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For: Didelot X, Wilson DJ. ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLoS Comput Biol 2015;11:e1004041. [PMID: 25675341 PMCID: PMC4326465 DOI: 10.1371/journal.pcbi.1004041] [Citation(s) in RCA: 607] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 11/16/2014] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
601
Ingle DJ, Tauschek M, Edwards DJ, Hocking DM, Pickard DJ, Azzopardi KI, Amarasena T, Bennett-Wood V, Pearson JS, Tamboura B, Antonio M, Ochieng JB, Oundo J, Mandomando I, Qureshi S, Ramamurthy T, Hossain A, Kotloff KL, Nataro JP, Dougan G, Levine MM, Robins-Browne RM, Holt KE. Evolution of atypical enteropathogenic E. coli by repeated acquisition of LEE pathogenicity island variants. Nat Microbiol 2016;1:15010. [PMID: 27571974 DOI: 10.1038/nmicrobiol.2015.10] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 11/02/2015] [Indexed: 01/25/2023]
602
Deng X, den Bakker HC, Hendriksen RS. Genomic Epidemiology: Whole-Genome-Sequencing-Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens. Annu Rev Food Sci Technol 2016;7:353-74. [PMID: 26772415 DOI: 10.1146/annurev-food-041715-033259] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
603
Dearlove BL, Cody AJ, Pascoe B, Méric G, Wilson DJ, Sheppard SK. Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections. ISME JOURNAL 2015;10:721-9. [PMID: 26305157 PMCID: PMC4677457 DOI: 10.1038/ismej.2015.149] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 06/20/2015] [Accepted: 07/21/2015] [Indexed: 12/12/2022]
604
Pettengill JB. The Time to Most Recent Common Ancestor Does Not (Usually) Approximate the Date of Divergence. PLoS One 2015;10:e0128407. [PMID: 26273822 PMCID: PMC4537086 DOI: 10.1371/journal.pone.0128407] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 04/17/2015] [Indexed: 11/18/2022]  Open
605
Stasiewicz MJ, den Bakker HC, Wiedmann M. Genomics tools in microbial food safety. Curr Opin Food Sci 2015. [DOI: 10.1016/j.cofs.2015.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
606
Walker TM, Kohl TA, Omar SV, Hedge J, Del Ojo Elias C, Bradley P, Iqbal Z, Feuerriegel S, Niehaus KE, Wilson DJ, Clifton DA, Kapatai G, Ip CLC, Bowden R, Drobniewski FA, Allix-Béguec C, Gaudin C, Parkhill J, Diel R, Supply P, Crook DW, Smith EG, Walker AS, Ismail N, Niemann S, Peto TEA. Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study. THE LANCET. INFECTIOUS DISEASES 2015;15:1193-1202. [PMID: 26116186 PMCID: PMC4579482 DOI: 10.1016/s1473-3099(15)00062-6] [Citation(s) in RCA: 424] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/03/2015] [Accepted: 05/15/2015] [Indexed: 12/14/2022]
607
Genomics Reveals the Worldwide Distribution of Multidrug-Resistant Serotype 6E Pneumococci. J Clin Microbiol 2015;53:2271-85. [PMID: 25972423 PMCID: PMC4473186 DOI: 10.1128/jcm.00744-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/06/2015] [Indexed: 02/02/2023]  Open
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