KPop: accurate and scalable comparative analysis of microbial genomes by sequence embeddings by Xavier Didelot, Paolo Ribeca

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ClonalFrameML: efficient inference of recombination in whole bacterial genomes. by Xavier Didelot, Daniel J Wilson

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Estimating the fitness cost and benefit of cefixime resistance in Neisseria gonorrhoeae to inform prescription policy: A modelling study. by Lilith K Whittles, Peter J White, Xavier Didelot

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Bayesian Inference of Pathogen Phylogeography using the Structured Coalescent Model. by Ian Roberts, Richard G Everitt, Jere Koskela, Xavier Didelot

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Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks. by Don Klinkenberg, Jantien A Backer, Xavier Didelot, Caroline Colijn, Jacco Wallinga

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Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data. by Thibaut Jombart, Anne Cori, Xavier Didelot, Simon Cauchemez, Christophe Fraser, Neil Ferguson

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Recombination and population structure in Salmonella enterica. by Xavier Didelot, Rory Bowden, Teresa Street, Tanya Golubchik, Chris Spencer, Gil McVean, Vartul Sangal, Muna F Anjum, Mark Achtman, Daniel Falush, Peter Donnelly

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Clinical Clostridium difficile: clonality and pathogenicity locus diversity. by Kate E Dingle, David Griffiths, Xavier Didelot, Jessica Evans, Alison Vaughan, Melina Kachrimanidou, Nicole Stoesser, Keith A Jolley, Tanya Golubchik, Rosalind M Harding, Tim E Peto, Warren Fawley, A Sarah Walker, Mark Wilcox, Derrick W Crook

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