J C Fay

Summary

Affiliation: Washington University School of Medicine
Country: USA

Publications

  1. pmc A catalog of neutral and deleterious polymorphism in yeast
    Scott W Doniger
    Computational Biology Program, Washington University, St Louis, Missouri, United States of America
    PLoS Genet 4:e1000183. 2008
  2. pmc Is transcription factor binding site turnover a sufficient explanation for cis-regulatory sequence divergence?
    Sandeep Venkataram
    Department of Genetics, Washington University, St Louis, Missouri, USA
    Genome Biol Evol 2:851-8. 2010
  3. pmc Fine-mapping an association of FSHR with preterm birth in a Finnish population
    Sung Chun
    Computational and Systems Biology Program, Washington University, St Louis, Missouri, United States of America
    PLoS ONE 8:e78032. 2013
  4. pmc Evidence for hitchhiking of deleterious mutations within the human genome
    Sung Chun
    Computational and Systems Biology Program, Washington University, St Louis, Missouri, United States of America
    PLoS Genet 7:e1002240. 2011
  5. pmc Divergence of the yeast transcription factor FZF1 affects sulfite resistance
    Elizabeth K Engle
    Molecular Genetics and Genomics Program, Washington University, St Louis, Missouri, United States of America
    PLoS Genet 8:e1002763. 2012
  6. pmc A noncomplementation screen for quantitative trait alleles in saccharomyces cerevisiae
    Hyun Seok Kim
    Department of Genetics, Washington University, St Louis, Missouri 63108, USA
    G3 (Bethesda) 2:753-60. 2012
  7. pmc The molecular basis of phenotypic variation in yeast
    Justin C Fay
    Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University, St Louis, MO, United States Electronic address
    Curr Opin Genet Dev 23:672-7. 2013
  8. ncbi Tapping into yeast diversity
    Justin C Fay
    Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University, St Louis, MO 63108, USA
    Mol Ecol 21:5387-9. 2012
  9. pmc Phylogeny based discovery of regulatory elements
    Jason Gertz
    Department of Genetics, Washington University School of Medicine, 4444 Forest Park Parkway, St Louis, MO 63108, USA
    BMC Bioinformatics 7:266. 2006
  10. ncbi Evaluating the role of natural selection in the evolution of gene regulation
    J C Fay
    Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA
    Heredity (Edinb) 100:191-9. 2008

Collaborators

Detail Information

Publications25

  1. pmc A catalog of neutral and deleterious polymorphism in yeast
    Scott W Doniger
    Computational Biology Program, Washington University, St Louis, Missouri, United States of America
    PLoS Genet 4:e1000183. 2008
    ..Our results show that the genome sequences of both closely and distantly related species provide a means of identifying deleterious polymorphisms that disrupt functionally conserved coding and noncoding sequences...
  2. pmc Is transcription factor binding site turnover a sufficient explanation for cis-regulatory sequence divergence?
    Sandeep Venkataram
    Department of Genetics, Washington University, St Louis, Missouri, USA
    Genome Biol Evol 2:851-8. 2010
    ..Our results imply that binding site turnover is not a sufficient explanation for cis-regulatory sequence evolution...
  3. pmc Fine-mapping an association of FSHR with preterm birth in a Finnish population
    Sung Chun
    Computational and Systems Biology Program, Washington University, St Louis, Missouri, United States of America
    PLoS ONE 8:e78032. 2013
    ....
  4. pmc Evidence for hitchhiking of deleterious mutations within the human genome
    Sung Chun
    Computational and Systems Biology Program, Washington University, St Louis, Missouri, United States of America
    PLoS Genet 7:e1002240. 2011
    ..Our results suggest that positive selection has had a significant impact on deleterious polymorphism and may be partly responsible for the high frequency of certain human disease alleles...
  5. pmc Divergence of the yeast transcription factor FZF1 affects sulfite resistance
    Elizabeth K Engle
    Molecular Genetics and Genomics Program, Washington University, St Louis, Missouri, United States of America
    PLoS Genet 8:e1002763. 2012
    ..Both coding and noncoding changes also affect the expression of many other genes. Our results show how divergence in the coding and promoter region of a transcription factor alters the response to an environmental stress...
  6. pmc A noncomplementation screen for quantitative trait alleles in saccharomyces cerevisiae
    Hyun Seok Kim
    Department of Genetics, Washington University, St Louis, Missouri 63108, USA
    G3 (Bethesda) 2:753-60. 2012
    ..Our results highlight the difficulty of identifying small-effect alleles but support the use of noncomplementation as a rapid means of identifying quantitative trait alleles of large effect...
  7. pmc The molecular basis of phenotypic variation in yeast
    Justin C Fay
    Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University, St Louis, MO, United States Electronic address
    Curr Opin Genet Dev 23:672-7. 2013
    ..The profile of quantitative trait alleles has proven useful to reverse quantitative genetics approaches and supports the use of systems genetics approaches to synthesize the molecular basis of trait variation across multiple strains. ..
  8. ncbi Tapping into yeast diversity
    Justin C Fay
    Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University, St Louis, MO 63108, USA
    Mol Ecol 21:5387-9. 2012
    ..These lineages substantially expand our knowledge of wild yeast diversity and will be a boon to elucidating the ecology, evolution and domestication of this academic and industrial workhorse...
  9. pmc Phylogeny based discovery of regulatory elements
    Jason Gertz
    Department of Genetics, Washington University School of Medicine, 4444 Forest Park Parkway, St Louis, MO 63108, USA
    BMC Bioinformatics 7:266. 2006
    ....
  10. ncbi Evaluating the role of natural selection in the evolution of gene regulation
    J C Fay
    Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA
    Heredity (Edinb) 100:191-9. 2008
    ....
  11. 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...
  12. pmc Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae
    Justin C Fay
    Department of Genome Sciences, Life Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Rd, Berkeley, CA 94720, USA
    Genome Biol 5:R26. 2004
    ....
  13. pmc Weighing the evidence for adaptation at the molecular level
    Justin C Fay
    Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University, St Louis, MO, USA
    Trends Genet 27:343-9. 2011
    ..Based on these considerations it is argued that the common assumption of independence among sites must be relaxed before abandoning the neutral theory of molecular evolution...
  14. 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...
  15. 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...
  16. pmc A combined-cross analysis reveals genes with drug-specific and background-dependent effects on drug sensitivity in Saccharomyces cerevisiae
    Hyun Seok Kim
    Computational Biology Program, Washington University, St Louis, Missouri 63108, USA
    Genetics 183:1141-51. 2009
    ..Our results suggest that drug response may often depend on interactions between genes with multi-drug and drug-specific effects...
  17. pmc Dissecting the pleiotropic consequences of a quantitative trait nucleotide
    Hyun Seok Kim
    Department of Genetics, Washington University School of Medicine, 444 Forest Park Ave, St Louis, MO 63108, USA
    FEMS Yeast Res 9:713-22. 2009
    ..Our results show that a single quantitative trait polymorphism can generate a complex set of downstream changes, providing a molecular basis for pleiotropy...
  18. pmc Quantification of rare allelic variants from pooled genomic DNA
    Todd E Druley
    Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, USA
    Nat Methods 6:263-5. 2009
    ..Our base-calling algorithm, SNPSeeker, derived from large deviation theory, detected single-nucleotide polymorphisms present at frequencies below the raw error rate of the sequencing platform...
  19. 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...
  20. ncbi 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...
  21. doi Preventing preterm birth: the past limitations and new potential of animal models
    Christine K Ratajczak
    Molecular Cell Biology Program, Washington University, St Louis, MO 63110, USA
    Dis Model Mech 3:407-14. 2010
    ....
  22. 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...
  23. 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...
  24. ncbi 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...

Research Grants7

  1. Evolution of cis-regulatory sequences
    Justin Fay; Fiscal Year: 2007
    ....
  2. Evolution of cis-regulatory sequences
    Justin Fay; Fiscal Year: 2009
    ....
  3. GENES AND GENETIC INTERACTIONS UNDERLYING PHARMACOLOGICAL VARIATION IN YEAST
    Justin Fay; Fiscal Year: 2009
    ..The proposed research will develop and evaluate a method of identifying multiple genes that contribute to complex traits and a model to predict their dependence on genetic background using gene expression data. ..
  4. Evolution of cis-regulatory sequences
    Justin C Fay; Fiscal Year: 2010
    ....
  5. Evolution of cis-regulatory sequences
    Justin Fay; Fiscal Year: 2009
    ....
  6. GENES AND GENETIC INTERACTIONS UNDERLYING PHARMACOLOGICAL VARIATION IN YEAST
    Weixiong Zhang; Fiscal Year: 2010
    ..The proposed research will develop and evaluate a method of identifying multiple genes that contribute to complex traits and a model to predict their dependence on genetic background using gene expression data. ..