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Publications

  1. Vilgalys TP, Klunk J, Demeure CE, Cheng X, Shiratori M, Madej J, Beau R, Elli D, Patino MI, Redfern R, DeWitte SN, Gamble JA, Boldsen JL, Carmichael A, Varlik N, Eaton K, Grenier J-C, Golding GB, Devault A, Rouillard J-M, Yotova V, Sindeaux R, Ye CJ, Bikaran M, Dumaine A, Brinkworth JF, Missiakas D, Rouleau GA, Steinrücken M, Pizarro-Cerdá J, Poinar H^, Barreiro LB^. Reply to Barton et al: signatures of natural selection during the Black Death. bioRxiv doi:10.1101/2023.04.06.535944.
  2. Woitowich NC*, Hengel SR*, Vilgalys TP, Babdor J, Tyrrell DJ. Analysis of NIH K99/R00 Awards and the Career Progression of Awardees. eLife 12:RP88984. doi:10.7554/eLife.88984.1. 
  3. Klunk J*, Vilgalys TP*, Demeure CE, Cheng X, Shiratori M, Madej J, Beau R, Elli D, Patino MI, Redfern R, DeWitte SN, Gamble JA, Boldsen JL, Carmichael A, Varlik N, Eaton K, Grenier J-C, Golding GB, Devault A, Rouillard J-M, Yotova V, Sindeaux R, Ye CJ, Bikaran M, Dumaine A, Brinkworth JF, Missiakas D, Rouleau GA, Steinrücken M, Pizarro-Cerdá J, Poinar H^, Barreiro LB^. 2022. Evolution of immune genes is associated with the Black Death. Nature 611: 312–319, doi.  
  4. Vilgalys TP*, Fogel AS*, Anderson JA, Mututua RF, Warutere JK, Kim SY, Voyles TN, Robinson JA, Wall JD, Archie EA, Alberts SC, Tung J. 2022. Selection against admixture and gene regulatory divergence in a long-term primate field study. Science​ 377(6606): 635-641, doi.org/10.1126/science.abm4917​. ​
  5. Batra SS, Levy-Sakin M, Robinson JA, Guillory J, Durinck S, Vilgalys TP, Kwok PY, Cox LA, Seshagiri S, Song YS, Wall JD. 2020. Accurate assembly of the olive baboon (Papio anubis) genome using long-read and Hi-C data. Gigascience 9(12): giaa134, doi.org/10.1093/gigascience/giaa134. 
  6. Anderson JA, Vilgalys TP, Tung J. 2020. Broadening primate genomics: new insights into the ecology and evolution of primate gene regulation. Current Opinions in Genetics & Development 62: 16-22, doi.org/10.1016/j.gde.2020.05.009. 
  7. Fan Y, Vilgalys TP, Sun S, Peng Q, Tung J, Zhou X. 2019. IMAGE: high-powered detection of genetic effects on DNA methylation using integrated methylation QTL mapping and allele-specific analysis. Genome Biology 20: 220, doi.org/10.1186/s13059-019-1813-1.
  8. Vilgalys TP, Rogers J, Jolly C, Mukherjee S, Baboon Genome Analysis Consortium, Tung J. 2019. Evolution of DNA methylation in Papio baboons. Molecular Biology & Evolution 36(3): 527-540, doi.org/10.1093/molbev/msy227.
  9. ​Rogers J, et al., Baboon Genome Analysis Consortium (including Vilgalys TP). 2019. The comparative genomics and complex population history of Papio baboons. Science Advances 5(1): eaau6947. 
  10. Watts HE, Jiminez D, Pacheco V, Vilgalys TP. 2018. Temperature-correlated shifts in the timing of egg laying in house finches Haemorhous mexicanus. International Journal of Avian Science: doi.org/10.1111/ibi.12676.
  11. Watts HE, Jiminez D, Pacheco V, Vilgalys TP. 2018. Effects of temperature on the timing of breeding and molt transitions in house finches. Journal of Experimental Biology 221: 185058. 
  12. Lea AJ, Vilgalys TP, Durst PAP, Tung J. 2017. Maximizing ecological and evolutionary insight from bisulfite sequencing data sets. Nature Ecology & Evolution 1(8): 1074. 
  13. ​Vilgalys TP, Sears R, Hand E, Morlege-Hampton S, Carmona-Galindo V. 2014. Exploration of climate influences on the abundance of galls on red willows (Salix laevitigata) across two riparian communities in Southern California. Journal of Ecology and the Natural Environment 5(5): 164-169.