J C Fay
Affiliation: Washington University School of Medicine
- Tapping into yeast diversityJustin 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...
- Phylogeny based discovery of regulatory elementsJason Gertz
Department of Genetics, Washington University School of Medicine, 4444 Forest Park Parkway, St Louis, MO 63108, USA
BMC Bioinformatics 7:266. 2006....
- Weighing the evidence for adaptation at the molecular levelJustin 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...
- Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiaeJustin 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....
- Hypervariable noncoding sequences in Saccharomyces cerevisiaeJustin 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...
- Evaluating the role of natural selection in the evolution of gene regulationJ C Fay
Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA
Heredity (Edinb) 100:191-9. 2008....
- Identification of functional transcription factor binding sites using closely related Saccharomyces speciesScott 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...
- Frequent gain and loss of functional transcription factor binding sitesScott 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...
- Quantification of rare allelic variants from pooled genomic DNATodd 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...
- Dissecting the pleiotropic consequences of a quantitative trait nucleotideHyun 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...
- A combined-cross analysis reveals genes with drug-specific and background-dependent effects on drug sensitivity in Saccharomyces cerevisiaeHyun 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...
- Genetic variation in the cysteine biosynthesis pathway causes sensitivity to pharmacological compoundsHyun 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...
- Sequence divergence, functional constraint, and selection in protein evolutionJustin 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...
- Preventing preterm birth: the past limitations and new potential of animal modelsChristine K Ratajczak
Molecular Cell Biology Program, Washington University, St Louis, MO 63110, USA
Dis Model Mech 3:407-14. 2010....
- DNA variability and divergence at the notch locus in Drosophila melanogaster and D. simulans: a case of accelerated synonymous site divergenceVanessa 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...
- A catalog of neutral and deleterious polymorphism in yeastScott 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...
- Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genomeZiva 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...
- Testing the neutral theory of molecular evolution with genomic data from DrosophilaJustin 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...
- Evolution of cis-regulatory sequencesJustin C Fay; Fiscal Year: 2010....
- Evolution of cis-regulatory sequencesJustin Fay; Fiscal Year: 2009....
- GENES AND GENETIC INTERACTIONS UNDERLYING PHARMACOLOGICAL VARIATION IN YEASTWeixiong 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. ..