Michael Baym, PhD

Michael Baym, PhD

Associate Professor of Biomedical Informatics

10 Shattuck Street #303, Boston, MA 02115

Baym Lab

Michael Baym received his PhD in Mathematics from MIT and was a postdoctoral fellow at Harvard Medical School in Systems Biology. Baym's research is centered around the problem of antibiotic resistance, at the intersection of experimental, theoretical and computational techniques. His work ranges from understanding the basic mechanisms of evolution to the development of algorithms for computation on massive biological datasets.


DBMI Research Areas
From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance.
Authors: Souque C, González Ojeda I, Baym M.
Annu Rev Microbiol
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Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data.
Authors: Sutcliffe SG, Kraemer SA, Ellmen I, Knapp JJ, Overton AK, Nash D, Nissimov JI, Charles TC, Dreifuss D, Topolsky I, Baykal PI, Fuhrmann L, Jablonski KP, Beerenwinkel N, Levy JI, Olabode AS, Becker DG, Gugan G, Brintnell E, Poon AFY, Valieris R, Drummond RD, Defelicibus A, Dias-Neto E, Rosales RA, Tojal da Silva I, Orfanou A, Psomopoulos F, Pechlivanis N, Pipes L, Chen Z, Baaijens JA, Baym M, Shapiro BJ.
Microb Genom
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Diverse and abundant phages exploit conjugative plasmids.
Authors: Quinones-Olvera N, Owen SV, McCully LM, Marin MG, Rand EA, Fan AC, Martins Dosumu OJ, Paul K, Sanchez Castaño CE, Petherbridge R, Paull JS, Baym M.
Nat Commun
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Changing fitness effects of mutations through long-term bacterial evolution.
Authors: Couce A, Limdi A, Magnan M, Owen SV, Herren CM, Lenski RE, Tenaillon O, Baym M.
Science
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Resolving Deleterious and Near-Neutral Effects Requires Different Pooled Fitness Assay Designs.
Authors: Limdi A, Baym M.
J Mol Evol
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Diverse and Abundant Viruses Exploit Conjugative Plasmids.
Authors: Quinones-Olvera N, Owen SV, McCully LM, Marin MG, Rand EA, Fan AC, Dosumu OJM, Paul K, Castaño CES, Petherbridge R, Paull JS, Baym M.
bioRxiv
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Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression.
Authors: Bå Inda K, Lima L, Pignotti S, Quinones-Olvera N, Salikhov K, Chikhi R, Kucherov G, Iqbal Z, Baym M.
bioRxiv
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A swapped genetic code prevents viral infections and gene transfer.
Authors: Nyerges A, Vinke S, Flynn R, Owen SV, Rand EA, Budnik B, Keen E, Narasimhan K, Marchand JA, Baas-Thomas M, Liu M, Chen K, Chiappino-Pepe A, Hu F, Baym M, Church GM.
Nature
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Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection.
Authors: Dulberger CL, Guerrero-Bustamante CA, Owen SV, Wilson S, Wuo MG, Garlena RA, Serpa LA, Russell DA, Zhu J, Braunecker BJ, Squyres GR, Baym M, Kiessling LL, Garner EC, Rubin EJ, Hatfull GF.
Nat Microbiol
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Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques.
Authors: Baaijens JA, Zulli A, Ott IM, Nika I, van der Lugt MJ, Petrone ME, Alpert T, Fauver JR, Kalinich CC, Vogels CBF, Breban MI, Duvallet C, McElroy KA, Ghaeli N, Imakaev M, Mckenzie-Bennett MF, Robison K, Plocik A, Schilling R, Pierson M, Littlefield R, Spencer ML, Simen BB, Hanage WP, Grubaugh ND, Peccia J, Baym M.
Genome Biol
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