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Michael Baym, Ph.D.

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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. 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. Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques. Genome Biol. 2022 Nov 08; 23(1):236. PMID: 36348471; PMCID: PMC9643916.
    Citations: 1     Fields:    Translation:HumansCellsPHPublic Health
  2. Herren CM, Baym M. Decreased thermal niche breadth as a trade-off of antibiotic resistance. ISME J. 2022 07; 16(7):1843-1852. PMID: 35422477; PMCID: PMC9213455.
    Citations:    Fields:    Translation:Cells
  3. Silpe JE, Wong JWH, Owen SV, Baym M, Balskus EP. The bacterial toxin colibactin triggers prophage induction. Nature. 2022 03; 603(7900):315-320. PMID: 35197633; PMCID: PMC8907063.
    Citations:    Fields:    Translation:Cells
  4. Owen SV, Wenner N, Dulberger CL, Rodwell EV, Bowers-Barnard A, Quinones-Olvera N, Rigden DJ, Rubin EJ, Garner EC, Baym M, Hinton JCD. Prophages encode phage-defense systems with cognate self-immunity. Cell Host Microbe. 2021 11 10; 29(11):1620-1633.e8. PMID: 34597593.
    Citations: 7     Fields:    Translation:Cells
  5. 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. Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification. medRxiv. 2021 Sep 02. PMID: 34494031; PMCID: PMC8423229.
    Citations:    
  6. Rowe AR, Salimijazi F, Trutschel L, Sackett J, Adesina O, Anzai I, Kugelmass LH, Baym MH, Barstow B. Identification of a pathway for electron uptake in Shewanella oneidensis. Commun Biol. 2021 08 11; 4(1):957. PMID: 34381156.
    Citations: 4     Translation:Cells
  7. Brinda K, Baym M, Kucherov G. Simplitigs as an efficient and scalable representation of de Bruijn graphs. Genome Biol. 2021 04 06; 22(1):96. PMID: 33823902.
    Citations: 4     Fields:    
  8. Kennedy-Shaffer L, Baym M, Hanage WP. Perfect as the enemy of good: tracing transmissions with low-sensitivity tests to mitigate SARS-CoV-2 outbreaks. Lancet Microbe. 2021 05; 2(5):e219-e224. PMID: 33748803; PMCID: PMC7954468.
    Citations: 6     Translation:HumansCellsPHPublic Health
  9. Kim J, Bae JH, Baym M, Zhang DY. Metastable hybridization-based DNA information storage to allow rapid and permanent erasure. Nat Commun. 2020 10 06; 11(1):5008. PMID: 33024123.
    Citations:    Fields:    Translation:Cells
  10. Qian J, Lu ZX, Mancuso CP, Jhuang HY, Del Carmen Barajas-Ornelas R, Boswell SA, Ramírez-Guadiana FH, Jones V, Sonti A, Sedlack K, Artzi L, Jung G, Arammash M, Pettit ME, Melfi M, Lyon L, Owen SV, Baym M, Khalil AS, Silver PA, Rudner DZ, Springer M. Barcoded microbial system for high-resolution object provenance. Science. 2020 06 05; 368(6495):1135-1140. PMID: 32499444.
    Citations: 7     Fields:    Translation:CellsPHPublic Health
  11. Russ D, Glaser F, Shaer Tamar E, Yelin I, Baym M, Kelsic ED, Zampaloni C, Haldimann A, Kishony R. Escape mutations circumvent a tradeoff between resistance to a beta-lactam and resistance to a beta-lactamase inhibitor. Nat Commun. 2020 04 24; 11(1):2029. PMID: 32332717.
    Citations: 9     Fields:    Translation:Cells
  12. Brinda K, Callendrello A, Ma KC, MacFadden DR, Charalampous T, Lee RS, Cowley L, Wadsworth CB, Grad YH, Kucherov G, O'Grady J, Baym M, Hanage WP. Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing. Nat Microbiol. 2020 03; 5(3):455-464. PMID: 32042129.
    Citations: 30     Fields:    Translation:HumansCells
  13. Canals R, Chaudhuri RR, Steiner RE, Owen SV, Quinones-Olvera N, Gordon MA, Baym M, Ibba M, Hinton JCD. The fitness landscape of the African Salmonella Typhimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid. PLoS Pathog. 2019 09; 15(9):e1007948. PMID: 31560731.
    Citations: 6     Fields:    Translation:AnimalsCells
  14. Anzai IA, Shaket L, Adesina O, Baym M, Barstow B. Rapid curation of gene disruption collections using Knockout Sudoku. Nat Protoc. 2017 Oct; 12(10):2110-2137. PMID: 28906493.
    Citations: 3     Fields:    Translation:Cells
  15. Riglar DT, Giessen TW, Baym M, Kerns SJ, Niederhuber MJ, Bronson RT, Kotula JW, Gerber GK, Way JC, Silver PA. Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation. Nat Biotechnol. 2017 Jul; 35(7):653-658. PMID: 28553941; PMCID: PMC5658125.
    Citations: 88     Fields:    Translation:AnimalsCells
  16. Myhrvold C, Baym M, Hanikel N, Ong LL, Gootenberg JS, Yin P. Barcode extension for analysis and reconstruction of structures. Nat Commun. 2017 03 13; 8:14698. PMID: 28287117.
    Citations: 5     Fields:    Translation:Cells
  17. Baym M, Shaket L, Anzai IA, Adesina O, Barstow B. Rapid construction of a whole-genome transposon insertion collection for Shewanella oneidensis by Knockout Sudoku. Nat Commun. 2016 11 10; 7:13270. PMID: 27830751.
    Citations: 15     Fields:    Translation:Cells
  18. Stone LK, Baym M, Lieberman TD, Chait R, Clardy J, Kishony R. Compounds that select against the tetracycline-resistance efflux pump. Nat Chem Biol. 2016 Nov; 12(11):902-904. PMID: 27642863; PMCID: PMC5069154.
    Citations: 17     Fields:    Translation:Cells
  19. Baym M, Lieberman TD, Kelsic ED, Chait R, Gross R, Yelin I, Kishony R. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 2016 09 09; 353(6304):1147-51. PMID: 27609891.
    Citations: 137     Fields:    Translation:Cells
  20. Baym M, Stone LK, Kishony R. Multidrug evolutionary strategies to reverse antibiotic resistance. Science. 2016 Jan 01; 351(6268):aad3292. PMID: 26722002.
    Citations: 193     Fields:    Translation:HumansCells
  21. Palmer AC, Toprak E, Baym M, Kim S, Veres A, Bershtein S, Kishony R. Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes. Nat Commun. 2015 Jun 10; 6:7385. PMID: 26060115.
    Citations: 64     Fields:    
  22. Baym M, Kryazhimskiy S, Lieberman TD, Chung H, Desai MM, Kishony R. Inexpensive multiplexed library preparation for megabase-sized genomes. PLoS One. 2015; 10(5):e0128036. PMID: 26000737.
    Citations: 270     Fields:    
  23. Klein DJ, Baym M, Eckhoff P. The Separatrix Algorithm for synthesis and analysis of stochastic simulations with applications in disease modeling. PLoS One. 2014; 9(7):e103467. PMID: 25078087.
    Citations: 2     Fields:    Translation:Humans
  24. Daniels NM, Gallant A, Peng J, Cowen LJ, Baym M, Berger B. Compressive genomics for protein databases. Bioinformatics. 2013 Jul 01; 29(13):i283-90. PMID: 23812995.
    Citations: 15     Fields:    
  25. Loh PR, Baym M, Berger B. Compressive genomics. Nat Biotechnol. 2012 Jul 10; 30(7):627-30. PMID: 22781691.
    Citations: 42     Fields:    Translation:HumansAnimals
  26. Park D, Singh R, Baym M, Liao CS, Berger B. IsoBase: a database of functionally related proteins across PPI networks. Nucleic Acids Res. 2011 Jan; 39(Database issue):D295-300. PMID: 21177658.
    Citations: 21     Fields:    Translation:HumansAnimals
  27. Lun DS, Rockwell G, Guido NJ, Baym M, Kelner JA, Berger B, Galagan JE, Church GM. Large-scale identification of genetic design strategies using local search. Mol Syst Biol. 2009; 5:296. PMID: 19690565.
    Citations: 55     Fields:    Translation:Cells
  28. Liao CS, Lu K, Baym M, Singh R, Berger B. IsoRankN: spectral methods for global alignment of multiple protein networks. Bioinformatics. 2009 Jun 15; 25(12):i253-8. PMID: 19477996.
    Citations: 94     Fields:    
  29. Baym M, Hübler AW. Conserved quantities and adaptation to the edge of chaos. Phys Rev E Stat Nonlin Soft Matter Phys. 2006 May; 73(5 Pt 2):056210. PMID: 16803029.
    Citations: 1     Fields:    
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.