Publications

Publications and patents are also listed at Google Scholar, Pubmed and Google Patents.
If you have difficulty obtaining any of the papers listed here, please email Michael for a copy.

 

Reviews and Perspectives

  1. B. Spellberg, D.N. Gilbert, M. Baym, G. Bearman, T. Boyles, A. Casadevall, G.N. Forrest, S. Freling, B. Ghanem, F. Hamilton, B. Luna, J. Moore, D.M. Musher, T.B. Nielsen, P. Nori, M.C. Phillips, L.-A. Pirofski, A.F. Shorr, S.Y.C. Tong, T.C. Lee, E.G. McDonald, Sustainable Solutions to the Continuous Threat of Antimicrobial Resistance, Health Affairs Scholar, qxaf012 (2025). (PDF)
  2. C. Souque†, I. González Ojeda, M. Baym†, From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance, Annual Review of Microbiology, 78 (2024). (PDF)
  3. M. Baym, Sustainable Stewardship Needs Evolution, Cell Host and Microbe, 26(1):8 (2019). (PDF)
  4. M. Baym*, L.K. Stone*, R. Kishony, Multidrug evolutionary strategies to reverse antibiotic resistance, Science, 351, 6268 (2016). (PDF)

Articles and Preprints

  1. K. Břinda, L. Lima, S. Pignotti, N. Quinones-Olvera, K. Salikhov, R. Chikhi, G. Kucherov, Z. Iqbal, M. Baym, Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression, Nature Methods, 22, 692–697 (2025) (PDF)
  2. F. Rossine, C. Sanchez, D. Eaton, J. Paulsson, M. Baym, Intracellular competition shapes plasmid population dynamics, (2025)
    Preprint: https://www.biorxiv.org/content/10.1101/2025.02.19.639193
  3. K. Mears*, F. Rossine*, N. Quinones-Olvera, C. Souque, M. Baym, RNA-guided nucleases enable a gene drive of insertion sequences in plasmids, (2025)
    Preprint: https://www.biorxiv.org/content/10.1101/2025.02.20.638934
  4. A. Kaul, C. Souque, M. Holland, M. Baym, Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics, (2025)
    Preprint: https://www.biorxiv.org/content/10.1101/2025.01.16.633422
  5. E.A. Rand, S.V. Owen, N. Quinones-Olvera, K. Jean, C. Hernandez-Perez, M. Baym, Phage DisCo: targeted discovery of bacteriophages by co-culture, (2024)
    Preprint: https://www.biorxiv.org/content/10.1101/2024.11.22.624878
  6. N. Quinones-Olvera*, S.V. Owen*, L.M. McCully, M.G. Marin, E.A. Rand, A.C. Fan, O.J. Martins Dosumu, K. Paul, C.E. Sanchez Castaño, R. Petherbridge, J.S. Paull, M. Baym, Diverse and abundant phages exploit conjugative plasmids, Nature Communications, 15, 3197 (2024)
  7. A. Couce*, A. Limdi*, M. Magnan, S.V. Owen, C.M. Herren, R.E. Lenski, O. Tenaillon†, M. Baym†, Changing fitness effects of mutations through long-term bacterial evolution, Science, 383, eadd1417 (2024) (PDF)
    Research Highlight in Nature Reviews Genetics.
  8. S.G. Sutcliffe, S.A. Kraemer, I. Ellmen, J.J. Knapp, A.K. Overton, D. Nash, J.I. Nissimov, T.C. Charles, D. Dreifuss, I. Topolsky, P.I. Baykal, L. Fuhrmann, K.P. Jablonski, N. Beerenwinkel, J.I. Levy, A.S. Olabode, D.G. Becker, G. Gugan, E. Britnell, A.F.Y. Poon, R. Valieris, R.D. Drummond, A. Defelicibus, E. Dias-Neto, R.A. Rosales, I.T. Silva, A. Orfanou, F. Psomopoulos, N. Pechlivanis, L. Pipes, Z. Chen, J.A. Baaijens, M. Baym, B.J. Shapiro, Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data, Microbial Genomics, 10(5), 001249 (2024)
  9. A. Limdi, M. Baym, Resolving deleterious and near-neutral effects requires different pooled fitness assay designs, Journal of Molecular Evolution, 91, 325-333 (2023) (PDF)
  10. A. Nyerges, S. Vinke, R. Flynn, S.V. Owen, E.A. Rand, B. Budnik, E. Keen, K. Narasimhan, J.A. Marchand, M. Baas-Thomas, M. Liu, K. Chen, A. Chiappino-Pepe, F. Hu, M. Baym, G.M. Church, A swapped genetic code prevents viral infections and gene transfer, Nature 615, 720–727 (2023) (PDF)
  11. C.L. Dulberger*, C.A. Guerrero-Bustamante*, S.V. Owen, S. Wilson, M.G. Wuo, R.A. Garlena, L.A. Serpa, D.A. Russell, J. Zhu, B.J. Braunecker, G.R. Squyres, M. Baym, L. Kiessling, E.C. Garner, E.J. Rubin†, G.F. Hatfull†, Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection, Nature Microbiology 8, 695–710 (2023)
  12. J.A. Baaijens*, A. Zulli*, I.M. Ott*, M.E. Petrone, T. Alpert, J.R. Fauver, C.C. Kalinich, C.B.F. Vogels, M.I. Breban, C. Duvallet, K. McElroy, N. Ghaeli, M. Imakaev, M. Mckenzie-Bennett, K. Robison, A. Plocik, R. Schilling, M. Pierson, R. Littlefield, M. Spencer, B.B. Simen, Yale SARS-CoV-2 Genomic Surveillance Initiative, W.P. Hanage, N.D. Grubaugh†, J. Peccia†, M. Baym†, Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques, Genome Biology, 23, 236 (2022)
  13. C.M. Herren, M. Baym, Decreased thermal niche breadth as a trade-off of antibiotic resistance, The ISME Journal, 16, 1843–1852 (2022)
  14. J.E. Silpe*, J.W.H. Wong*, S.V. Owen, M. Baym, E.P. Balskus, The bacterial toxin colibactin triggers prophage induction, Nature, 603, 315–320 (2022)
  15. S.V. Owen*, N. Wenner*, C. Dulberger, E. Rodwell, A. Bowers-Barnard, N. Quinones-Olvera, D.J. Rigden, E.J. Rubin, E.C. Garner, M. Baym†, J.C.D. Hinton†, Prophages encode phage-defense systems with cognate self-immunity, Cell Host & Microbe, 29, 1620-1633 (2021)
  16. A.R. Rowe, F. Salimijazi, L. Trutschel, J. Sackett, O. Adesina, I. Anzai, L.H. Kugelmass, M. Baym, B. Barstow, Identification of a Pathway for Electron Uptake in Shewanella oneidensis, Communications Biology, 4, 957 (2021)
  17. K. Břinda, M. Baym*, G. Kucherov*, Simplitigs as an efficient and scalable representation of de Bruijn graphs, Genome Biology, 22, 96 (2021)
  18. L. Kennedy-Shaffer, M. Baym, W.P. Hanage, Perfect as the enemy of good: tracing transmissions with low-sensitivity tests to mitigate SARS-CoV-2 outbreaks, The Lancet Microbe, 2, e219-24 (2021)
  19. J. Kim, J.H. Bae, M. Baym, D.Y. Zhang, Metastable Hybridization-based DNA Information Storage to Allow Rapid and Permanent Erasure, Nature Communications, 11, 5008 (2020).
  20. J. Qian*, Z.-X. Lu*, C.P. Mancuso*, H.-Y. Jhuang*, R. del Carmen Barajas-Ornelas*, S. Boswell*, F.H. Ramírez-Guadiana, V. Jones, A. Sonti, K. Sedlack, L. Artzi, G. Jung, M. Arammash, M.E. Pettit, M. Melfi, L. Lyon, S.V. Owen, M. Baym, A.S. Khalil, P. Silver, D. Rudner, M. Springer, Barcoded microbial system for high-resolution object provenance, Science, 368, 1135-1140 (2020). (PDF)
  21. K. Břinda, A. Callendrello, K.C. Ma, D.R. MacFadden, T. Charalampous, R.S. Lee, L. Cowley, C.B. Wadsworth, Y.H. Grad, G. Kucherov, J. O’Grady, M. Baym & W.P. Hanage, Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing, Nature Microbiology 5, 455-464 (2020)
  22. R. Canals, R.R. Chaudhuri, R.E. Steiner, S.V. Owen, N. Quinones-Olvera, M.A. Gordon, M. Baym, M. Ibba, J.C.D. Hinton, The fitness landscape of the African Salmonella Typhimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid, PLOS Pathogens, 15(9), e1007948 (2019)
  23. I. A. Anzai, L. Shaket, O. Adesina, M. Baym†, B. Barstow†, Rapid curation of gene disruption collections using Knockout Sudoku, Nature Protocols, 12, 2110–2137 (2017) (PDF)
  24. D. Russ, F. Glaser, E.S. Tamar, I. Yelin, M. Baym, E.D. Kelsic, C. Zampaloni, A. Haldimann, R. Kishony, Escape mutations circumvent a tradeoff between resistance to a beta-lactam and resistance to a beta-lactamase inhibitor, Nature Communications, 11, 2029 (2020)
  25. D.T. Riglar, T.W. Giessen, M. Baym, S.J. Kerns, M.J. Niederhuber, R.T. Bronson, J.W. Kotula, G.K. Gerber, J.C. Way, P.A. Silver, Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation, Nature Biotechnology, 35, 653–658 (2017). (PDF)
  26. C. Myhrvold, M. Baym, N. Hanikel, L.L. Ong, J.S. Gootenberg, P. Yin, Barcode Extension for Analysis and Reconstruction of Structures, Nature Communications, 8, 14698 (2017). (PDF)
  27. Y. J. Jiao*, M. Baym*, A. Veres, R. Kishony, Population diversity can jeopardize the efficacy of antibiotic cycling, (2017)
    Preprint: www.biorxiv.org/content/early/2016/10/20/082107
  28. M. Baym*, L. Shaket, I.A. Anzai, O. Adesina, B. Barstow*, Rapid Construction of a Whole-genome Transposon Insertion Collection for Shewanella oneidensis by Knockout Sudoku, Nature Communications, 7, 13270 (2016). (PDF)
  29. L.K. Stone, M. Baym, T.D. Lieberman, R. Chait, J. Clardy, R. Kishony, Compounds that select against the tetracycline resistance efflux pump, Nature Chemical Biology, 12, 902–904 (2016). (PDF)
  30. M. Baym, T.D. Lieberman, E.D. Kelsic, R. Chait, R. Gross, I. Yelin, R. Kishony, Spatiotemporal microbial evolution on antibiotic landscapes, Science, 353, 1147–1151 (2016). (PDF)
    Media attention including: PBS News Hour, CNN, NPR, The Atlantic, Haaretz, The Scientist, Smithsonian, Vox, Vice Motherboard, Wired, Gizmodo, Slate
  31. A. Palmer*, E. Toprak*, M. Baym, S. Kim, A. Veres, S. Bershtein, R. Kishony, Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes, Nature Communications, 6, 7385 (2015). (PDF)
  32. M. Baym*, S. Kryazhimskiy*, T.D. Lieberman*, H. Chung*, M.M. Desai, R. Kishony, Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes, PLoS ONE, 10, e0128036 (2015). (PDF)
  33. D.J. Klein, M. Baym, and P. Eckhoff, The Separatrix Algorithm for Synthesis and Analysis of Stochastic Simulations with Applications in Disease Modeling, PLoS ONE 9, e103467 (2014). (PDF)
  34. N.M. Daniels, A. Gallant, J. Peng, L.J. Cowen, M. Baym, and B. Berger, Compressive genomics for protein databases, Bioinformatics 29:13 i283–i290 (2013). (PDF)
  35. M. Baym and D.B. West, Bounds on the k-dimension of Products of Special Posets, Order 30 779–796 (2013). (PDF)
  36. P.-R. Loh*, M. Baym*†, and B. Berger†, Compressive Genomics, Nature Biotechnology 30 627–630 (2012). (PDF)
    Selected for Highlights Track at RECOMB 2013 and ISMB 2013
  37. D. Park, R. Singh, M. Baym, C. Liao, and B. Berger, IsoBase: A Database of Functionally Related Proteins across PPI Networks, Nucleic Acids Research, 39 D295–300 (2011). (PDF)
  38. D.S. Lun, G. Rockwell, N.J. Guido, M. Baym, J.A. Kelner, B. Berger, J.E. Galagan, and G.M. Church, Large-scale identification of genetic design strategies using local search, Molecular Systems Biology 5:296 (2009). (PDF)
  39. C.-S.Liao, K. Lu, M. Baym, R. Singh, and B. Berger, IsoRankN: Spectral methods for global alignment of multiple protein networks, Bioinformatics, 25(12): i253–258 (2009). (PDF)
  40. M. Baym*, C. Bakal*, N. Perrimon and B. Berger, High-Resolution Modeling of Cellular Signaling Networks, Proceedings of the 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB) LNBI 4955: 257–271 (2008). (PDF)
  41. M. Baym and A.W. Hübler, Conserved quantities and adaptation to the edge of chaos, Phys. Rev. E. 73, 056210 (2006). (PDF)

   *Authors contributed equally. †Corresponding author.