Daniel A Pollard

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments
    Daniel A Pollard
    Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA
    BMC Bioinformatics 7:376. 2006
  2. pmc Large-scale turnover of functional transcription factor binding sites in Drosophila
    Alan M Moses
    Graduate Group in Biophysics, University of California Berkeley, Berkeley, California, United States of America
    PLoS Comput Biol 2:e130. 2006
  3. pmc MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
    Alan M Moses
    Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA
    Genome Biol 5:R98. 2004
  4. pmc Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting
    Daniel A Pollard
    Graduate Group in Biophysics, University of California Berkeley, Berkeley, California, USA
    PLoS Genet 2:e173. 2006
  5. pmc Benchmarking tools for the alignment of functional noncoding DNA
    Daniel A Pollard
    Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
    BMC Bioinformatics 5:6. 2004
  6. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
  7. pmc Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm
    Xiao Yong Li
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
    PLoS Biol 6:e27. 2008

Detail Information

Publications7

  1. pmc Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments
    Daniel A Pollard
    Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA
    BMC Bioinformatics 7:376. 2006
    ..Yet how multiple alignment accuracy varies across sequence types, tree topologies, divergences and tools, and further how this variation impacts specific inferences, remains unclear...
  2. pmc Large-scale turnover of functional transcription factor binding sites in Drosophila
    Alan M Moses
    Graduate Group in Biophysics, University of California Berkeley, Berkeley, California, United States of America
    PLoS Comput Biol 2:e130. 2006
    ..Finally, we show that binding-site gains and losses are asymmetrically distributed with respect to D. melanogaster, consistent with lineage-specific acquisition and loss of Zeste-responsive regulatory elements...
  3. pmc MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
    Alan M Moses
    Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA
    Genome Biol 5:R98. 2004
    ..Using genomes from the genus Saccharomyces, we illustrate how the significance of real sites increases with evolutionary distance and explore the relationship between conservation and function...
  4. pmc Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting
    Daniel A Pollard
    Graduate Group in Biophysics, University of California Berkeley, Berkeley, California, USA
    PLoS Genet 2:e173. 2006
    ..Methods to infer the correct species tree, the history of every base in the genome, and comparative methods that control for and/or utilize this information will be valuable advancements for the field of comparative genomics...
  5. pmc Benchmarking tools for the alignment of functional noncoding DNA
    Daniel A Pollard
    Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
    BMC Bioinformatics 5:6. 2004
    ..For noncoding sequences, where such independent validation is lacking, simulation provides an effective means to generate "correct" alignments with which to benchmark alignment tools...
  6. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  7. pmc Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm
    Xiao Yong Li
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
    PLoS Biol 6:e27. 2008
    ....