Main Projects:

  1. Hittinger C.T., et al. (2015) Genomics and the making of yeast biodiversity. Dec 2015; 35:100-9.
  2. Lopes M.R., et al. (2016) Genomic analysis and D-xylose fermentation of three novel Spathaspora species: Spathaspora girioi sp. nov., Spathaspora haerdaliae f. a., sp. nov. and Spathaspora gorwiae f. a., sp. nov. Jun 2016; 16(4). pii fow044.
  3. Riley R., et al. (2016). Comparative genomics of biotechnologically important yeasts. Proc Natl Acad Sci USA. 30 Aug 2016; 113(35):9882-7.
  4. Zhou X, Peris D, Kominek J, Kurtzman CP, Hittinger CT@, Rokas A@. 2016. in silico Whole Genome Sequencer & Analyzer (iWGS): a computational pipeline to guide the design and analysis of de novo genome sequencing studies. G3 (Bethesda) 6: 3655-62.
  5. Shen XX, Zhou X, Kominek J, Kurtzman CP@, Hittinger CT@, Rokas A@. 2016. Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data. G3 (Bethesda) 6: 3927-39.
  6. Haase MAB, Kominek J, Langdon QK, Kurtzman CP, Hittinger CT. 2017. Genome sequence and physiological analysis of Yamadazyma laniorum f.a. sp. nov. and a reevaluation of the apocryphal xylose fermentation of its sister species, Candida tenuis. FEMS Yeast Res 17: fox019.
  7. Morais CG, Batista TM, Kominek J, Borelli BM, Furtado C, Moreira RG, Franco GR, Rosa LH, Fonseca C, Hittinger CT, Lachance MA, Rosa CA. 2017 Spathaspora boniae sp. nov., a D-xylose-fermenting species in the Candida albicans/Lodderomyces clade. Int J Syst Evol Microbiol 67: 3798–805.
  8. Opulente DA, Rollinson EJ, Bernick-Roehr C, Hulfachor AB, Rokas A, Kurtzman CP, Hittinger CT. 2018. Factors driving metabolic diversity in the budding yeast subphylum. BMC Biol 16: 26.
  9. Gonçalves C, Wisecaver JH, Kominek J, Oom MS, Leandro MJ, Shen XX, Opulente DA, Zhou X, Peris D, Kurtzman CP, Hittinger CT, Rokas A, Gonçalves P. 2018. Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage. eLife 7: e33034.
  10. Krassowski T, Coughlan AY, Shen XX, Zhou X, Kominek J, Opulente DA, Riley R, Grigoriev IV, Maheshwari N, Shields DC, Kurtzman CP, Hittinger CT, Rokas A, Wolfe KH. 2018. Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. Nat Commun 9: 1887.
  11. Krause DJ, Kominek J, Opulente DA, Shen XX, Zhou X, Langdon QK, DeVirgilio J, Hulfachor AB, Kurtzman CP, Rokas A, Hittinger CT@. Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts. Proc Natl Acad Sci USA 115: 11030-11035.
  12. Shen XX&, Opulente DA&, Kominek J&, Zhou X&, Steenwyk JL, Buh KV, Haase MAB, Wisecaver JH, Wang M, Doering DT, Boudouris JT, Schneider RM, Langdon QK, Ohkuma M, Endoh R, Takashima M, Manabe RI, Cadez N, Libkind D, Rosa CA, DeVirgilio J, Hulfachor AB, Groenewald M, Kurtzman CP, Hittinger CT@, Rokas A@. 2018. Tempo and mode of genome evolution in the budding yeast subphylum. Cell 175: 1533-45.
  13. Kominek J&, Doering DT&, Opulente DA, Shen XX, Zhou X, DeVirgilio J, Hulfachor AB, Groenewald M, Mcgee MA, Karlen SD, Kurtzman CP, Rokas A, Hittinger CT@. 2019. Eukaryotic acquisition of a bacterial operon. Cell 176: 1356-66.
  14. Steenwyk JL, Opulente DA, Kominek J, Shen XX, Zhou X, Labella AL, Bradley NP, Eichman BF, Cadez N, Libkind D, DeVirgilio J, Hulfachor AB, Kurtzman CP, Hittinger CT@, Rokas A@. 2019. Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts. PLoS Biol 17: e3000255.
  15. Krassowski T, Kominek J, Shen XX, Opulente DA, Zhou X, Rokas A, Hittinger CT, Wolfe KH. 2019. Multiple reinventions of mating-type switching during budding yeast evolution. Curr Biol 29: 2555-62.
  16. Labella AL, Opulente DA, Steenwyk JL, Hittinger CT, Rokas A. 2019. Variation and selection on codon usage bias across an entire subphylum. PLoS Genet epub: https://doi.org/10.1371/journal.pgen.1008304.

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