Alan M Moses

Summary

Affiliation: University of California
Country: USA

Publications

  1. 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
  2. pmc Conservation and evolution of cis-regulatory systems in ascomycete fungi
    Audrey P Gasch
    Genome Sciences Department, Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    PLoS Biol 2:e398. 2004
  3. 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
  4. pmc Position specific variation in the rate of evolution in transcription factor binding sites
    Alan M Moses
    Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA
    BMC Evol Biol 3:19. 2003
  5. 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
  6. pmc Primate-specific evolution of an LDLR enhancer
    Qian Fei Wang
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genome Biol 7:R68. 2006
  7. 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
  8. pmc Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis
    Ryan K Shultzaberger
    Department of Molecular and Cell Biology, University of California, Berkeley, United States of America
    PLoS ONE 2:e1199. 2007
  9. pmc Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts
    Derek Y Chiang
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Genome Biol 4:R43. 2003
  10. ncbi request reprint In vivo enhancer analysis of human conserved non-coding sequences
    Len A Pennacchio
    US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 444:499-502. 2006

Detail Information

Publications12

  1. 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...
  2. pmc Conservation and evolution of cis-regulatory systems in ascomycete fungi
    Audrey P Gasch
    Genome Sciences Department, Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    PLoS Biol 2:e398. 2004
    ..Our results suggest that the DNA binding specificity of these proteins has coevolved with the sequences found upstream of the Rpn4p target genes and suggest that Rpn4p has a different function in N. crassa...
  3. 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...
  4. pmc Position specific variation in the rate of evolution in transcription factor binding sites
    Alan M Moses
    Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA
    BMC Evol Biol 3:19. 2003
    ..Comparison of non-coding DNA from related species has shown considerable promise in identifying these functional non-coding sequences, even though relatively little is known about their evolution...
  5. 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...
  6. pmc Primate-specific evolution of an LDLR enhancer
    Qian Fei Wang
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genome Biol 7:R68. 2006
    ..Sequence changes in regulatory regions have often been invoked to explain phenotypic divergence among species, but molecular examples of this have been difficult to obtain...
  7. 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...
  8. pmc Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis
    Ryan K Shultzaberger
    Department of Molecular and Cell Biology, University of California, Berkeley, United States of America
    PLoS ONE 2:e1199. 2007
    ..Interestingly, we found that the major determinant of Met4 regulation was the sum of the strength of the Cbf1 and Met31 binding sites and that the energetic costs associated with spacing appeared to be minimal...
  9. pmc Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts
    Derek Y Chiang
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Genome Biol 4:R43. 2003
    ..We extend this concept of functional conservation to higher-order features of transcription control regions...
  10. ncbi request reprint In vivo enhancer analysis of human conserved non-coding sequences
    Len A Pennacchio
    US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 444:499-502. 2006
    ....
  11. pmc Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase
    Alan M Moses
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
    Genome Biol 8:R23. 2007
    ..Our data suggest that regulatory modules may exist in protein sequence as clusters of short sequence motifs...
  12. pmc Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites
    Alan M Moses
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1HH, United Kingdom
    Proc Natl Acad Sci U S A 104:17713-8. 2007
    ..Our results begin to explore the dynamics of regulatory evolution at the posttranslational level and show interesting similarities to recent observations of regulatory evolution at the level of transcription...