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2021
Aluru C, Singh M. Improved inference of tandem domain duplications. Bioinformatics. 2021 ;37(Suppl_1):i133-i141.
2020
Tareen A, Wingreen NS, Mukhopadhyay R. Asymmetry between Activators and Deactivators in Functional Protein Networks. Sci Rep. 2020 ;10(1):10131.
Ramundo S, Asakura Y, Salomé PA, Strenkert D, Boone M, Mackinder LCM, et al.. Coexpressed subunits of dual genetic origin define a conserved supercomplex mediating essential protein import into chloroplasts. Proc Natl Acad Sci U S A. 2020 ;117(51):32739-32749.
Kapheim KM, Jones BM, Pan H, Li C, Harpur BA, Kent CF, et al. Developmental plasticity shapes social traits and selection in a facultatively eusocial bee. Proc Natl Acad Sci U S A. 2020 ;117(24):13615-13625.
Saad-Roy CM, Arinaminpathy N, Wingreen NS, Levin SA, Akey JM, Grenfell BT. Implications of localized charge for human influenza A H1N1 hemagglutinin evolution: Insights from deep mutational scans. PLoS Comput Biol. 2020 ;16(6):e1007892.
2019
Federspiel JD, Tandon P, Wilczewski CM, Wasson L, Herring LE, Venkatesh SS, et al. Conservation and divergence of protein pathways in the vertebrate heart. PLoS Biol. 2019 ;17(9):e3000437.
Gaska JM, Parsons L, Balev M, Cirincione A, Wang W, Schwartz RE, et al. Conservation of cell-intrinsic immune responses in diverse nonhuman primate species. Life Sci Alliance. 2019 ;2(5).
Wang S-W, Bitbol A-F, Wingreen NS. Revealing evolutionary constraints on proteins through sequence analysis. PLoS Comput Biol. 2019 ;15(4):e1007010.
Schober AF, Mathis AD, Ingle C, Park JO, Chen L, Rabinowitz JD, et al. A Two-Enzyme Adaptive Unit within Bacterial Folate Metabolism. Cell Rep. 2019 ;27(11):3359-3370.e7.
2018
Hoegler KJ, Hecht MH. Artificial Gene Amplification in Escherichia coli Reveals Numerous Determinants for Resistance to Metal Toxicity. J Mol Evol. 2018 ;86(2):103-110.
Ali MZulfikar, Wingreen NS, Mukhopadhyay R. Hidden long evolutionary memory in a model biochemical network. Phys Rev E. 2018 ;97(4-1):040401.
Schumer M, Xu C, Powell DL, Durvasula A, Skov L, Holland C, et al. Natural selection interacts with recombination to shape the evolution of hybrid genomes. Science. 2018 ;360(6389):656-660.
Douam F, Fusil F, Enguehard M, Dib L, Nadalin F, Schwaller L, et al. A protein coevolution method uncovers critical features of the Hepatitis C Virus fusion mechanism. PLoS Pathog. 2018 ;14(3):e1006908.
2017
Cleard F, Wolle D, Taverner AM, Aoki T, Deshpande G, Andolfatto P, et al. Different Evolutionary Strategies To Conserve Chromatin Boundary Function in the Bithorax Complex. Genetics. 2017 ;205(2):589-603.
McCulloch KJ, Yuan F, Zhen Y, Aardema ML, Smith G, Llorente-Bousquets J, et al. Sexual Dimorphism and Retinal Mosaic Diversification following the Evolution of a Violet Receptor in Butterflies. Mol Biol Evol. 2017 ;34(9):2271-2284.
2016
Greco TM, Cristea IM. The Biochemical Evolution of Protein Complexes. Trends Biochem Sci. 2016 ;41(1):4-6.
Koch IJanowitz, Clark MM, Thompson MJ, Deere-Machemer KA, Wang J, Duarte L, et al. The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves. Mol Ecol. 2016 ;25(8):1838-55.
Hoegler KJ, Hecht MH. A de novo protein confers copper resistance in Escherichia coli. Protein Sci. 2016 ;25(7):1249-59.
Schweizer RM, vonHoldt BM, Harrigan R, Knowles JC, Musiani M, Coltman D, et al. Genetic subdivision and candidate genes under selection in North American grey wolves. Mol Ecol. 2016 ;25(1):380-402.
Elyashiv E, Sattath S, Hu TT, Strutsovsky A, McVicker G, Andolfatto P, et al. A Genomic Map of the Effects of Linked Selection in Drosophila. PLoS Genet. 2016 ;12(8):e1006130.
Aardema ML, Andolfatto P. Phylogenetic incongruence and the evolutionary origins of cardenolide-resistant forms of Na(+) ,K(+) -ATPase in Danaus butterflies. Evolution. 2016 ;70(8):1913-21.
Webb CJ, Zakian VA. Telomerase RNA is more than a DNA template. RNA Biol. 2016 ;13(8):683-9.
2015
Smith BA, Mularz AE, Hecht MH. Divergent evolution of a bifunctional de novo protein. Protein Sci. 2015 ;24(2):246-52.
Ghosh R, Bloom JS, Mohammadi A, Schumer ME, Andolfatto P, Ryu W, et al. Genetics of Intraspecies Variation in Avoidance Behavior Induced by a Thermal Stimulus in Caenorhabditis elegans. Genetics. 2015 ;200(4):1327-39.
Nadimpalli S, Persikov AV, Singh M. Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PLoS Genet. 2015 ;11(3):e1005011.