@article {740756, title = {Sex Speeds Adaptation by Altering the Dynamics of Molecular Evolution}, journal = {Nature}, volume = {in press}, year = {2016}, author = {McDonald, M. J and Rice, D. P. and M. M. Desai} } @article {740711, title = {The competition between simple and complex evolutionary trajectories in asexual populations.}, journal = {BMC Evolutionary Biology}, volume = {15}, year = {2015}, pages = {55}, author = {Ochs, I. E. and M. M. Desai} } @article {740746, title = {Crowded Growth Leads to the Spontaneous Evolution of Semi-Stable Coexistence in Laboratory Yeast Populations.}, journal = {PNAS}, volume = {112}, year = {2015}, pages = {11306-13111}, url = {http://www.pnas.org/content/112/36/11306.abstract}, author = {Frenkel, E. M. and M. J. McDonald and J. D. van Dyken and K. Kosheleva and G. I. Lang and M. M. Desai} } @article {740726, title = {The evolutionarily stable distribution of fitness effects.}, journal = {Genetics }, volume = {200}, year = {2015}, pages = {321-329}, url = {http://www.genetics.org/content/early/2015/03/10/genetics.114.173815}, author = {Rice, D. P. and B. H. Good and M. M. Desai} } @article {740751, title = {Fate of a Mutation in a Fluctuating Environment.}, journal = {PNAS}, volume = {112}, year = {2015}, pages = {E5021-E5028}, url = {http://www.pnas.org/content/112/36/E5021.abstract}, author = {Cvijovic, I. and B. H. Good and E. R. Jerison and M. M. Desai} } @article {740721, title = {Flexible Gene Pools.}, journal = {Science}, volume = {348}, year = {2015}, pages = {977-978}, url = {http://www.sciencemag.org/content/348/6238/977}, author = {M. M. Desai and A. M. Walczak} } @article {740706, title = {Functional characterization of bacteria isolated from ancient arctic soil exposes diverse resistance mechanisms to modern antibiotics.}, journal = {PLoS One}, volume = {10}, year = {2015}, pages = {1-19}, url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069533}, author = {Perron, G. G. and L. Whyte and P. J. Turnbaugh and J. Goordial and W. P. Hanage and G. Dantas and M. M. Desai} } @article {740736, title = {Genomic investigations of evolutionary dynamics and epistasis in microbial evolution experiments.}, journal = {Current Opinion in Genetics and Development}, volume = {35}, year = {2015}, pages = {33-39}, author = {Jerison, E. R and M. M. Desai} } @article {506886, title = {The impact of macroscopic epistasis on long-term evolutionary dynamics}, journal = {Genetics}, volume = {199}, year = {2015}, pages = {177-190}, url = {http://www.genetics.org/content/199/1/177.abstract}, author = {Good, BH and Desai, MM} } @article {740716, title = {Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes.}, journal = {PLoS One}, volume = {10:e0128036 }, year = {2015}, url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0128036}, author = {Baym, M. and S. Kryazhimskiy and T. Lieberman and H. Chung and M. M. Desai and R. Kishony} } @article {506896, title = {Deleterious Passengers in Adapting Populations}, journal = {Genetics}, volume = {198}, year = {2014}, pages = {1183-1208}, url = {Genetics}, author = {Good, BH and Desai, MM} } @article {506916, title = {The Fates of Mutant Lineages and the Distribution of Fitness Effects of Beneficial Mutations in Laboratory Budding Yeast Populations}, journal = {Genetics}, volume = {196}, year = {2014}, pages = {1217-1226}, url = {http://www.genetics.org/content/196/4/1217.full}, author = {Frenkel, EM and Good, BH and Desai, MM} } @article {506921, title = {Genetic Diversity in the Interference Selection Limit}, journal = {PLoS Genetics}, year = {2014}, url = {http://www.oeb.harvard.edu/faculty/desai/PDFs/goodwalczakneherdesai14.pdf}, author = {Good, BH and Walczak, AM and Neher, RA and Desai, MM} } @article {506906, title = {Genomic Evolutionary Approach Reveals Unexpected Metabolic Switch in Malaria Drug Resistance}, journal = {Genome Biology}, volume = {15}, year = {2014}, pages = {511}, author = {Herman, JD and Rice, DP and Ribacke, U and Deik, AA and Moss, E and Nearfsey, D and Desai, MM and Clish, CB and Mazitschek, R and Wirth, DF} } @article {506926, title = {Refining a key metabolic innovation in Escherichia coli}, journal = {PNAS}, volume = {111}, year = {2014}, pages = {2056-2057}, url = {http://www.pnas.org/content/111/6/2056.full}, author = {S. Kryazhimskiy and Desai, MM} } @article {506911, title = {Global Epistasis Makes Adaptation Predictable Despite Sequence-Level Stochasticity}, journal = {Science}, volume = {344}, year = {2014}, pages = {1519-1522}, url = {http://www.sciencemag.org/cgi/rapidpdf/344/6191/1519?ijkey=nZiFADaPb3Kck\&keytype=ref\&siteid=sci}, author = {S. Kryazhimskiy and Rice, DP and Jerison, ER and Desai, MM} } @article {506891, title = {The spectrum of adaptive mutations in experimental evolution}, journal = {Genomics}, volume = {104}, year = {2014}, pages = {412-416}, author = {Lang, GI and Desai, MM} } @article {506936, title = {Distortions in Genealogies Due to Purifying Selection and Recombination}, journal = {Genetics}, volume = {195}, year = {2013}, pages = {221-230}, url = {http://www.genetics.org/content/195/1/221.full}, author = {Nicolaisen, LE and Desai, MM} } @article {506931, title = {The Dynamics of Genetic Draft in Rapidly Adapting Populations}, journal = {Genetics}, volume = {195}, year = {2013}, pages = {1007-1025}, url = {http://www.genetics.org/content/195/3/1007.full}, author = {Kosheleva, K and Desai, MM} } @article {506956, title = {Genetic Diversity and the Structure of Genealogies in Rapidly Adapting Populations}, journal = {Genetics}, volume = {193}, year = {2013}, pages = {565-585}, url = {http://www.genetics.org/content/193/2/565.full.pdf+html}, author = {Desai, MM and Walczak, AM and Fisher, DS} } @article {506941, title = {Pervasive Genetic Hitchhiking and Clonal Interference in Forty Evolving Yeast Populations}, journal = {Nature}, volume = {500}, year = {2013}, pages = {571-574}, url = {http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12344.html}, author = {Lang, GI and Rice, DP and Hickman, MJ and Sodergren, E and Weinstock, GM and Botstein, D and Desai, MM} } @article {506951, title = {Fluctuations in Fitness Distributions and the Effects of Weak Linked Selection on Sequence Evolution}, journal = {Theoretical Population Biology}, volume = {85}, year = {2013}, pages = {86-102}, url = {http://www.sciencedirect.com/science/article/pii/S0040580913000063}, author = {Good, BH and Desai, MM} } @article {506961, title = {Statistical Questions in Experimental Evolution}, journal = {Journal of Statistical Mechanics}, year = {2013}, url = {http://www.oeb.harvard.edu/faculty/desai/PDFs/desai13.pdf}, author = {Desai, MM} } @article {506946, title = {Spatial Population Expansion Promotes the Evolution of Cooperation in an Experimental Prisoner{\textquoteright}s Dilemma}, journal = {Current Biology}, volume = {23}, year = {2013}, pages = {919-923}, url = {http://www.sciencedirect.com/science/article/pii/S096098221300434X}, author = {Van Dyken,JD and Muller, MJI and Mack, KML and Desai, MM} } @article {506966, title = {Distortions in Genealogies Due to Purifying Selection}, journal = {Molecular Biology and Evolution}, volume = {29}, year = {2012}, pages = {3589-3600}, url = {http://mbe.oxfordjournals.org/content/29/11/3589.abstract?etoc}, author = {Nicolaisen, LE and Desai, MM} } @article {506981, title = {Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations}, journal = {PNAS}, volume = {109}, year = {2012}, pages = {4950-4955}, url = {http://www.pnas.org/content/109/13/4950.short}, author = {Good, BH and Rouzine, IM and Balick, DJ and Hallatschek, O and Desai, MM} } @article {506971, title = {Dynamic Mutation-Selection Balance as an Evolutionary Attractor}, journal = {Genetics}, volume = {191}, year = {2012}, pages = {1309-1319}, url = {http://www.genetics.org/content/191/4/1309.short}, author = {Goyal, S and Balick, DJ and Jerison, ER and Neher, RA and Shraiman, BI and Desai, MM} } @article {506976, title = {Population Subdivision and Adaptation in Asexual Populations of Saccharomyces cerevisiae}, journal = {Evolution}, volume = {66}, year = {2012}, pages = {1931-1941}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2011.01569.x/full}, author = {Kryazhimskiy, SK and Rice, DP and Desai, MM} } @article {506986, title = {The Structure of Allelic Diversity in the Presence of Purifying Selection}, journal = {Theoretical Population Biology}, volume = {81}, year = {2012}, pages = {144-157}, url = {http://www.sciencedirect.com/science/article/pii/S0040580911001055}, author = {Desai, MM and Nicolaisen, LE and Walczak, AM and Plotkin, JB} } @article {506991, title = {The Structure of Genealogies in the Presence of Purifying Selection: A "Fitness-Class Coalescent"}, journal = {Genetics}, volume = {190}, year = {2012}, pages = {753}, url = {http://www.genetics.org/content/190/2/753.short}, author = {Walczak, AM and Nicolaisen, LE and Plotkin, JB and Desai, MM} } @article {506996, title = {The Balance Between Mutators and Nonmutators in Asexual Populations}, journal = {Genetics}, volume = {188}, year = {2011}, pages = {997-1014}, url = {http://www.oeb.harvard.edu/faculty/desai/PDFs/desaifisher11.pdf}, author = {Desai, MM and Nicolaisen, LE and Walczak, AM and Plotkin, JB} } @article {507001, title = {Genetic Variation And the Fate of Individual Beneficial Mutations in Asexual Populations}, journal = {Genetics}, volume = {188}, year = {2011}, pages = {647-661}, url = {http://www.oeb.harvard.edu/faculty/desai/PDFs/langbotsteindesai11.pdf}, author = {Lang, GI and Botstein, D and Desai, MM} } @article {507006, title = {The Rate at Which Asexual Populations Cross Fitness Valleys}, journal = {Theoretical Population Biology}, volume = {75}, year = {2009}, pages = {286-300}, url = {http://www.oeb.harvard.edu/faculty/desai/PDFs/weissmandesaifisherfeldman09.pdf}, author = {Weissman, DW and Desai, MM and Fisher, DS and Feldman, MW} } @article {507011, title = {Reverse Evolution and Evolutionary Memory}, journal = {Nature Genetics}, volume = {41}, year = {2009}, pages = {142-143}, url = {http://www.oeb.harvard.edu/faculty/desai/PDFs/desai09.pdf}, author = {Desai, MM} } @article {507026, title = {Clonal Interference, Multiple Mutations, and Adaptation in Large Asexual Populations}, journal = {Genetics}, volume = {180}, year = {2008}, pages = {2163-2173}, url = {http://www.oeb.harvard.edu/faculty/desai/PDFs/foglenagledesai08.pdf}, author = {Fogle, CA and Nagle, JL and Desai, MM} } @article {507021, title = {The Polymorphism Frequency Spectrum of Finitely Many Sites Under Selection}, journal = {Genetics}, volume = {180}, year = {2008}, pages = {2185-2191}, url = {http://www.oeb.harvard.edu/faculty/desai/PDFs/desaiplotkin08.pdf}, author = {Desai, MM and Plotkin, JB} } @article {507016, title = {The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast}, journal = {PLoS Genetics}, year = {2008}, url = {http://www.oeb.harvard.edu/faculty/desai/PDFs/greshamdesaituckerjenqpaiwarddesovobotsteindunham08.pdf}, author = {Gresham, D and Desai, MM and Tucker, CM and Jenq, HT and Pai, DA and Ware, A and DeSevo, CG and Botstein, D and Dunham, MJ} } @article {507036, title = {Beneficial Mutation-Selection Balance and the Effect of Linkage on Positive Selection}, journal = {Genetics}, volume = {176}, year = {2007}, pages = {1759-1798}, url = {http://www.oeb.harvard.edu/faculty/desai/PDFs/desaifisher07.pdf}, author = {Desai, MM and Fisher, DS} } @article {507031, title = {Evolution Can Favor Antagonistic Epistasis}, journal = {Genetics}, volume = {177}, year = {2007}, pages = {1001-1010}, url = {http://www.oeb.harvard.edu/faculty/desai/PDFs/desaiweissmanfeldman07.pdf}, author = {Desai, MM and Weissman, DW and Feldman, MW} } @article {507041, title = {The Speed of Evolution and Maintenance of Variation in Asexual Populations}, journal = {Current Biology}, volume = {17}, year = {2007}, pages = {385-394}, url = {http://www.oeb.harvard.edu/faculty/desai/PDFs/desaifishermurray07.pdf}, author = {Desai, MM and Fisher, DS and Murray, AW} } @article {507051, title = {Codon Usage and Selection on Proteins}, journal = {Journal of Molecular Evolution}, volume = {63}, year = {2006}, pages = {635-653}, url = {http://www.oeb.harvard.edu/faculty/desai/PDFs/plotkinsdushoffdesaifraser06a.pdf}, author = {Plotkin, JB and Dushoff, J and Desai, MM and Fraser, HB} } @article {507061, title = {Estimating Selection Pressures from Limited Comparative Data}, journal = {Molecular Biology and Evolution}, volume = {23}, year = {2006}, pages = {1457-1459}, url = {http://www.oeb.harvard.edu/faculty/desai/PDFs/plotkinsdushoffdesaifraser06a.pdf}, author = {Plotkin, JB and Dushoff, J and Desai, MM and Fraser, HB} } @article {507056, title = {Ploidy Controls the Success of Mutators and Nature of Mutations During Budding Yeast Evolution}, journal = {Current Biology}, volume = {16}, year = {2006}, pages = {1581-1590}, url = {http://www.oeb.harvard.edu/faculty/desai/PDFs/thompsondesaimurray06.pdf}, author = {Thompson, DA and Desai, MM and Murray, AW} } @article {507066, title = {A Quasispecies on a Moving Oasis}, journal = {Theoretical Population Biology}, volume = {67}, year = {2005}, pages = {33-45}, url = {http://www.oeb.harvard.edu/faculty/desai/PDFs/desainelson05.pdf}, author = {Desai, MM and Nelson, DR} }