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Items: 18

1.

Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing.

Břinda 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.

Nat Microbiol. 2020 Feb 10. doi: 10.1038/s41564-019-0656-6. [Epub ahead of print]

PMID:
32042129
2.

The fitness landscape of the African Salmonella Typhimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid.

Canals R, Chaudhuri RR, Steiner RE, Owen SV, Quinones-Olvera N, Gordon MA, Baym M, Ibba M, Hinton JCD.

PLoS Pathog. 2019 Sep 27;15(9):e1007948. doi: 10.1371/journal.ppat.1007948. eCollection 2019 Sep.

3.

Rapid curation of gene disruption collections using Knockout Sudoku.

Anzai IA, Shaket L, Adesina O, Baym M, Barstow B.

Nat Protoc. 2017 Oct;12(10):2110-2137. doi: 10.1038/nprot.2017.073. Epub 2017 Sep 14.

PMID:
28906493
4.

Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation.

Riglar DT, Giessen TW, Baym M, Kerns SJ, Niederhuber MJ, Bronson RT, Kotula JW, Gerber GK, Way JC, Silver PA.

Nat Biotechnol. 2017 Jul;35(7):653-658. doi: 10.1038/nbt.3879. Epub 2017 May 29.

5.

Barcode extension for analysis and reconstruction of structures.

Myhrvold C, Baym M, Hanikel N, Ong LL, Gootenberg JS, Yin P.

Nat Commun. 2017 Mar 13;8:14698. doi: 10.1038/ncomms14698.

6.

Rapid construction of a whole-genome transposon insertion collection for Shewanella oneidensis by Knockout Sudoku.

Baym M, Shaket L, Anzai IA, Adesina O, Barstow B.

Nat Commun. 2016 Nov 10;7:13270. doi: 10.1038/ncomms13270.

7.

Compounds that select against the tetracycline-resistance efflux pump.

Stone LK, Baym M, Lieberman TD, Chait R, Clardy J, Kishony R.

Nat Chem Biol. 2016 Nov;12(11):902-904. doi: 10.1038/nchembio.2176. Epub 2016 Sep 19.

8.

Spatiotemporal microbial evolution on antibiotic landscapes.

Baym M, Lieberman TD, Kelsic ED, Chait R, Gross R, Yelin I, Kishony R.

Science. 2016 Sep 9;353(6304):1147-51. doi: 10.1126/science.aag0822.

9.

Multidrug evolutionary strategies to reverse antibiotic resistance.

Baym M, Stone LK, Kishony R.

Science. 2016 Jan 1;351(6268):aad3292. doi: 10.1126/science.aad3292. Review.

10.

Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes.

Palmer AC, Toprak E, Baym M, Kim S, Veres A, Bershtein S, Kishony R.

Nat Commun. 2015 Jun 10;6:7385. doi: 10.1038/ncomms8385.

11.

Inexpensive multiplexed library preparation for megabase-sized genomes.

Baym M, Kryazhimskiy S, Lieberman TD, Chung H, Desai MM, Kishony R.

PLoS One. 2015 May 22;10(5):e0128036. doi: 10.1371/journal.pone.0128036. eCollection 2015. Erratum in: PLoS One. 2015;10(6):e0131262.

12.

The Separatrix Algorithm for synthesis and analysis of stochastic simulations with applications in disease modeling.

Klein DJ, Baym M, Eckhoff P.

PLoS One. 2014 Jul 31;9(7):e103467. doi: 10.1371/journal.pone.0103467. eCollection 2014.

13.

Compressive genomics for protein databases.

Daniels NM, Gallant A, Peng J, Cowen LJ, Baym M, Berger B.

Bioinformatics. 2013 Jul 1;29(13):i283-90. doi: 10.1093/bioinformatics/btt214.

14.

Compressive genomics.

Loh PR, Baym M, Berger B.

Nat Biotechnol. 2012 Jul 10;30(7):627-30. doi: 10.1038/nbt.2241. No abstract available.

PMID:
22781691
15.

IsoBase: a database of functionally related proteins across PPI networks.

Park D, Singh R, Baym M, Liao CS, Berger B.

Nucleic Acids Res. 2011 Jan;39(Database issue):D295-300. doi: 10.1093/nar/gkq1234.

16.

Large-scale identification of genetic design strategies using local search.

Lun DS, Rockwell G, Guido NJ, Baym M, Kelner JA, Berger B, Galagan JE, Church GM.

Mol Syst Biol. 2009;5:296. doi: 10.1038/msb.2009.57. Epub 2009 Aug 18.

17.

IsoRankN: spectral methods for global alignment of multiple protein networks.

Liao CS, Lu K, Baym M, Singh R, Berger B.

Bioinformatics. 2009 Jun 15;25(12):i253-8. doi: 10.1093/bioinformatics/btp203.

18.

Conserved quantities and adaptation to the edge of chaos.

Baym M, Hübler AW.

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 May;73(5 Pt 2):056210. Epub 2006 May 26.

PMID:
16803029

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