Rich A, Carvunis AR. (2023) De nova gene increases brain sizeNature Ecology & Evolution.

Cui X, Xue Y, McCormack C, Garces A, Rachman TW, Yi Y, Stolzer M, Durand D. (2022) Simulating domain architecture evolutionBioinformatics.

Xue-Ping Wang, Deidra M Balchak, Clayton Gentilcore, Nathan L Clark, Ossama B Kashlan. (2022)  Activation by cleavage of the epithelial Na+ channel α and γ subunits independently coevolved with the vertebrate terrestrial migrationElife.

Shields RK, Stellfox ME, Kline EG, Samanta P, Van Tyne D. (2022) Evolution of Imipenem-Relebactam Resistance Following Treatment of Multidrug-Resistant Pseudomonas aeruginosa Pneumonia. Clin Infect Dis.

Elgrail MM, Chen E, Shaffer MG, Srinivasa V, Griffith MP, Mustapha MM, Shields RK, Van Tyne D, Culyba MJ. (2022) Convergent Evolution of Antibiotic Tolerance in Patients with Persistent Methicillin-Resistant Staphylococcus aureus Bacteremia. Infect Immun.

Van Oss SB, Parikh SB, Castilho Coelho N, Wacholder A, Belashov I, Zdancewicz S, Michaca M, Xu J, Kang YP, Ward NP, Yoon SJ, McCourt KM, McKee J, Ideker T, VanDemark AP, DeNicola GM, Carvunis AR. (2022) On the illusion of auxotrophy: met15⌂ yeast cells can grow on inorganic sulfur thanks to the previously uncharacterized homocysteine synthase YII058wJournal of Biological Chemistry.

Iovleva A, Mustapha MM, Griffith MP, Komarow L, Luterbach C, Evans DR, Cober E, Richter SS, Rydell K, Arias CA, Jacob JT, Salata RA, Satlin MJ, Wong D, Bonomo RA, van Duin D, Cooper VS, Van Tyne D, Doi Y.  (2022) Carbapenem-Resistant Acinetobacter baumannii in U.S. Hospitals: Diversification of Circulating Lineages and Antimicrobial Resistance. mBio.

Parikh SB, Houghton C, Van Oss SB, Wacholder A, Carvunis AR.  (2022) Origins, evolution, and physiological implications of de novo genes in yeast.  Yeast.

Nordstrom HR, Evans DR, Finney AG, Westbrook KJ, Zamora PF, Hofstaedter CE, Yassin MH, Pradhan A, Iovleva A, Ernst RK, Bomberger JM, Shields RK, Doi Y, Van Tyne D. (2022) Genomic characterization of lytic bacteriophages targeting genetically diverse Pseudomonas aeruginosa clinical isolates.  iScience.

Mudge JM, Carvuins AR, van Heesch S. (2022) Standardized annotation of translated open reading frames.  Nature Biotechnology.

Mustapha MM, Srinivasa VR, Griffith MP, Cho ST, Evans DR, Waggle K, Ezeonwuka C, Snyder DJ, Marsh JW, Harrison LH, Cooper VS, Van Tyne D. (2022) Genomic Diversity of Hospital-Acquired Infections Revealed through Prospective Whole-Genome Sequencing-Based Surveillance. mSystems.

Guenole A, Velilla F, Chartier A, Rich A, Carvunis AR, Sardet C, Simonelig M, Sobhian B.  (2022) RNF219 regulates CCR4-NOT function in mRNA translation and deadenylationScientific Reports.

Smith AB, Jenior ML, Keenan O, Hart JL, Specker J, Abbas A, Rangel PC, Di C, Green J, Bustin KA, Gaddy JA, Nicholson MR, Laut C, Kelly BJ, Matthews ML, Evans DR, Van Tyne D, Furth EE, Papin JA, Bushman FD, Erlichman J, Baldassano RN, Silverman MA, Dunny GM, Prentice BM, Skaar EP, Zackular JP.  (2022) Enterococci enhance Clostridioides difficile pathogenesis. Nature.

Beckley AM, Wright ES. (2021). Identification of antibiotic pairs that evade concurrent resistance via a retrospective analysis of antimicrobial susceptibility test results. The Lancet.

Morgenthaler AB, Kinney WR, Ebmeier CC, Walsh CM, Snyder DJ, Cooper VS, Old WM, Copley SD.  (2019) Mutations that improve efficiency of a weak-link enzyme are rare compared to adaptive mutations elsewhere in the genomeElife.

Patel RK, Weir MC, Shen K, Snyder D, Cooper VS, Smithgall TE.  (2019) Expression of myeloid Src-family kinases is associated with poor prognosis in AML and influences Flt3-ITD kinase inhibitor acquired resistancePLoS One.

Kim J, Flood JJ, Kristofich MR, Gidfar C, Morgenthaler AB, Fuhrer T, Sauer U, Snyder D, Cooper VS, Ebmeier CC, Old WM, Copley SD. (2019) Hidden resources in the Escherichia coli genome restore PLP synthesis and robust growth after deletion of the essential gene pdxB. Proc Natl Acad Sci USA.

Turner CB, Buskirk SW, Harris KB, Cooper VS.  (2019) Negative frequency-dependent selection maintains coexisting genotypes during fluctuating selection. Mol Ecol.

Bias AS, Kostka D. (2019)  scds: Computational Annotation of Doublets in Single-Cell RNA Sequencing DataBioinformatics.

Benton ML, Talipineni SC, Kostka D, Capra Ja.  (2019)  Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function.  BMC Genomics.

Korandla DR, Wozniak JM, Campeau A, Gonzalez DJ, Wright ES. (2019) AssessORF: combining evolutionary conservation and proteomics to assess prokaryotic gene predictionsBioinformatics.

Santos-Lopez A, Marshall CW, Scribner MR, Snyder DJ, Cooper VS. (2019) Evolutionary pathways to antibiotic resistance are dependent upon environmental structure and bacterial lifestyle. Elife 13;8. doi: 10.7554/eLife.47612.

Hall AE, Karkare K, Cooper VS, Bank C, Cooper TF, Moore FB. (2019) Environment changes epistasis to alter trade-offs along alternative evolutionary paths. Evolution. doi: 10.1111/evo.13825.

Van Oss SB, Carvunis A-R (2019) De novo gene birth. PLoS Genet 15(5): e1008160.

Lin Y, May GE, Kready H, Nazzaro L, Mao M, Spealman P, Creeger Y, McManus CJ. (2019) Impacts of uORF codon identity and position on translation regulationNucleic Acids Research.

Turner CB, Marshall CW, Cooper VS. Parallel genetic adaptation across environments differing in mode of growth or resource availability. Evol Lett. 2(4):355-367. doi: 10.1002/evl3.75. eCollection 2018 Aug.

Gloag ES, Marshall CW, Snyder D, Lewin GR, Harris J, Santos-Lopez A, Chaney SB, Whiteley M, Cooper VS, Wozniak DJ. Pseudomonas aeruginosa Interstrain Dynamics and Selection of Hyperbiofilm Mutants during a Chronic Infection. MBio. 2019 Aug 13;10(4). pii: e01698-19. doi: 10.1128/mBio.01698-19.

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