The Desai Lab

Publications

  • Alpay, B. A. and M. M. Desai. Effects of selection stringency on the outcomes of directed evolution. PLOS One 19:1-16 (2024). [pdf]
  • Alpay, B. A., J. M. Higgins, and M. M. Desai. Some statistical theory for interpreting reference distributions. medRxiv 24309680 (2024). [pdf]
  • Dupic, T., A. M. Phillips, and M. M. Desai. Protein landscapes are not so simple: on reference-free versus reference-based inference. bioRxiv 577800 (2024). [pdf]
  • Melissa, M. J. and M. M. Desai. A dynamical limit to evolutionary adaptation. PNAS 121:e2312845121 (2024). [pdf]
  • Johnson, M. S., G. Reddy, and M. M. Desai. Epistasis and evolution: recent advances and an outlook for prediction. BMC Biology 21:1-12 (2023). [pdf]
  • Petti, S.*, G. Reddy*, and M. M. Desai. Inferring sparse structure in genotype–phenotype maps. Genetics 225:iyad127 (2023). [pdf]
  • Phillips, A. M.*, D. P. Maurer*, C. Brooks, T. Dupic, A. G. Schmidt, and M. M. Desai. Hierarchical sequence-affinity landscapes shape the evolution of breadth in an anti-influenza receptor binding site antibody. eLife 12:e83628 (2023). [pdf]
  • Rego-Costa, A., I.-T. Huang, M. M. Desai, and A. K. Gombert. Yeast population dynamics in Brazilian bioethanol production. G3 13:jkad104 (2023). [pdf]
  • Moulana, A.*, T. Dupic*, A. M. Phillips, and M. M. Desai. Genotype–phenotype landscapes for immune–pathogen coevolution. Trends in Immunology (2023). [pdf]
  • Chen, V., M. S. Johnson, L. Hérissant, P. T. Humphrey, D.C. Yuan, Y. Li, A. Agarwala, S. B. Hoelscher, D. A. Petrov, M. M. Desai, and G. Sherlock. Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments. eLife 12:e92899 (2023). [pdf]
  • Moulana, A.*, T. Dupic*, A. M. Phillips*, J. Chang*, A. Roffler, A. J. Greaney, T. N. Starr, J. D. Bloom, and M. M. Desai. The landscape of antibody binding affinity in SARS-CoV-2 Omicron BA. 1 evolution. eLife 12:e83442 (2023). [pdf]
  • Kates-Harbeck, J., and M. M. Desai. Social network structure and the spread of complex contagions from a population genetics perspective. Physical Review E 108:024306 (2023). [pdf]
  • Wortel, M., D. Agashe, S. Bailey, C. Bank, K. Bisschop, T. Blankers, J. Cairns, E. S. Colizzi, D. Cusseddu, M. M. Desai, B. van Dijk, M. Egas, J. Ellers, A. Groot, D. Heckel, M. Johnson, K. Kraaijeveld, J. Krug, L. Laan, M. Lässig, P. Lind, J. Meijer, L. Noble, S. Okasha, P. Rainey, D. Rozen, S. Shitut, S. Tans, O. Tenaillon, H. Teotónio, J. A. G. M. de Visser, M. Visser, R. Vroomans, G. Werner, B. Wertheim, and P. Pennings. Towards evolutionary predictions: Current promises and challenges. Evolutionary Applications 16:3-21 (2023). [pdf]
  • Moulana, A.*, T. Dupic*, A. M. Phillips*, J. Chang*, S. Nieves, A. Roffler, A. J. Greaney, T. N. Starr, J. D. Bloom, and M. M. Desai. Compensatory epistasis maintains ACE2 binding during antibody escape in SARS-CoV-2 Omicron BA.1. Nature Communications 13:7011 (2022). [pdf]
  • Nguyen Ba, A. N.*, K. R. Lawrence*, A. Rego-Costa*, S. Gopalakrishnan, and M. M. Desai. Barcoded Bulk QTL Mapping Reveals Highly Polygenic and Epistatic Architecture of Complex Traits in Yeast. eLife 11:e73983 (2022). [pdf]
  • Bakerlee, C. W.*, A. N. Nguyen Ba*, Y. Shulgina, J. I. R. Echenique, and M. M. Desai. Idiosyncratic Epistasis Leads to Global Fitness-Correlated Trends. Science 376: 630-635 (2022). [pdf]
  • Beukenhorst, A. L., J. Frallicciardi, C. M. Koch, A. Phillips, M. M. Desai, K. Wichapong, G. Nicolaes, W. Koudstaal, G. Alter, and J. Goudsmit. The influenza hemagglutinin stem antibody CR9114: evidence for a narrow evolutionary path towards universal protection. Frontiers in Virology 2:1049134 (2022). [pdf]
  • Min, J., M. Gupta, M. M. Desai, and D. B. Weissman. Spatial structure alters the site frequency spectrum produced by hitchhiking. Genetics 222:iyac139 (2022). [pdf]
  • Johnson, M. S. and M. M. Desai. Mutational Robustness Changes During Long-Term Adaptation in Laboratory Budding Yeast Populations. eLife 11: e76491 (2022). [pdf]
  • Melissa, M. J., B. H. Good, D. S. Fisher, and M. M. Desai. Population genetics of polymorphism and divergence in rapidly evolving populations. Genetics 221: iyac053 (2022). [pdf]
  • Bakerlee, C. W.*, A. M. Phillips*, Nguyen Ba, A. N., and M. M. Desai. Dynamics and variability in the pleiotropic effects of adaptation in laboratory budding yeast populations. eLife 10:e70918 (2021). [pdf]
  • Phillips, A. M.*, K. R. Lawrence*, A. Moulana, T. Dupic, J. Chang, M. S. Johnson, I. Cvijovic, T. Mora, A. M. Walczak, and M. M. Desai. Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies. eLife 10:e71393 (2021). [pdf]
  • Tung, S.*, C. W. Bakerlee*, A. M. Phillips, A. N. Nguyen Ba, and M. M. Desai. The Genetic Basis of Differential Autodiploidization in Evolving Yeast Populations. G3 11:jkab192 (2021). [pdf]
  • Reddy, G., and M. M. Desai. Global epistasis emerges from a generic model of a complex trait. eLife 10:e64740 (2021). [pdf]
  • Johnson, M. S., S. Gopalkrishnan, J. Gohal, M. E. Dillingham, C. W. Bakerlee, P. T. Humphrey, T. Jagdish, E. R. Jerison, K. Kosheleva, K. R. Lawrence, J. Min, A. Moulana, A. M. Phillips, J. C. Piper, R. Purkanti, A. Rego-Costa, M. J. McDonald, A. N. Nguyen Ba, and M. M. Desai. Phenotypic and molecular evolution across 10,000 generations in laboratory budding yeast populations. eLife 10:e63910 (2021). [pdf]
  • Jerison, E. R., A. N. Nguyen Ba, M. M. Desai†, and S. Kryazhimskiy†. Chance and Necessity in the Pleiotropic Consequences of Adaptation for Budding Yeast. Nature Ecology and Evolution 4:601-611 (2020). [pdf]
  • Desai, M. M. Haigh (1978) and Muller's ratchet. Theoretical Population Biology 133:19-20 (2020). [pdf]
  • Nguyen Ba, A. N.*, I. Cvijovic*, J. I. R. Echenique*, K. R. Lawrence, A. Rego-Costa, X. Liu, S. F. Levy, and M. M. Desai. High-Resolution Lineage Tracking Reveals Traveling Wave of Adaptation in Laboratory Yeast. Nature 575:494-499 (2019). [pdf]
  • Johnson, M. S., A. Martsul, S. Kryazhimskiy†, and M. M. Desai†. Higher fitness yeast genotypes are less robust to deleterious mutations. Science 366:490-493 (2019). [pdf]
  • Strauss, S. K., D. Schirman, G. Jona, A. N. Brooks, A. M. Kunjapur, A. N. Nguyen Ba, A. Flint, A. Solt, A. Mershin, A. Dixit, A. H. Yona, B. Csörgő, B. Busby, B. P. Hennig, C. Pál, D. Schraivogel, D. Schultz, D. G. Wernick, D. Agashe, D. Levi, D. Zabezhinsky, D. Russ, E. Sass, E. Tamar, E. Herz, E. D. Levy, G. M. Church, I. Yelin, I. Nachman, J. Gerst, J. M. Georgeson, K.ate Adamala, L. M. Steinmetz, M. Rübsam, M. Ralser, M. Klutstein, M. M. Desai, N. Walunjkar, N. Yin, N. A. Hefetz1, N. Jakimo, O. Snitser, O. Adini, P. Kumar, R. S. H. Smith, R. Zeidan, R. Hazan, R. Rak, R. Kishony, S. Johnson, S. Nouriel, S. C. Vonesch, S. Foster, T. Dagan, T. Wein, T. Karydis, T. M. Wannier, T. Stiles, V. Olin-Sandoval, W. F. Mueller, Y. M. Bar-On, O. Dahan, Y. Pilpel. Evolthon: A Community Endeavor to Evolve Lab Evolution. PLoS Biology 17:e3000182 (2019). [pdf]
  • Echenique, J. I. R. Echenique, S. Kryazhimskiy, A. N. Nguyen Ba, and M. M. Desai. Modular Epistasis and the Compensatory Evolution of Gene Deletion Mutants. PLoS Genetics 15:e1007958 (2019). [pdf]
  • Cvijovic, I., A. N. Nguyen Ba, and M. M. Desai. Experimental Studies of Evolutionary Dynamics in Microbes. Trends in Genetics 34: 693-703 (2018). [pdf]
  • Cvijovic, I., B. H. Good, and M. M. Desai. The Effect of Strong Purifying Selection on Genetic Diversity. Genetics 209:1235-1278 (2018). [pdf]
  • Wannier, T. M., A. M. Kunjapur, D. P. Rice, M. J. McDonald, M. M. Desai, and G. M. Church. Adaptive Evolution of Genomically Recoded Escherichia coli. PNAS 115:3090-3095 (2018). [pdf]
  • Kosheleva, K. and M. M. Desai. Recombination Alters the Dynamics of Adaptation on Standing Variation in Laboratory Yeast Populations. Molecular Biology and Evolution 35:180-201 (2018). [pdf]
  • Good, B. H., McDonald, M. J., Barrick, J. E., Lenski, R. E. and Desai, M. M. The Dynamics of Molecular Evolution Over 60,000 Generations. Nature 551:45-50 (2017). [pdf]
  • Jerison, E. J. , S. Kryazhimskiy, J. K. Mitchell, J. S. Bloom, L. Kruglyak, and M. M. Desai. Genetic Variation in Adaptability and Pleiotropy in Budding Yeast. eLife 6:e27167 (2017). [pdf]
  • Good, B. H. and M. M. Desai. Evolution of Mutation Rates in Rapidly Adapting Asexual Populations. Genetics 204:1249-1266 (2016). [pdf]
  • McDonald, M. J., D. P. Rice, and M. M. Desai. Sex Speeds Adaptation by Altering the Dynamics of Molecular Evolution. Nature 531:233-236 (2016). [pdf]
  • Cvijovic, I., B. H. Good, E. R. Jerison, and M. M. Desai. Fate of a Mutation in a Fluctuating Environment. PNAS 112:E5021-E5028 (2015). [pdf]
  • Frenkel, E. M., M. J. McDonald, J. D. van Dyken, K. Kosheleva, G. I. Lang, and M. M. Desai. Crowded Growth Leads to the Spontaneous Evolution of Semi-Stable Coexistence in Laboratory Yeast Populations. PNAS 112:11306-13111 (2015). [pdf]
  • Jerison, E. R. and M. M. Desai. Genomic Investigations of Evolutionary Dynamics and Epistasis in Microbial Evolution Experiments. Current Opinion in Genetics and Development 35:33-39 (2015). [pdf]
  • Rice, D. P., B. H. Good, and M. M. Desai. The Evolutionarily Stable Distribution of Fitness Effects. Genetics 200:321-329 (2015). [pdf]
  • Desai, M. M. and A. M. Walczak. Flexible Gene Pools. Science 348:977-978 (2015). [pdf]
  • Baym, M., S. Kryazhimskiy, T. Lieberman, H. Chung, M. M. Desai, and R. Kishony. Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes. PLoS One 10:e0128036 (2015). [pdf]
  • Ochs, I. E. and M. M. Desai. The Competition Between Simple and Complex Evolutionary Trajectories in Asexual Populations. BMC Evolutionary Biology 15:55 (2015). [pdf]
  • Perron, G. G., L. Whyte, P. J. Turnbaugh, J. Goordial, W. P. Hanage, G. Dantas, and M. M. Desai. Functional Characterization of Bacteria Isolated From Ancient Arctic Soil Exposes Diverse Resistance Mechanisms to Modern Antibiotics. PLoS One 10:e0069533 (2015). [pdf]
  • Good, B. H. and M. M. Desai. The Impact of Macroscopic Epistasis on Long-term Evolutionary Dynamics. Genetics 199:177-190 (2015). [pdf]
  • Lang, G. I. and M. M. Desai. The Spectrum of Adaptive Mutations in Experimental Evolution. Genomics 104:412-416 (2014). [pdf]
  • Good, B. H. and M. M. Desai. Deleterious Passengers in Adapting Populations. Genetics 198:1183-1208 (2014). [pdf]
  • Herman, J. D., D. P. Rice, U. Ribacke, A. A. Deik, E. Moss, D. Neafsey, M. M. Desai, C. B. Clish, R. Mazitschek, and D. F. Wirth. Genomic Evolutionary Approach Reveals Unexpected Metabolic Switch in Malaria Drug Resistance. Genome Biology 15:511 (2014). [pdf]
  • Kryazhimskiy, S., D. P. Rice, E. R. Jerison, and M. M. Desai. Global Epistasis Makes Adaptation Predictable Despite Sequence-Level Stochasticity. Science 344:1519-1522 (2014). [pdf]
  • Frenkel, E. M., B. H. Good, and M. M. Desai. The Fates of Mutant Lineages and the Distribution of Fitness Effects of Beneficial Mutations in Laboratory Budding Yeast Populations. Genetics 196:1217-1226 (2014). [pdf]
  • Good, B. H., A. M. Walczak, R. A. Neher, and M. M. Desai. Genetic Diversity in the Interference Selection Limit. PLoS Genetics 10:e1004222 (2014). [software]. [pdf]
  • Kryazhimskiy, S. and M. M. Desai. Refining a Key Metabolic Innovation in Escherichia coli. PNAS 111:2056-2057 (2014). [pdf]
  • Kosheleva, K. and M. M. Desai. The Dynamics of Genetic Draft in Rapidly Adapting Populations. Genetics 195:1007-1025 (2013). [pdf]
  • Nicolaisen, L. E. and M. M. Desai. Distortions in Genealogies Due to Purifying Selection and Recombination. Genetics 195:221-230 (2013). [pdf]
  • Lang, G. I.*, D. P. Rice*, M. J. Hickman, E. Sodergren, G. M. Weinstock, D. Botstein†, and M. M. Desai†. Pervasive Genetic Hitchhiking and Clonal Interference in Forty Evolving Yeast Populations. Nature 500:571-574 (2013). [pdf]
  • Van Dyken, J. D., M. J. I. Muller, K. M. L. Mack, and M. M. Desai.  Spatial Population Expansion Promotes the Evolution of Cooperation in an Experimental Prisoner's Dilemma. Current Biology 23:919-923 (2013). [pdf]
  • Good, B. H. and M. M. Desai. Fluctuations in Fitness Distributions and the Effects of Weak Linked Selection on Sequence Evolution. Theoretical Population Biology 85:86-102 (2013). [software]. [pdf]
  • Desai, M. M.*, A. M. Walczak*, and D. S. Fisher. Genetic Diversity and the Structure of Genealogies in Rapidly Adapting Populations. Genetics 193:565-585 (2013). [pdf]
  • Desai, M. M. Statistical Questions in Experimental Evolution. Journal of Statistical Mechanics P01003 (2013). [pdf]
  • Nicolaisen, L. E. and M. M. Desai. Distortions in Genealogies Due to Purifying Selection. Molecular Biology and Evolution 29:3589-3600 (2012). [pdf]
  • Goyal, S., D. J. Balick, E. R. Jerison, R. A. Neher, B. I. Shraiman, and M. M. Desai. Dynamic Mutation-Selection Balance as an Evolutionary Attractor. Genetics 191:1309-1319 (2012). [pdf]
  • Kryazhimskiy, S. K., D. P. Rice, and M. M. Desai. Population Subdivision and Adaptation in Asexual Populations of Saccharomyces Cerevisiae. Evolution 66:1931-1941 (2012). [pdf]
  • Good, B. H., I. M. Rouzine, D. J. Balick, O. Hallatschek, and M. M. Desai. Distribution of Fixed Beneficial Mutations and the Rate of Adaptation in Asexual Populations. PNAS 109:4950-4955 (2012). [pdf]
  • Desai, M. M.*, L. E. Nicolaisen*, A. M. Walczak, and J. B. Plotkin. The Structure of Allelic Diversity in the Presence of Purifying Selection.  Theoretical Population Biology 81:144-157 (2012). [pdf]
  • Walczak, A. M.*, L. E. Nicolaisen*, J. B. Plotkin, and M. M. Desai. The Structure of Genealogies in the Presence of Purifying Selection:  A "Fitness-Class Coalescent".  Genetics 190:753 (2012). [pdf]
  • Desai, M. M. and D. S. Fisher. The Balance Between Mutators and Nonmutators in Asexual Populations.  Genetics 188:997-1014 (2011). [pdf]
  • Lang, G. I., D. Botstein, and M. M. Desai. Genetic Variation and the Fate of Individual Beneficial Mutations in Asexual Populations. Genetics 188:647-661 (2011). [pdf]
  • Weissman, D. W., M. M. Desai, D. S. Fisher, and M. W. Feldman. The Rate at Which Asexual Populations Cross Fitness Valleys. Theoretical Population Biology.  75:286-300 (2009). [pdf]
  • Desai, M. M. Reverse Evolution and Evolutionary Memory. Nature Genetics 41:142-3 (2009). [pdf]
  • Gresham, D., M. M. Desai, C. M. Tucker, H. T. Jenq, D. A. Pai, A. Ware, C. G. DeSevo, D. Botstein, and M. J. Dunham. The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast. PLoS Genetics 4: e1000303 (2008). [pdf]
  • Desai, M. M. and J. B. Plotkin. The Polymorphism Frequency Spectrum of Finitely Many Sites Under Selection. Genetics 180:2175-91 (2008). [pdf]
  • Fogle, C. A., J. L. Nagle, and M. M. Desai. Clonal Interference, Multiple Mutations, and Adaptation in Large Asexual Populations. Genetics 180:2163-73 (2008).  [pdf]
  • Desai, M. M., D. W. Weissman, and M. W. Feldman. Evolution Can Favor Antagonistic Epistasis.  Genetics 177:1001-10 (2007). [pdf]
  • Desai, M. M. and D. S. Fisher. Beneficial Mutation-Selection Balance and the Effect of Linkage on Positive Selection. Genetics 176:1759-98 (2007). [pdf]
  • Desai, M. M., D. S. Fisher, and A. W. Murray. The Speed of Evolution and Maintenance of Variation in Asexual Populations. Current Biology 17:385-94 (2007). [pdf]
  • Plotkin, J. B., J. Dushoff, M. M. Desai, and H. B. Fraser. Codon Usage and Selection on Proteins. Journal of Molecular Evolution 63:635-53 (2006). [pdf] 
  • Thompson, D. A., M. M. Desai, and A. W. Murray. Ploidy Controls the Success of Mutators and Nature of Mutations During Budding Yeast Evolution. Current Biology 16:1581-90 (2006). [pdf]
  • Plotkin, J. B., J. Dushoff, M. M. Desai, and H. B. Fraser. Estimating Selection Pressures from Limited Comparative Data. Molecular Biology and Evolution 23:1457-9 (2006). [pdf]
  • Desai, M. M. and D. R. Nelson. A Quasispecies on a Moving Oasis.  Theoretical Population Biology 67:33-45 (2005). [pdf]
[Current/Former lab members in bold. *Co-first authors. †Co-senior authors.]