research Grants

  1. Evolutionary Modeling/Prediction of ncRNA Genes in Flies
    Ian Holmes; Fiscal Year: 2007
  2. Evolutionary Modeling/Prediction of ncRNA Genes in Flies
    Ian Holmes; Fiscal Year: 2009
  3. Enhancement of the GBrowse Genome Annotation Browser
    Ian Holmes; Fiscal Year: 2009
  4. Evolutionary Modeling/Prediction of ncRNA Genes in Flies
    Ian H Holmes; Fiscal Year: 2010
  5. Enhancement of the GBrowse Genome Annotation Browser
    Ian H Holmes; Fiscal Year: 2010

Detail Information

Publications15

  1. ncbi Tools for simulating evolution of aligned genomic regions with integrated parameter estimation
    Avinash Varadarajan
    Biophysics Graduate Group, University of California Berkeley, CA 94720 3200, USA
    Genome Biol 9:R147. 2008
    ..All three tools out-perform the leading neutral DNA simulator (DAWG) in benchmarks. The programs are available at http://biowiki.org/SimulationTools...
  2. ncbi XRate: a fast prototyping, training and annotation tool for phylo-grammars
    Peter S Klosterman
    Department of Bioengineering, University of California, Berkeley CA, USA
    BMC Bioinformatics 7:428. 2006
    ..Previously, phylo-grammars have required considerable effort to implement, limiting their adoption by computational biologists...
  3. ncbi A probabilistic model for the evolution of RNA structure
    Ian Holmes
    Department of Bioengineering, University of California, Berkeley 94720 1762, USA
    BMC Bioinformatics 5:166. 2004
    ....
  4. ncbi Using evolutionary Expectation Maximization to estimate indel rates
    Ian Holmes
    Department of Statistics, 1 South Parks Road, Oxford OX1 3TG, UK
    Bioinformatics 21:2294-300. 2005
    ..Recently, we showed how to do this for the point substitution component of the evolutionary process; here, we extend these results to the indel process...
  5. ncbi Accelerated probabilistic inference of RNA structure evolution
    Ian Holmes
    Department of Bioengineering, University of California, Berkeley, CA 94720 1762, USA
    BMC Bioinformatics 6:73. 2005
    ..It is therefore desirable to constrain such algorithms, by pre-processing the sequences and using this first pass to limit the range of structures and/or alignments that can be considered...
  6. ncbi Phylocomposer and phylodirector: analysis and visualization of transducer indel models
    Ian Holmes
    Department of Bioengineering, University of California, Berkeley, CA, USA
    Bioinformatics 23:3263-4. 2007
    ..AVAILABILITY: Phylocomposer and phylodirector are freely available at http://biowiki.org/PhyloComposer and http://biowiki.org/PhyloDirector..
  7. ncbi Evolutionary triplet models of structured RNA
    Robert K Bradley
    Biophysics Graduate Group, University of California, Berkeley, California, United States of America
    PLoS Comput Biol 5:e1000483. 2009
    ..For more exact probabilistic inference, we discuss the use of transducer composition for ML (or MCMC) inference on phylogenies, including possible ways to make the core operations tractable...
  8. ncbi xREI: a phylo-grammar visualization webserver
    Lars Barquist
    Department of Bioengineering, University of California, Berkeley, USA
    Nucleic Acids Res 36:W65-9. 2008
    ..It is hoped that this application will serve as a valuable tool to those developing phylo-grammars, and as a means for the exploration and dissemination of such models. xREI is available at http://harmony.biowiki.org/xrei/..
  9. ncbi JBrowse: a next-generation genome browser
    Mitchell E Skinner
    Department of Bioengineering, University of California at Berkeley, Berkeley, California 94720, USA
    Genome Res 19:1630-8. 2009
    ....
  10. ncbi Setting up the JBrowse genome browser
    Mitchell E Skinner
    University of California at Berkeley, Berkeley, California, USA
    Curr Protoc Bioinformatics . 2010
    ..After completing the protocols described in this unit, the reader will have a Web site that other users can visit to browse the genomic data...
  11. ncbi Fast statistical alignment
    Robert K Bradley
    Department of Mathematics, University of California Berkeley, Berkeley, California, United States of America
    PLoS Comput Biol 5:e1000392. 2009
    ..The FSA program and a companion visualization tool for exploring uncertainty in alignments can be used via a web interface at http://orangutan.math.berkeley.edu/fsa/, and the source code is available at http://fsa.sourceforge.net/...
  12. ncbi Specific alignment of structured RNA: stochastic grammars and sequence annealing
    Robert K Bradley
    Biophysics Graduate Group, Department of Mathematics and Department of Bioengineering, University of California, Berkeley, CA 94720, USA
    Bioinformatics 24:2677-83. 2008
    ..This leads to a new software program, Stemloc-AMA, that is both accurate and specific in the alignment of multiple related RNA sequences...
  13. ncbi Colorstock, SScolor, Ratón: RNA alignment visualization tools
    Yuri R Bendaña
    Department of Bioengineering, UC Berkeley, Berkeley, CA, USA
    Bioinformatics 24:579-80. 2008
    ..AVAILABILITY: All source code is freely available under the GPL. The source code can be downloaded and a prototype of Ratón can be accessed at http://biowiki.org/RnaAlignmentViewers...
  14. ncbi Accurate detection of recombinant breakpoints in whole-genome alignments
    Oscar Westesson
    Department of Bioengineering, University of California Berkeley, Berkeley, California, United States of America
    PLoS Comput Biol 5:e1000318. 2009
    ..In all cases, we confirm the breakpoint predictions of previous studies, and in many cases we offer novel predictions...
  15. ncbi Evolutionary modeling and prediction of non-coding RNAs in Drosophila
    Robert K Bradley
    Biophysics Graduate Group, University of California, Berkeley, CA, USA
    PLoS ONE 4:e6478. 2009
    ..5 Kbp spanned by the predicted tandem array is contained within a FlyBase-annotated cDNA...

Research Grants9

  1. Evolutionary Modeling/Prediction of ncRNA Genes in Flies
    Ian Holmes; Fiscal Year: 2007
    ..All our software will be freely available online. ..
  2. Evolutionary Modeling/Prediction of ncRNA Genes in Flies
    Ian Holmes; Fiscal Year: 2009
    ..All our software will be freely available online. ..
  3. Enhancement of the GBrowse Genome Annotation Browser
    Ian Holmes; Fiscal Year: 2009
    ..We wish to rectify this situation by establishing a full-time support center responsible for GMOD packaging, documentation, end-user education and outreach. ..
  4. Evolutionary Modeling/Prediction of ncRNA Genes in Flies
    Ian H Holmes; Fiscal Year: 2010
    ..All our software will be freely available online. ..
  5. Enhancement of the GBrowse Genome Annotation Browser
    Ian H Holmes; Fiscal Year: 2010
    ..We wish to rectify this situation by establishing a full-time support center responsible for GMOD packaging, documentation, end-user education and outreach. ..