Michael Baym, PhD
Michael Baym, PhD
Assistant 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
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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Decreased thermal niche breadth as a trade-off of antibiotic resistance.
Authors: Herren CM, Baym M.
ISME J
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The bacterial toxin colibactin triggers prophage induction.
Authors: Silpe JE, Wong JWH, Owen SV, Baym M, Balskus EP.
Nature
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Prophages encode phage-defense systems with cognate self-immunity.
Authors: Owen SV, Wenner N, Dulberger CL, Rodwell EV, Bowers-Barnard A, Quinones-Olvera N, Rigden DJ, Rubin EJ, Garner EC, Baym M, Hinton JCD.
Cell Host Microbe
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Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification.
Authors: Baaijens JA, Zulli A, Ott IM, Petrone ME, Alpert T, Fauver JR, Kalinich CC, Vogels CBF, Breban MI, Duvallet C, McElroy K, Ghaeli N, Imakaev M, Mckenzie-Bennett M, Robison K, Plocik A, Schilling R, Pierson M, Littlefield R, Spencer M, Simen BB, Hanage WP, Grubaugh ND, Peccia J, Baym M.
medRxiv
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