Colin N Dewey

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Evolution at the nucleotide level: the problem of multiple whole-genome alignment
    Colin N Dewey
    Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA
    Hum Mol Genet 15:R51-6. 2006
  2. pmc Genomic variation in natural populations of Drosophila melanogaster
    Charles H Langley
    Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
    Genetics 192:533-98. 2012
  3. pmc Parametric alignment of Drosophila genomes
    Colin N Dewey
    Department of Electrical Engineering and Computer Sciences, University of California Berkeley, Berkeley, California, USA
    PLoS Comput Biol 2:e73. 2006
  4. ncbi request reprint Aligning multiple whole genomes with Mercator and MAVID
    Colin N Dewey
    Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, USA
    Methods Mol Biol 395:221-36. 2007
  5. ncbi request reprint A genome-wide map of conserved microRNA targets in C. elegans
    Sabbi Lall
    Center for Comparative Functional Genomics, Department of Biology, New York University, New York, New York 10003, USA
    Curr Biol 16:460-71. 2006
  6. pmc Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
    Elliott H Margulies
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Res 17:760-74. 2007
  7. pmc Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans
    David J Begun
    Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
    PLoS Biol 5:e310. 2007
  8. pmc Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns
    Colin N Dewey
    National Center for Biotechnology Information NLM, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Genomics 7:311. 2006
  9. pmc Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
    Alexander Stark
    The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02140, USA
    Nature 450:219-32. 2007
  10. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007

Detail Information

Publications10

  1. ncbi request reprint Evolution at the nucleotide level: the problem of multiple whole-genome alignment
    Colin N Dewey
    Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA
    Hum Mol Genet 15:R51-6. 2006
    ..Within this framework, we review the current methods available for the alignment of multiple large genomes. We then describe a subset of tools that make biological inferences from multiple whole-genome alignments...
  2. pmc Genomic variation in natural populations of Drosophila melanogaster
    Charles H Langley
    Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
    Genetics 192:533-98. 2012
    ..Comparison of the variation among these genomes to variation among genomes from D. simulans suggests that many targets of directional selection are shared between these species...
  3. pmc Parametric alignment of Drosophila genomes
    Colin N Dewey
    Department of Electrical Engineering and Computer Sciences, University of California Berkeley, Berkeley, California, USA
    PLoS Comput Biol 2:e73. 2006
    ..We also show how whole genome parametric alignment can be used to quantitatively assess the dependence of branch length estimates on alignment parameters...
  4. ncbi request reprint Aligning multiple whole genomes with Mercator and MAVID
    Colin N Dewey
    Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, USA
    Methods Mol Biol 395:221-36. 2007
    ..This tutorial will guide the researcher through the steps required for whole-genome alignment with Mercator and MAVID...
  5. ncbi request reprint A genome-wide map of conserved microRNA targets in C. elegans
    Sabbi Lall
    Center for Comparative Functional Genomics, Department of Biology, New York University, New York, New York 10003, USA
    Curr Biol 16:460-71. 2006
    ..Metazoan miRNAs regulate protein-coding genes by binding the 3' UTR of cognate mRNAs. Identifying targets for the 115 known C. elegans miRNAs is essential for understanding their function...
  6. pmc Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
    Elliott H Margulies
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Res 17:760-74. 2007
    ..Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization...
  7. pmc Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans
    David J Begun
    Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
    PLoS Biol 5:e310. 2007
    ..simulans...
  8. pmc Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns
    Colin N Dewey
    National Center for Biotechnology Information NLM, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Genomics 7:311. 2006
    ..We explored the connections between the length of vertebrate introns, the strength of splice sites, exonic splicing signals, and evolution of flanking exons...
  9. pmc Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
    Alexander Stark
    The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02140, USA
    Nature 450:219-32. 2007
    ..We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies...
  10. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...