Publications

Selected publications by topic (below), complete list: Google Scholar Profile

Genetic basis of thermal divergence in yeast

  • Williams KM, Liu P, Fay JC. 2015. Evolution of ecological dominance of yeast species in high-sugar environments. Evolution 69:2079-83. PMC4751874
  • Li XC, Peris D, Hittinger CT, Sia EA, Fay JC. 2019. Mitochondria-encoded genes contribute to evolution of heat and cold tolerance in yeast. Sci Adv 5:aav1848. PMC6353624
  • Baker EP, Peris D, Moriarty RV, Li XC, Fay JC, Hittinger CT. 2019. Mitochondrial DNA and temperature tolerance in lager yeasts. Sci Adv. 5:eaav1869. PMC6353617
  • Li XC, Fay JC. 2017. Cis-regulatory divergence in gene expression between two thermally divergent yeast species. Genome Biol Evol 9:1120-1129. PMC5554586

Diversification and domestication of yeast

  • Fay JC, Benavides JA. 2005. Evidence for domesticated and wild populations of Saccharomyces cerevisiae. PLoS Genetics 1: 66-71. PMC1183524
  • 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. PMC3852379
  • Hyma KE, Fay JC. 2013. Mixing of vineyard and oak-tree ecotypes of Saccharomyces cerevisiae in North American vineyards. Mol Ecol 22: 2917-30. PMC3620907
  • Fay JC, Liu P, Ong GT, Dunham MJ, Cromie GA, Jeffery EW, Ludlow CL, Dudley AM. 2019. A polyploid admixed origin of beer yeasts derived from European and Asian wine populations. PLoS Biol 17:e3000147. PMC6400334

Evolution of cis-regulatory sequences

  • Doniger SW, Fay JC. 2007. Frequency gain and loss of functional transcription factor binding sites. PloS Comput. Biol. 3: e99. PMC1876492
  • 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. PMC2515631
  • Engle EK, Fay JC. 2012. Divergence of the yeast transcription factor FZF1 affects sulfite resistance. PLoS Genet. 8: e1002763. PMC3375221
  • Bergen AC, Olsen GM, Fay JC. 2016. Divergent MLS1 promoters lie on a fitness plateau for gene expression. Mol Biol Evol 33:1270-9. PMC4839218
  • Shih CH, Fay JC. 2021. Cis-regulatory variants affect gene expression dynamics in yeast. eLife 10:e68469.

Population genomics

  • 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.
  • Chun S, Fay JC. 2009. Identification of deleterious mutations within three human genomes. Genome Res 19:1553-1561.
  • Chun S, Fay JC. 2011. Evidence for hitchhiking of deleterious mutations within the human genome. PLoS Genet 7:e1002240.
  • Kono TJ, Lei L, Shih CH, Hoffman PJ, Morrell PL, Fay JC. 2018. Comparative genomics approaches accurately predict deleterious variants in plants. G3 (Bethesda) 8:3321-3329.
  • Tortelli BA, Lewis AL, Fay JC. 2021. The structure and diversity of strain-level variation in vaginal bacteria. Microbial genomics 7:mgen000543.