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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. Brinda K, Baym M, Kucherov G. Simplitigs as an efficient and scalable representation of de Bruijn graphs. Genome Biol. 2021 Apr 06; 22(1):96. PMID: 33823902.
    Citations: 1     Fields:    
  2. 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 May; 2(5):e219-e224. PMID: 33748803.
    Citations: 1     
  3. 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
  4. 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: 4     Fields:    Translation:CellsPHPublic Health
  5. 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: 4     Fields:    Translation:Cells
  6. 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: 12     Fields:    Translation:HumansCells
  7. 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: 3     Fields:    Translation:AnimalsCells
  8. 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: 1     Fields:    Translation:Cells
  9. 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.
    Citations: 46     Fields:    Translation:AnimalsCells
  10. 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: 3     Fields:    Translation:Cells
  11. 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: 7     Fields:    Translation:Cells
  12. 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.
    Citations: 12     Fields:    Translation:Cells
  13. 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: 94     Fields:    Translation:Cells
  14. Baym M, Stone LK, Kishony R. Multidrug evolutionary strategies to reverse antibiotic resistance. Science. 2016 Jan 01; 351(6268):aad3292. PMID: 26722002.
    Citations: 130     Fields:    Translation:HumansCells
  15. 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: 51     Fields:    
  16. 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: 163     Fields:    
  17. 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
  18. 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: 12     Fields:    
  19. Loh PR, Baym M, Berger B. Compressive genomics. Nat Biotechnol. 2012 Jul 10; 30(7):627-30. PMID: 22781691.
    Citations: 35     Fields:    Translation:HumansAnimals
  20. 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: 18     Fields:    Translation:HumansAnimals
  21. 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: 49     Fields:    Translation:Cells
  22. 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: 77     Fields:    
  23. 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:    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.