| Year |
Citation |
Score |
| 2024 |
Alpay BA, Desai MM. Effects of selection stringency on the outcomes of directed evolution. Biorxiv : the Preprint Server For Biology. PMID 38895455 DOI: 10.1101/2024.06.09.598029 |
0.366 |
|
| 2024 |
Dupic T, Phillips AM, Desai MM. Protein sequence landscapes are not so simple: on reference-free versus reference-based inference. Biorxiv : the Preprint Server For Biology. PMID 38352387 DOI: 10.1101/2024.01.29.577800 |
0.624 |
|
| 2024 |
Melissa MJ, Desai MM. A dynamical limit to evolutionary adaptation. Proceedings of the National Academy of Sciences of the United States of America. 121: e2312845121. PMID 38241432 DOI: 10.1073/pnas.2312845121 |
0.522 |
|
| 2023 |
Chen V, Johnson MS, Hérissant L, Humphrey PT, Yuan DC, Li Y, Agarwala A, Hoelscher SB, Petrov DA, Desai MM, Sherlock G. Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments. Elife. 12. PMID 37861305 DOI: 10.7554/eLife.92899 |
0.477 |
|
| 2023 |
Melissa MJ, Desai MM. A dynamical limit to evolutionary adaptation. Biorxiv : the Preprint Server For Biology. PMID 37577473 DOI: 10.1101/2023.07.31.551320 |
0.522 |
|
| 2023 |
Johnson MS, Reddy G, Desai MM. Epistasis and evolution: recent advances and an outlook for prediction. Bmc Biology. 21: 120. PMID 37226182 DOI: 10.1186/s12915-023-01585-3 |
0.348 |
|
| 2023 |
Moulana A, Dupic T, Phillips AM, Desai MM. Genotype-phenotype landscapes for immune-pathogen coevolution. Trends in Immunology. PMID 37024340 DOI: 10.1016/j.it.2023.03.006 |
0.629 |
|
| 2023 |
Moulana A, Dupic T, Phillips AM, Chang J, Roffler AA, Greaney AJ, Starr TN, Bloom JD, Desai MM. The landscape of antibody binding affinity in SARS-CoV-2 Omicron BA.1 evolution. Elife. 12. PMID 36803543 DOI: 10.7554/eLife.83442 |
0.699 |
|
| 2023 |
Phillips AM, Maurer DP, Brooks C, Dupic T, Schmidt AG, Desai MM. Hierarchical sequence-affinity landscapes shape the evolution of breadth in an anti-influenza receptor binding site antibody. Elife. 12. PMID 36625542 DOI: 10.7554/eLife.83628 |
0.679 |
|
| 2022 |
Moulana A, Dupic T, Phillips AM, Chang J, Nieves S, Roffler AA, Greaney AJ, Starr TN, Bloom JD, Desai MM. Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1. Nature Communications. 13: 7011. PMID 36384919 DOI: 10.1038/s41467-022-34506-z |
0.722 |
|
| 2022 |
Min J, Gupta M, Desai MM, Weissman DB. Spatial structure alters the site frequency spectrum produced by hitchhiking. Genetics. PMID 36094352 DOI: 10.1093/genetics/iyac139 |
0.76 |
|
| 2022 |
Johnson MS, Desai MM. Mutational robustness changes during long-term adaptation in laboratory budding yeast populations. Elife. 11. PMID 35880743 DOI: 10.7554/eLife.76491 |
0.468 |
|
| 2022 |
Bakerlee CW, Nguyen Ba AN, Shulgina Y, Rojas Echenique JI, Desai MM. Idiosyncratic epistasis leads to global fitness-correlated trends. Science (New York, N.Y.). 376: 630-635. PMID 35511982 DOI: 10.1126/science.abm4774 |
0.392 |
|
| 2022 |
Melissa MJ, Good BH, Fisher DS, Desai MM. Population genetics of polymorphism and divergence in rapidly evolving populations. Genetics. PMID 35389471 DOI: 10.1093/genetics/iyac053 |
0.681 |
|
| 2021 |
Tung S, Bakerlee CW, Phillips AM, Nguyen Ba AN, Desai MM. The genetic basis of differential autodiploidization in evolving yeast populations. G3 (Bethesda, Md.). 11. PMID 34849811 DOI: 10.1093/g3journal/jkab192 |
0.697 |
|
| 2021 |
Bakerlee CW, Phillips AM, Nguyen Ba AN, Desai MM. Dynamics and variability in the pleiotropic effects of adaptation in laboratory budding yeast populations. Elife. 10. PMID 34596043 DOI: 10.7554/eLife.70918 |
0.712 |
|
| 2021 |
Phillips AM, Lawrence KR, Moulana A, Dupic T, Chang J, Johnson MS, Cvijovic I, Mora T, Walczak AM, Desai MM. Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies. Elife. 10. PMID 34491198 DOI: 10.7554/eLife.71393 |
0.677 |
|
| 2021 |
Reddy G, Desai MM. Global epistasis emerges from a generic model of a complex trait. Elife. 10. PMID 33779543 DOI: 10.7554/eLife.64740 |
0.427 |
|
| 2021 |
Johnson MS, Gopalakrishnan S, Goyal J, Dillingham ME, Bakerlee CW, Humphrey PT, Jagdish T, Jerison ER, Kosheleva K, Lawrence KR, Min J, Moulana A, Phillips AM, Piper JC, Purkanti R, ... ... Desai MM, et al. Phenotypic and molecular evolution across 10,000 generations in laboratory budding yeast populations. Elife. 10. PMID 33464204 DOI: 10.7554/eLife.63910 |
0.76 |
|
| 2020 |
Jerison ER, Nguyen Ba AN, Desai MM, Kryazhimskiy S. Chance and necessity in the pleiotropic consequences of adaptation for budding yeast. Nature Ecology & Evolution. PMID 32152531 DOI: 10.1038/S41559-020-1128-3 |
0.805 |
|
| 2019 |
Nguyen Ba AN, Cvijović I, Rojas Echenique JI, Lawrence KR, Rego-Costa A, Liu X, Levy SF, Desai MM. High-resolution lineage tracking reveals travelling wave of adaptation in laboratory yeast. Nature. PMID 31723263 DOI: 10.1038/S41586-019-1749-3 |
0.519 |
|
| 2019 |
Johnson MS, Martsul A, Kryazhimskiy S, Desai MM. Higher-fitness yeast genotypes are less robust to deleterious mutations. Science (New York, N.Y.). 366: 490-493. PMID 31649199 DOI: 10.1126/Science.Aay4199 |
0.786 |
|
| 2019 |
Kaminski Strauss S, Schirman D, Jona G, Brooks AN, Kunjapur AM, Nguyen Ba AN, Flint A, Solt A, Mershin A, Dixit A, Yona AH, Csörgő B, Busby BP, Hennig BP, Pál C, ... ... Desai MM, et al. Evolthon: A community endeavor to evolve lab evolution. Plos Biology. 17: e3000182. PMID 30925180 DOI: 10.1371/Journal.Pbio.3000182 |
0.452 |
|
| 2019 |
Rojas Echenique JI, Kryazhimskiy S, Nguyen Ba AN, Desai MM. Modular epistasis and the compensatory evolution of gene deletion mutants. Plos Genetics. 15: e1007958. PMID 30768593 DOI: 10.1371/Journal.Pgen.1007958 |
0.761 |
|
| 2018 |
Cvijović I, Nguyen Ba AN, Desai MM. Experimental Studies of Evolutionary Dynamics in Microbes. Trends in Genetics : Tig. PMID 30025666 DOI: 10.1016/J.Tig.2018.06.004 |
0.366 |
|
| 2018 |
Cvijović I, Good BH, Desai MM. The Effect of Strong Purifying Selection on Genetic Diversity. Genetics. PMID 29844134 DOI: 10.1534/Genetics.118.301058 |
0.569 |
|
| 2018 |
Wannier TM, Kunjapur AM, Rice DP, McDonald MJ, Desai MM, Church GM. Adaptive evolution of genomically recoded. Proceedings of the National Academy of Sciences of the United States of America. PMID 29440500 DOI: 10.1073/Pnas.1715530115 |
0.474 |
|
| 2017 |
Kosheleva K, Desai MM. Recombination alters the dynamics of adaptation on standing variation in laboratory yeast populations. Molecular Biology and Evolution. PMID 29069452 DOI: 10.1093/Molbev/Msx278 |
0.578 |
|
| 2017 |
Good BH, McDonald MJ, Barrick JE, Lenski RE, Desai MM. The dynamics of molecular evolution over 60,000 generations. Nature. PMID 29045390 DOI: 10.1038/Nature24287 |
0.492 |
|
| 2017 |
Jerison ER, Kryazhimskiy S, Mitchell JK, Bloom JS, Kruglyak L, Desai MM. Genetic variation in adaptability and pleiotropy in budding yeast. Elife. 6. PMID 28826486 DOI: 10.7554/Elife.27167 |
0.74 |
|
| 2017 |
Jerison ER, Kryazhimskiy S, Mitchell JK, Bloom JS, Kruglyak L, Desai MM. Author response: Genetic variation in adaptability and pleiotropy in budding yeast Elife. DOI: 10.7554/Elife.27167.025 |
0.703 |
|
| 2016 |
Good BH, Desai MM. Evolution of Mutation Rates in Rapidly Adapting Asexual Populations. Genetics. PMID 27646140 DOI: 10.1534/Genetics.116.193565 |
0.578 |
|
| 2016 |
McDonald MJ, Rice DP, Desai MM. Sex speeds adaptation by altering the dynamics of molecular evolution. Nature. PMID 26909573 DOI: 10.1038/Nature17143 |
0.543 |
|
| 2015 |
Jerison ER, Desai MM. Genomic investigations of evolutionary dynamics and epistasis in microbial evolution experiments. Current Opinion in Genetics & Development. 35: 33-39. PMID 26370471 DOI: 10.1016/J.Gde.2015.08.008 |
0.454 |
|
| 2015 |
Cvijović I, Good BH, Jerison ER, Desai MM. Fate of a mutation in a fluctuating environment. Proceedings of the National Academy of Sciences of the United States of America. 112: E5021-8. PMID 26305937 DOI: 10.1073/Pnas.1505406112 |
0.566 |
|
| 2015 |
Frenkel EM, McDonald MJ, Van Dyken JD, Kosheleva K, Lang GI, Desai MM. Crowded growth leads to the spontaneous evolution of semistable coexistence in laboratory yeast populations. Proceedings of the National Academy of Sciences of the United States of America. PMID 26240355 DOI: 10.1073/Pnas.1506184112 |
0.398 |
|
| 2015 |
Desai MM, Walczak AM. Microbiology. Flexible gene pools. Science (New York, N.Y.). 348: 977-8. PMID 26023126 DOI: 10.1126/Science.Aab3957 |
0.416 |
|
| 2015 |
Baym M, Kryazhimskiy S, Lieberman TD, Chung H, Desai MM, Kishony R. Inexpensive multiplexed library preparation for megabase-sized genomes. Plos One. 10: e0128036. PMID 26000737 DOI: 10.1371/Journal.Pone.0128036 |
0.677 |
|
| 2015 |
Ochs IE, Desai MM. The competition between simple and complex evolutionary trajectories in asexual populations. Bmc Evolutionary Biology. 15: 55. PMID 25881244 DOI: 10.1186/S12862-015-0334-0 |
0.582 |
|
| 2015 |
Rice DP, Good BH, Desai MM. The evolutionarily stable distribution of fitness effects. Genetics. 200: 321-9. PMID 25762525 DOI: 10.1534/Genetics.114.173815 |
0.565 |
|
| 2015 |
Good BH, Desai MM. The impact of macroscopic epistasis on long-term evolutionary dynamics. Genetics. 199: 177-90. PMID 25395665 DOI: 10.1534/Genetics.114.172460 |
0.537 |
|
| 2015 |
Baym M, Kryazhimskiy S, Lieberman TD, Chung H, Desai MM, Kishony R. Correction: Inexpensive multiplexed library preparation for megabase-sized genomes Plos One. 10. DOI: 10.1371/journal.pone.0131262 |
0.645 |
|
| 2014 |
Herman JD, Rice DP, Ribacke U, Silterra J, Deik AA, Moss EL, Broadbent KM, Neafsey DE, Desai MM, Clish CB, Mazitschek R, Wirth DF. A genomic and evolutionary approach reveals non-genetic drug resistance in malaria. Genome Biology. 15: 511. PMID 25395010 DOI: 10.1186/S13059-014-0511-2 |
0.34 |
|
| 2014 |
Lang GI, Desai MM. The spectrum of adaptive mutations in experimental evolution. Genomics. 104: 412-6. PMID 25269377 DOI: 10.1016/J.Ygeno.2014.09.011 |
0.568 |
|
| 2014 |
Good BH, Desai MM. Deleterious passengers in adapting populations. Genetics. 198: 1183-208. PMID 25194161 DOI: 10.1534/Genetics.114.170233 |
0.574 |
|
| 2014 |
Kryazhimskiy S, Rice DP, Jerison ER, Desai MM. Microbial evolution. Global epistasis makes adaptation predictable despite sequence-level stochasticity. Science (New York, N.Y.). 344: 1519-22. PMID 24970088 DOI: 10.1126/Science.1250939 |
0.778 |
|
| 2014 |
Good BH, Walczak AM, Neher RA, Desai MM. Genetic diversity in the interference selection limit. Plos Genetics. 10: e1004222. PMID 24675740 DOI: 10.1371/Journal.Pgen.1004222 |
0.592 |
|
| 2014 |
Frenkel EM, Good BH, Desai MM. The fates of mutant lineages and the distribution of fitness effects of beneficial mutations in laboratory budding yeast populations. Genetics. 196: 1217-26. PMID 24514901 DOI: 10.1534/Genetics.113.160069 |
0.57 |
|
| 2014 |
Kryazhimskiy S, Desai MM. Refining a key metabolic innovation in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. 111: 2056-7. PMID 24459186 DOI: 10.1073/Pnas.1323189111 |
0.749 |
|
| 2013 |
Kosheleva K, Desai MM. The dynamics of genetic draft in rapidly adapting populations. Genetics. 195: 1007-25. PMID 24002646 DOI: 10.1534/Genetics.113.156430 |
0.581 |
|
| 2013 |
Lang GI, Rice DP, Hickman MJ, Sodergren E, Weinstock GM, Botstein D, Desai MM. Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature. 500: 571-4. PMID 23873039 DOI: 10.1038/Nature12344 |
0.6 |
|
| 2013 |
Nicolaisen LE, Desai MM. Distortions in genealogies due to purifying selection and recombination. Genetics. 195: 221-30. PMID 23821597 DOI: 10.1534/Genetics.113.152983 |
0.794 |
|
| 2013 |
Van Dyken JD, Müller MJ, Mack KM, Desai MM. Spatial population expansion promotes the evolution of cooperation in an experimental Prisoner's Dilemma. Current Biology : Cb. 23: 919-23. PMID 23664975 DOI: 10.1016/J.Cub.2013.04.026 |
0.414 |
|
| 2013 |
Good BH, Desai MM. Fluctuations in fitness distributions and the effects of weak linked selection on sequence evolution. Theoretical Population Biology. 85: 86-102. PMID 23337315 DOI: 10.1016/J.Tpb.2013.01.005 |
0.501 |
|
| 2013 |
Desai MM, Walczak AM, Fisher DS. Genetic diversity and the structure of genealogies in rapidly adapting populations. Genetics. 193: 565-85. PMID 23222656 DOI: 10.1534/Genetics.112.147157 |
0.689 |
|
| 2012 |
Nicolaisen LE, Desai MM. Distortions in genealogies due to purifying selection. Molecular Biology and Evolution. 29: 3589-600. PMID 22729750 DOI: 10.1093/Molbev/Mss170 |
0.819 |
|
| 2012 |
Kryazhimskiy S, Rice DP, Desai MM. Population subdivision and adaptation in asexual populations of Saccharomyces cerevisiae. Evolution; International Journal of Organic Evolution. 66: 1931-41. PMID 22671557 DOI: 10.1111/J.1558-5646.2011.01569.X |
0.787 |
|
| 2012 |
Goyal S, Balick DJ, Jerison ER, Neher RA, Shraiman BI, Desai MM. Dynamic mutation-selection balance as an evolutionary attractor. Genetics. 191: 1309-19. PMID 22661327 DOI: 10.1534/Genetics.112.141291 |
0.834 |
|
| 2012 |
Good BH, Rouzine IM, Balick DJ, Hallatschek O, Desai MM. Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations. Proceedings of the National Academy of Sciences of the United States of America. 109: 4950-5. PMID 22371564 DOI: 10.1073/Pnas.1119910109 |
0.833 |
|
| 2012 |
Desai MM, Nicolaisen LE, Walczak AM, Plotkin JB. The structure of allelic diversity in the presence of purifying selection. Theoretical Population Biology. 81: 144-57. PMID 22198521 DOI: 10.1016/J.Tpb.2011.12.002 |
0.804 |
|
| 2012 |
Walczak AM, Nicolaisen LE, Plotkin JB, Desai MM. The structure of genealogies in the presence of purifying selection: a fitness-class coalescent. Genetics. 190: 753-79. PMID 22135349 DOI: 10.1534/Genetics.111.134544 |
0.794 |
|
| 2011 |
Desai MM, Fisher DS. The balance between mutators and nonmutators in asexual populations. Genetics. 188: 997-1014. PMID 21652523 DOI: 10.1534/Genetics.111.128116 |
0.658 |
|
| 2011 |
Lang GI, Botstein D, Desai MM. Genetic variation and the fate of beneficial mutations in asexual populations. Genetics. 188: 647-61. PMID 21546542 DOI: 10.1534/Genetics.111.128942 |
0.566 |
|
| 2009 |
Weissman DB, Desai MM, Fisher DS, Feldman MW. The rate at which asexual populations cross fitness valleys. Theoretical Population Biology. 75: 286-300. PMID 19285994 DOI: 10.1016/J.Tpb.2009.02.006 |
0.818 |
|
| 2009 |
Desai MM. Reverse evolution and evolutionary memory. Nature Genetics. 41: 142-3. PMID 19174835 DOI: 10.1038/Ng0209-142 |
0.389 |
|
| 2008 |
Gresham D, Desai MM, Tucker CM, Jenq HT, Pai DA, Ward A, DeSevo CG, Botstein D, Dunham MJ. The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. Plos Genetics. 4: e1000303. PMID 19079573 DOI: 10.1371/Journal.Pgen.1000303 |
0.544 |
|
| 2008 |
Desai MM, Plotkin JB. The polymorphism frequency spectrum of finitely many sites under selection. Genetics. 180: 2175-91. PMID 18854590 DOI: 10.1534/Genetics.108.087361 |
0.705 |
|
| 2008 |
Fogle CA, Nagle JL, Desai MM. Clonal interference, multiple mutations and adaptation in large asexual populations. Genetics. 180: 2163-73. PMID 18832359 DOI: 10.1534/Genetics.108.090019 |
0.559 |
|
| 2007 |
Desai MM, Weissman D, Feldman MW. Evolution can favor antagonistic epistasis. Genetics. 177: 1001-10. PMID 17720923 DOI: 10.1534/Genetics.107.075812 |
0.796 |
|
| 2007 |
Desai MM, Fisher DS. Beneficial mutation selection balance and the effect of linkage on positive selection. Genetics. 176: 1759-98. PMID 17483432 DOI: 10.1534/Genetics.106.067678 |
0.708 |
|
| 2007 |
Desai MM, Fisher DS, Murray AW. The speed of evolution and maintenance of variation in asexual populations. Current Biology : Cb. 17: 385-94. PMID 17331728 DOI: 10.1016/J.Cub.2007.01.072 |
0.693 |
|
| 2006 |
Plotkin JB, Dushoff J, Desai MM, Fraser HB. Codon usage and selection on proteins. Journal of Molecular Evolution. 63: 635-53. PMID 17043750 DOI: 10.1007/S00239-005-0233-X |
0.714 |
|
| 2006 |
Thompson DA, Desai MM, Murray AW. Ploidy controls the success of mutators and nature of mutations during budding yeast evolution. Current Biology : Cb. 16: 1581-90. PMID 16920619 DOI: 10.1016/J.Cub.2006.06.070 |
0.493 |
|
| 2006 |
Plotkin JB, Dushoff J, Desai MM, Fraser HB. Estimating selection pressures from limited comparative data. Molecular Biology and Evolution. 23: 1457-9. PMID 16754640 DOI: 10.1093/Molbev/Msl021 |
0.606 |
|
| 2005 |
Desai MM, Nelson DR. A quasispecies on a moving oasis. Theoretical Population Biology. 67: 33-45. PMID 15649522 DOI: 10.1016/J.Tpb.2004.07.005 |
0.467 |
|
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