Publications

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

 

Articles and Preprints

  1. A. Limdi, S.V. Owen, C.M. Herren, R.E. Lenski, M. Baym, Parallel changes in gene essentiality over 50,000 generations of evolution, (2022)
    Preprint: https://www.biorxiv.org/content/10.1101/2022.05.17.492023
  2. C.M. Herren, M. Baym, Decreased thermal niche breadth as a trade-off of antibiotic resistance, The ISME Journal, 16, 1843–1852 (2022)
  3. 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)
  4. 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)
  5. 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†, Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification, (2021)
    Preprint: https://www.medrxiv.org/content/10.1101/2021.08.31.21262938v1
  6. 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)
  7. K. Břinda, M. Baym*, G. Kucherov*, Simplitigs as an efficient and scalable representation of de Bruijn graphs, Genome Biology, 22, 96 (2021)
  8. 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)
  9. 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).
  10. 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)
  11. 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)
  12. 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)
  13. 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)
  14. C.M. Herren, M. Baym, Stronger connectivity of the resident gut microbiome lends resistance to invading bacteria, (2018)
    Preprint: www.biorxiv.org/content/early/2018/02/08/261750
  15. 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)
  16. 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)
  17. 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)
  18. 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
  19. 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)
  20. 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)
  21. 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
  22. M. Baym*, L.K. Stone*, R. Kishony, Multidrug evolutionary strategies to reverse antibiotic resistance, Science, 351, 6268 (2016), review. (PDF)
  23. 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)
  24. 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)
  25. 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)
  26. 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)
  27. M. Baym and D.B. West, Bounds on the k-dimension of Products of Special Posets, Order 30 779–796 (2013). (PDF)
  28. 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
  29. 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)
  30. 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)
  31. 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)
  32. 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)
  33. 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.

Perspective

  1. M. Baym, Sustainable Stewardship Needs Evolution, Cell Host and Microbe, 26(1):8 (2019). (PDF)