1.
Schubert B, Maddamsetti R, Nyman J, Farhat MR, Marks DS. Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings. Nat Microbiol. 2019;4(2):328-338. doi:10.1038/s41564-018-0309-1.
1.
Groussin M, Poyet M, Sistiaga A, et al. Elevated rates of horizontal gene transfer in the industrialized human microbiome. Cell. 2021;184(8):2053-2067.e18. doi:10.1016/j.cell.2021.02.052.
1.
Zhang S, Lebreton F, Mansfield MJ, et al. Identification of a Botulinum Neurotoxin-like Toxin in a Commensal Strain of Enterococcus faecium. Cell Host Microbe. 2018;23(2):169-176.e6. doi:10.1016/j.chom.2017.12.018.
1.
Carey AF, Rock JM, Krieger IV, et al. TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities. PLoS Pathog. 2018;14(3):e1006939. doi:10.1371/journal.ppat.1006939.
1.
Chavez A, Pruitt BW, Tuttle M, et al. Precise Cas9 targeting enables genomic mutation prevention. Proc Natl Acad Sci U S A. 2018;115(14):3669-3673. doi:10.1073/pnas.1718148115.
1.
Manson AL, Abeel T, Galagan JE, et al. Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics. Clin Infect Dis. 2017;64(11):1494-1501. doi:10.1093/cid/cix169.
1.
Shapiro RS, Chavez A, Collins JJ. CRISPR-based genomic tools for the manipulation of genetically intractable microorganisms. Nat Rev Microbiol. 2018;16(6):333-339. doi:10.1038/s41579-018-0002-7.
1.
de Welzen L, Eldholm V, Maharaj K, Manson AL, Earl AM, Pym AS. Whole-Transcriptome and -Genome Analysis of Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolates Identifies Downregulation of as a Mechanism of Ethionamide Resistance. Antimicrob Agents Chemother. 2017;61(12). doi:10.1128/AAC.01461-17.
1.
Anyansi C, Keo A, Walker BJ, et al. QuantTB - a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data. BMC Genomics. 2020;21(1):80. doi:10.1186/s12864-020-6486-3.
1.
Nielsen KL, Stegger M, Kiil K, et al. Whole-genome comparison of urinary pathogenic Escherichia coli and faecal isolates of UTI patients and healthy controls. Int J Med Microbiol. 2017;307(8):497-507. doi:10.1016/j.ijmm.2017.09.007.