Colin N Dewey
Affiliation: University of California
- Evolution at the nucleotide level: the problem of multiple whole-genome alignmentColin 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...
- Genomic variation in natural populations of Drosophila melanogasterCharles 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...
- Parametric alignment of Drosophila genomesColin 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...
- Aligning multiple whole genomes with Mercator and MAVIDColin 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...
- A genome-wide map of conserved microRNA targets in C. elegansSabbi 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...
- Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genomeElliott 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...
- Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulansDavid J Begun
Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
PLoS Biol 5:e310. 2007..simulans...
- Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate intronsColin 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...
- Discovery of functional elements in 12 Drosophila genomes using evolutionary signaturesAlexander 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...
- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectEwan Birney
Nature 447:799-816. 2007..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...