Publications

Google Scholar Profile

  1. Li XC, Fay JC. 2017. Cis-Regulatory Divergence in Gene Expression between Two Thermally Divergent Yeast Species. Genome Biol Evol 9:1120-1129.
  2. Peris D, Moriarty RV, Alexander WG, Baker E, Sylvester K, Sardi M, Langdon QK, Libkind D, Wang QM, Bai FY, Leducq JB, Charron G, Landry CR, Sampaio JP, Gonçalves P, Hyma KE, Fay JC, Sato TK, Hittinger CT. 2017. Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production. Biotechnol Biofuels 10:78.
  3. Mezzetti F, Fay JC, Giudici P, De Vero L. 2017. Genetic variation and expression changes associated with molybdate resistance from a glutathione producing wine strain of Saccharomyces cerevisiae. PLoS One 12:e0180814.
  4. Ludlow CL, Cromie GA, Garmendia-Torres C, Sirr A, Hays M, Field C, Jeffery EW, Fay JC, Dudley AM. 2016. Independent Origins of Yeast Associated with Coffee and Cacao Fermentation. Curr Biol 26:965-71.
  5. Kono TJ, Fu F, Mohammadi M, Hoffman PJ, Liu C, Stupar RM, Smith KP, Tiffin P, Fay JC, Morrell PL. 2016. The Role of Deleterious Substitutions in Crop Genomes. Mol Biol Evol 33:2307-17.
  6. Bergen AC, Olsen GM, Fay JC. 2016. Divergent MLS1 promoters lie on a fitness plateau for gene expression. Mol Biol Evol 33:1270-9.
  7. Dashko S, Liu P, Volk H, Butinar L, Piškur J, Fay JC. 2016. Changes in the relative abundance of two Saccharomyces species from Oak forests to wine fermentations. Frontiers in Microbiology 7:215.
  8. Tsen SD, Kibler K, Jacobs B, Fay JC, Podolnikova NP, Ugarova TP, Achilefu S, Tsen KT. 2016. Selective photonic disinfection of cell culture using a visible ultrashort pulsed laser. IEEE J Sel Top Quantum Electron 22:7100508.
  9. Scienski K, Fay JC, Conant GC. 2015. Patterns of gene conversion in duplicated yeast histones suggest strong selection on a coadapted macromolecular complex. Genome Biology and Evol 7:3249-58.
  10. Williams KM, Liu P, Fay JC. 2015. Evolution of ecological dominance of yeast species in high-sugar environments. Evolution 69:2079-93.
  11. Nikolskiy I, Conrad DF, Chun S, Fay JC, Cheverud JM, Lawson HA. 2015. BMC Genomics 16:415.
  12. Swain Lenz D, Riles L, Fay JC. 2014. Heterochronic meiotic misexpression in an interspecific yeast hybrid. Mol Biol Evol 31:1333-42.
  13. Chun S, Plunkett J, Teramo K, Muglia LJ, Fay JC. 2013. Fine-mapping an association of FSHR with preterm birth in a Finnish population. PLoS One 8:e78032.
  14. Cromie GA, Hyma KE, Ludlow CL, Garmendia-Torres C, Gilbert TL, May P, Huang AA, Dudley AM, Fay JC. 2013. Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq. G3 (Bethesda) 3:2163-71.
  15. Engle EK, Fay JC. 2013. ZRT1 harbors an excess of nonsynonymous polymorphism and shows evidence of balancing selection. G3 (Bethesda) 3:665-73.
  16. Xiong Y, Brunson M, Huh J, Huang A, Coster A, Wendt K, Fay J, Qin D. 2013. The role of surface chemistry on the toxicity of ag nanoparticles. Small 9:2628-38.
  17. Hyma KE, Fay JC. 2013. Mixing of vineyard and oak-tree ecotypes of Saccharomyces cerevisiae in North American vineyards. Mol Ecol 22:2917-30.
  18. Kim HS, Huh J, Riles L, Reyes A, Fay JC. 2012. A noncomplementation screen for quantitative trait alleles in Saccharomyces cerevisiae. G3 (Bethesda) 2:753-60.
  19. Engle EK, Fay JC. 2012. Divergence of the yeast transcription factor FZF1 affects sulfite resistance. PLoS Genet 8:e1002763.
  20. Fay JC. 2011. Weighing the evidence for adaptation at the molecular level. Trends Genet 27:343-9.
  21. Chun S, Fay JC. 2011. Evidence for hitchhiking of deleterious mutations within the human genome. PLoS Genet 7:e1002240.
  22. Hyma KE, Saerens SM, Verstrepen KJ, Fay JC. 2011. Divergence in wine characteristics produced by wild and domesticated strains of Saccharmoyces cerevisiae. FEMS Yeast Res 11:540-51.
  23. Plunkett J, Doniger S, Orabona G, Morgan T, Haataja R, Hallman M, Puttonen H, Menon R, Kuczynski E, Norwitz E, Snegovskikh V, Palotie A, Peltonen L, Fellman V, DeFranco EA, Chaudhari BP, McGregor TL, McElroy JJ, Oetjens MT, Teramo K, Borecki I, Fay J, Muglia L. 2011. An evolutionary genomic approach to identify genes involved in human birth timing. PLoS Genet 7:e1001365.
  24. Plunkett J, Doniger S, Morgan T, Haataja R, Hallman M, Puttonen H, Menon R, Kuczynski E, Norwitz E, Snegovskikh V, Palotie A, Peltonen L, Fellman V, DeFranco EA, Chaudhari BP, Oates J, Boutaud O, McGregor TL, McElroy JJ, Teramo K, Borecki I, Fay JC, Muglia LJ. 2010. Primate-specific evolution of noncoding element insertion into PLA2G4C and human preterm birth. BMC Med Genomics 3:62.
  25. Venkataram S, Fay JC. 2010. Is transcription factor binding site turnover a sufficient explanation for cis-regulatory sequence divergence? Genome Biol Evol 2:851-58.
  26. Will JL, Kim HS, Clarke J, Painter JC, Fay JC, Gasch AP. 2010. Incipient balancing selection through adaptive loss of aquaporins in natural populations of Saccharomyces cerevisiae. PLoS Genet 6:e1000893.
  27. Kim HS, Fay JC. 2009. A combined cross analysis reveals genes with drug-specific and background-dependent effects on drug sensitivity in Saccharomyces cerevisiae. Genetics 183:1141-1151.
  28. Chun S, Fay JC. 2009. Identification of deleterious mutations within three human genomes. Genome Res 19:1553-1561.
  29. Kim HS, Huh J, Fay JC. 2009. Dissecting the pleiotropic consequences of a quantitative trait nucleotide. FEMS Yeast Research 9:713-722.
  30. Druley TE, Vallania FL, Wegner DJ, Varley KE, Knowles OL, Bonds JA, Robison SW, Doniger SW, Hamvas A, Cole FS, Fay JC, Mitra RD. 2009. Quantification of rare allelic variants from pooled genomic DNA. Nat Methods 6:263-265.
  31. Doniger SW, Kim HS, Swain D, Corcuera D, Williams M, Yang SP, Fay JC. 2008. A catalog of neutral and deleterious polymorphism in yeast. PLoS Genetics 4:e1000183.
  32. Misulovin Z, Schwartz YB, Li XY, Kahn TG, Gause M, Macarthur S, Fay JC, Eisen MB, Pirrotta V, Biggin MD, Dorsett D. 2008. Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome. Chromosoma 117:89-102.
  33. Kim HS, Fay JC. 2007. Genetic variation in the cysteine biosynthesis pathway causes sensitivity to pharmacological compounds. Proc Natl Acad Sci USA 104:19387-91.
  34. Doniger SW, Fay JC. 2007. Frequency gain and loss of functional transcription factor binding sites. PloS Comput Biol 3:e99.
  35. Gertz J, Fay JC, Cohen BA. 2006. Phylogeny based discovery of regulatory elements. BMC Bioinformatics 7:266.
  36. Fay JC, Benavides JA. 2005. Hypervariable noncoding sequences in Saccharomyces cerevisiae. Genetics 170:1575-87.
  37. Fay JC, Benavides JA. 2005. Evidence for domesticated and wild populations of Saccharomyces cerevisiae. PLoS Genetics 1:66-71.
  38. Doniger SW, Huh J, Fay JC. 2005. Identification of functional transcription factor binding sites using closely related Saccharomyces species. Genome Research 15:701-709.
  39. DuMont VB, Fay JC, Calabrese PP, Aquadro CF. 2004. DNA variability and divergence at the notch locus in Drosophila melanogaster and D. simulans:a case of accelerated synonymous site divergence. Genetics 167:171-185.
  40. Fay JC, McCullough HL, Sniegowski PD, Eisen MB. 2004. Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae. Genome Biol 5:R26.
  41. Fay JC, Wyckoff GJ, Wu C-I. 2002. Testing the neutral theory of molecular evolution with genomic data from Drosophila. Nature 415:1024-1026.
  42. Fay JC, Wyckoff GJ, Wu C-I. 2001. Positive and negative selection on the human genome. Genetics 155:1227-1234.
  43. Fay JC, Wu C-I. 2000. Hitchhiking under positive Darwinian selection. Genetics 155:1405-1413.
  44. Fay JC, Wu C-I. 1999. A human population bottleneck can account for the discordance between patterns of mitochondrial and nuclear DNA variation. Mol Biol Evol 16:1003-1005.
  45. Fay JC, Fry WE. 1997. 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.