Robert K Bradley

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc 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. pmc 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. pmc 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
  4. pmc 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
  5. pmc Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species
    Robert K Bradley
    Department of Mathematics, University of California Berkeley, Berkeley, California, United States of America
    PLoS Biol 8:e1000343. 2010

Collaborators

Detail Information

Publications5

  1. pmc 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. pmc 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. pmc 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/...
  4. pmc 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...
  5. pmc Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species
    Robert K Bradley
    Department of Mathematics, University of California Berkeley, Berkeley, California, United States of America
    PLoS Biol 8:e1000343. 2010
    ....