J C Fay

Summary

Affiliation: Lawrence Berkeley National Laboratory
Country: USA

Publications

  1. ncbi request reprint The neutral theory in the genomic era
    J C Fay
    Committee on Genetics, University of Chicago, 1101 East 57th Street, Chicago, Illinois 60637, USA
    Curr Opin Genet Dev 11:642-6. 2001
  2. ncbi request reprint Testing the neutral theory of molecular evolution with genomic data from Drosophila
    Justin C Fay
    Committee on Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Nature 415:1024-6. 2002
  3. ncbi request reprint Sequence divergence, functional constraint, and selection in protein evolution
    Justin C Fay
    Department of Genome Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Annu Rev Genomics Hum Genet 4:213-35. 2003
  4. pmc Hitchhiking under positive Darwinian selection
    J C Fay
    Committee on Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Genetics 155:1405-13. 2000
  5. pmc Positive and negative selection on the human genome
    J C Fay
    Committee on Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Genetics 158:1227-34. 2001
  6. pmc DNA variability and divergence at the notch locus in Drosophila melanogaster and D. simulans: a case of accelerated synonymous site divergence
    Vanessa Bauer DuMont
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genetics 167:171-85. 2004
  7. pmc Identification of functional transcription factor binding sites using closely related Saccharomyces species
    Scott W Doniger
    Computational Biology Program, Washington University School of Medicine, St Louis, MO 63110, USA
    Genome Res 15:701-9. 2005
  8. pmc Hypervariable noncoding sequences in Saccharomyces cerevisiae
    Justin C Fay
    Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Genetics 170:1575-87. 2005
  9. pmc Frequent gain and loss of functional transcription factor binding sites
    Scott W Doniger
    Computational Biology Program, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS Comput Biol 3:e99. 2007
  10. pmc Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome
    Ziva Misulovin
    Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA
    Chromosoma 117:89-102. 2008

Collaborators

Detail Information

Publications11

  1. ncbi request reprint The neutral theory in the genomic era
    J C Fay
    Committee on Genetics, University of Chicago, 1101 East 57th Street, Chicago, Illinois 60637, USA
    Curr Opin Genet Dev 11:642-6. 2001
    ..Recently, these tests have been applied on a genomic scale and have provided estimates of the frequency of adaptive substitutions and a critical test of the neutral theory...
  2. ncbi request reprint Testing the neutral theory of molecular evolution with genomic data from Drosophila
    Justin C Fay
    Committee on Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Nature 415:1024-6. 2002
    ..A higher A/S ratio of divergence than of polymorphism is also observed in other species, which suggests a rate of adaptive evolution that is far higher than permitted by the neutral theory of molecular evolution...
  3. ncbi request reprint Sequence divergence, functional constraint, and selection in protein evolution
    Justin C Fay
    Department of Genome Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Annu Rev Genomics Hum Genet 4:213-35. 2003
    ..We relate these studies to our understanding of the neutral theory and adaptive evolution...
  4. pmc Hitchhiking under positive Darwinian selection
    J C Fay
    Committee on Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Genetics 155:1405-13. 2000
    ..Application of the H test to published surveys of Drosophila variation reveals an excess of high frequency variants that are likely to have been influenced by positive selection...
  5. pmc Positive and negative selection on the human genome
    J C Fay
    Committee on Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Genetics 158:1227-34. 2001
    ..The A/S ratio of fixed differences is greater than that of common SNPs and suggests that a large fraction of protein divergence is adaptive and driven by positive Darwinian selection...
  6. pmc DNA variability and divergence at the notch locus in Drosophila melanogaster and D. simulans: a case of accelerated synonymous site divergence
    Vanessa Bauer DuMont
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genetics 167:171-85. 2004
    ..melanogaster at this locus. These results suggest that positive selection, and not simply relaxation of constraint on codon bias, has contributed to the higher levels of unpreferred divergence along the D. melanogaster lineage at Notch...
  7. pmc Identification of functional transcription factor binding sites using closely related Saccharomyces species
    Scott W Doniger
    Computational Biology Program, Washington University School of Medicine, St Louis, MO 63110, USA
    Genome Res 15:701-9. 2005
    ..Together these data imply that although sequence conservation can be reliably used to predict functional TFBSs, unconserved sequences might also make a significant contribution to a species' biology...
  8. pmc Hypervariable noncoding sequences in Saccharomyces cerevisiae
    Justin C Fay
    Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Genetics 170:1575-87. 2005
    ..Although hypervariable noncoding sequences could result from selection on regulatory mutations, they could also result from transient mutational hotspots...
  9. pmc Frequent gain and loss of functional transcription factor binding sites
    Scott W Doniger
    Computational Biology Program, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS Comput Biol 3:e99. 2007
    ..The frequent gain and loss of TFBSs implies that cis-regulatory sequences are labile and, in the absence of turnover, may contribute to species-specific patterns of gene expression...
  10. pmc Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome
    Ziva Misulovin
    Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA
    Chromosoma 117:89-102. 2008
    ..These mechanisms are likely involved in the etiology of Cornelia de Lange syndrome, in which mutation of one copy of the NIPBL gene encoding the human Nipped-B ortholog causes diverse structural and mental birth defects...
  11. pmc Genetic variation in the cysteine biosynthesis pathway causes sensitivity to pharmacological compounds
    Hyun Seok Kim
    Computational Biology Program, Washington University, St Louis, MO 63108
    Proc Natl Acad Sci U S A 104:19387-91. 2007
    ..These results implicate the cysteine/glutathione biosynthesis pathway as a significant, but not the sole contributor to pharmacological variation in yeast...