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Swain Lenz D, Riles L and Fay JC. Heterochronic meiotic misexpression in an interspecific yeast hybrid. Mol Biol Evol in press. pdf

Chun S, Plunkett J, Teramo K, Muglia LJ and Fay JC. Fine-mapping an association of FSHR with preterm birth in a Finnish population. PLoS ONE 8: e78032. pdf

Cromie GA, Hyma KE, Ludlow CL, Garmendia-Torre C et al. Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq. G3 (Bethesda) 3: 2163-2171. pdf

Fay JC. The molecular basis of phenotypic variation in yeast. Curr Opin Genet Dev 23: 672-7. pdf

Fay JC. Disease consequences of human adaptation. Applied & Translational Genomics 2: 42-7. pdf

Hyma KE and Fay JC. Mixing of vineyard and oak-tree ecotypes of Saccharomyces cerevisiae in North American vineyards. Mol Ecol 22: 2917-30. pdf

Engle EK and Fay JC. ZRT1 harbors an excess of nonsynonymous polymorphism and shows evidence of balancing selection in Saccharomyces cerevisiae. G3 (Bethesda) 3: 665-73. pdf

Kim HS, Huh J, Riles L, Reyes A and Fay JC. A noncomplementation screen for quantitative trait alleles in Saccharomyces cerevisiae. G3 (Bethesda) 2: 753-60. pdf

Engle EK and Fay JC. Divergence of the yeast transcription factor FZF1 affects sulfite resistance. PLoS Genet 8: e1002763. pdf

Hyma KE and Fay JC. Divergence in wine characteristics produced by wild and domesticated strains of Saccharomyces cerevisiae. FEMS Yeast Res 11: 540-51. pdf

Fay JC. Weighing evidence for adaptation at the molecular level. Trends Genet 27: 343-9. pdf

Chun S and Fay JC. Evidence for hitchhiking of deleterious mutations within the human genome. PLoS Genet 7: e1002240. pdf

Plunkett J, Doniger S, Orabona G, Morgan T et al. An evolutionary genomic approach to identify genes involved in human birth timing. PLoS Genet 7: e1001365. pdf

Plunkett J, Doniger S, Morgan T, Haataja R et al. Primate-specific evolution of noncoding element insertion into PLA2G4C and human preterm birth. BMC Med Genomics 3: 62. pdf

Venkataram S and Fay JC. Is transcription factor binding site turnover a sufficient explanation for cis-regulatory sequence divergence? Genome Biol Evol 2: 851-8. pdf

Chun S and Fay JC. Identification of deleterious mutations within three human genomes. Genome Research 19: 1553-1561. pdf
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Kim HS and Fay JC. A combined cross analysis reveals genes with drug-specific and background-dependent effects on drug-sensitivity in Saccharomyces cerevisiae. Genetics 183: 1141-51. pdf

Kim HS, Huh J and Fay JC. Dissecting the pleiotropic consequences of a quantitative trait nucleotide. FEMS Yeast Res 9: 713-722. pdf

Doniger SW, Kim HS, Swain D, Corcuera D et al. A catalog of neutral and deleterious polymorphism in yeast. PLoS Genetics 4: e1000183. pdf

Fay JC and Wittkopp PJ. Evaluating the role of natural selection in the evolution of gene regulation. Heredity 100: 191-9. pdf

Kim HS and Fay JC. Genetic variation in the cysteine biosynthesis pathway causes sensitivity to pharmacological compounds. Proc Natl Acad Sci U S A 104: 19387-91. pdf

Doniger SW and Fay JC. Frequent gain and loss of functional transcription factor binding sites. PLoS Comput Biol 3: e99. pdf

Fay JC and Kruglyak L. A white paper for sequencing multiple strains of Saccharomyces cerevisiae. pdf

Fay JC and Benavides JA. Hypervariable noncoding sequences in Saccharomyces cerevisiae. Genetics 170: 1575-87. pdf

Fay JC and Benavides JA. Evidence for domesticated and wild populations of Saccharomyces cerevisiae. PLoS Genetics 1: 66-71. pdf

Fay JC and Wu C-I. Detecting hitchhiking from patterns of DNA polymorphism. In Selective sweeps, Nurminsky, D., ed. Landes Biosciences, Georgetown, Texas. pdf

Doniger SW, Huh J and Fay JC. Identification of functional transcription factor binding sites using closely related Saccharomyces species. Genome Research 15: 701-709. pdf

Fay JC, McCullough HL, Sniegowski PD and Eisen MB. Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae. Genome Biology 5: R26. pdf

Fay JC and Wu C-I. Sequence divergence, functional constraint and selection in protein evolution. Annu Rev Genomics Hum Genet 3: 213-235. pdf

Fay JC, Wyckoff GJ and Wu C-I. Testing the neutral theory of molecular evolution with genomic data from Drosophila. Nature 415: 1024-1026. pdf

Fay JC and Wu C-I. The neutral theory in the genomic era. Curr Opin Genet Dev 11: 642-646. pdf

Fay JC, Wyckoff GJ and Wu C-I. Positive and negative selection on the human genome. Genetics 155: 1227-1234. pdf supplement

Fay JC and Wu C-I. Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413. pdf appendix


Fay JC and Wu C-I. A human population bottleneck can account for the discordance between patterns of mitochondrial and nuclear DNA variation. Mol Biol Evol 16: 1003-1005. pdf


Fay JC and Fry WE. Effects of hot and cold temperatures on the survival of oospores produced by United States strains of Phytophthora infestans. American Potato Journal 74: 315-323.