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ArticlesPeer ReviewedFull Text
Genome evolution and the emergence of pathogenicity in avian Escherichia coli
Author / Creator:Mageiros, Leonardos ; Méric, Guillaume ; Bayliss, Sion C. ; Pensar, Johan ; Pascoe, Ben ; Mourkas, Evangelos ; Calland, Jessica K. ; Yahara, Koji ; Murray, Susan ; Wilkinson, Thomas S. ; Williams, Lisa K. ; Hitchings, Matthew D. ; Porter, Jonathan ; Kemmett, Kirsty ; Feil, Edward J. ; Jolley, Keith A. ; Williams, Nicola J. ; Corander, Jukka ; Sheppard, Samuel K.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-02, Vol.12 (1), p.765-13, Article 765
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Rapid geographical source attribution of Salmonella enterica serovar Enteritidis genomes using hierarchical machine learning
Author / Creator:Bayliss, Sion C ; Locke, Rebecca K ; Jenkins, Claire ; Chattaway, Marie Anne ; Dallman, Timothy J ; Cowley, Lauren A
Publisher:England: eLife Sciences Publications, Ltd
Journal title:eLife, 2023-04, Vol.12
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Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages
Author / Creator:Calland, Jessica K ; Pascoe, Ben ; Bayliss, Sion C ; Mourkas, Evangelos ; Berthenet, Elvire ; Thorpe, Harry A ; Hitchings, Matthew D ; Feil, Edward J ; Corander, Jukka ; Blaser, Martin J ; Falush, Daniel ; Sheppard, Samuel K
Publisher:United States: Public Library of Science
Journal title:PLoS genetics, 2021-09, Vol.17 (9), p.e1009829
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Patterns of cross‐resistance and collateral sensitivity between clinical antibiotics and natural antimicrobials
Author / Creator:Colclough, Abigail ; Corander, Jukka ; Sheppard, Samuel K. ; Bayliss, Sion C. ; Vos, Michiel
Publisher:England: John Wiley & Sons, Inc
Journal title:Evolutionary applications, 2019-06, Vol.12 (5), p.878-887
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Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter
Author / Creator:Mourkas, Evangelos ; Yahara, Koji ; Bayliss, Sion C ; Calland, Jessica K ; Johansson, Håkan ; Mageiros, Leonardos ; Muñoz-Ramirez, Zilia Y ; Futcher, Grant ; Méric, Guillaume ; Hitchings, Matthew D ; Sandoval-Motta, Santiago ; Torres, Javier ; Jolley, Keith A ; Maiden, Martin C J ; Ellström, Patrik ; Waldenström, Jonas ; Pascoe, Ben ; Sheppard, Samuel K
Publisher:England: eLife Science Publications, Ltd
Journal title:eLife, 2022-02, Vol.11
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Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon
Author / Creator:Pascoe, Ben ; Schiaffino, Francesca ; Murray, Susan ; Méric, Guillaume ; Bayliss, Sion C ; Hitchings, Matthew D ; Mourkas, Evangelos ; Calland, Jessica K ; Burga, Rosa ; Yori, Pablo Peñataro ; Jolley, Keith A ; Cooper, Kerry K ; Parker, Craig T ; Olortegui, Maribel Paredes ; Kosek, Margaret N ; Sheppard, Samuel K
Publisher:United States: Public Library of Science
Journal title:PLoS neglected tropical diseases, 2020-08, Vol.14 (8), p.e0008533
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Author Correction: Genome evolution and the emergence of pathogenicity in avian Escherichia coli
Author / Creator:Mageiros, Leonardos ; Méric, Guillaume ; Bayliss, Sion C. ; Pensar, Johan ; Pascoe, Ben ; Mourkas, Evangelos ; Calland, Jessica K. ; Yahara, Koji ; Murray, Susan ; Wilkinson, Thomas S. ; Williams, Lisa K. ; Hitchings, Matthew D. ; Porter, Jonathan ; Kemmett, Kirsty ; Feil, Edward J. ; Jolley, Keith A. ; Williams, Nicola J. ; Corander, Jukka ; Sheppard, Samuel K.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-03, Vol.12 (1), p.1934-1934, Article 1934
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Campylobacter jejuni genotypes are associated with post-infection irritable bowel syndrome in humans
Author / Creator:Peters, Stephanie ; Pascoe, Ben ; Wu, Zuowei ; Bayliss, Sion C. ; Zeng, Ximin ; Edwinson, Adam ; Veerabadhran-Gurunathan, Sakteesh ; Jawahir, Selina ; Calland, Jessica K. ; Mourkas, Evangelos ; Patel, Robin ; Wiens, Terra ; Decuir, Marijke ; Boxrud, David ; Smith, Kirk ; Parker, Craig T. ; Farrugia, Gianrico ; Zhang, Qijing ; Sheppard, Samuel K. ; Grover, Madhusudan
Publisher:London: Nature Publishing Group UK
Journal title:Communications biology, 2021-08, Vol.4 (1), p.1015-1015, Article 1015
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Comparative Analyses of Selection Operating on Nontranslated Intergenic Regions of Diverse Bacterial Species
Author / Creator:Thorpe, Harry A ; Bayliss, Sion C ; Hurst, Laurence D ; Feil, Edward J
Publisher:United States: Genetics Society of America
Journal title:Genetics (Austin), 2017-05, Vol.206 (1), p.363-376
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Agricultural intensification and the evolution of host specialism in the enteric pathogen Campylobacter jejuni
Author / Creator:Mourkas, Evangelos ; Taylor, Aidan J. ; Meric, Guillaume ; Bayliss, Sion C. ; Pascoe, Ben ; Mageiros, Leonardos ; Calland, Jessica K. ; Hitchings, Matthew D. ; Ridley, Anne ; Vidal, Ana ; Forbes, Ken J. ; Strachan, Norval J. C. ; Parker, Craig T. ; Parkhill, Julian ; Jolley, Keith A. ; Cody, Alison J. ; Maiden, Martin C. J. ; Kelly, David J. ; Sheppard, Samuel K.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2020-05, Vol.117 (20), p.11018-11028
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Draft Genome Sequences of Salinivibrio proteolyticus, Salinivibrio sharmensis, Salinivibrio siamensis, Salinivibrio costicola subsp. alcaliphilus, Salinivibrio costicola subsp. vallismortis, and 29 Ne...
Author / Creator:López-Hermoso, Clara ; de la Haba Rafael R. ; Sánchez-Porro, Cristina ; Bayliss, Sion C ; Feil, Edward J ; Ventosa Antonio
Publisher:Washington: American Society for Microbiology
Journal title:Microbiology resource announcements, 2017-07, Vol.5 (27)
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ArticlesFull Text
Quantifying bacterial evolution in the wild: a birthday problem for Campylobacter lineages
Author / Creator:Calland, Jessica K ; Pascoe, Ben ; Bayliss, Sion C ; Mourkas, Evangelos ; Berthenet, Elvire ; Thorpe, Harry A ; Hitchings, Matthew D ; Feil, Edward J ; Corander, Jukka ; Blaser, Martin J ; Falush, Daniel ; Sheppard, Samuel K
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2021-08
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PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria
Author / Creator:Bayliss, Sion C ; Thorpe, Harry A ; Coyle, Nicola M ; Sheppard, Samuel K ; Feil, Edward J
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2019-04
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Gene composition as a potential barrier to large recombinations in the bacterial pathogen Klebsiella pneumoniae
Author / Creator:Comandatore, Francesco ; Sassera, Davide ; Bayliss, Sion C ; Scaltriti, Erika ; Gaiarsa, Stefano ; Cao, Xiaoli ; Gales, Ana ; Saito, Ryoichi ; Pongolini, Stefano ; Brisse, Sylvain ; Feil, Edward ; Bandi, Claudio
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2018-01
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Piggy: A Rapid, Large-Scale Pan-Genome Analysis Tool for Intergenic Regions in Bacteria
Author / Creator:Thorpe, Harry A ; Bayliss, Sion C ; Sheppard, Samuel K ; Feil, Edward J
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2017-08
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Rapid statistical methods for inferring intra- and inter-hospital transmission of nosocomial pathogens from whole genome sequence data
Author / Creator:Aspbury, Marianne ; Sciberas, James ; Corander, Jukka ; Bayliss, Sion ; Donker, Tjibbe ; Feil, Edward ; James, Richard
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2018-10
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The large majority of intergenic sites in bacteria are selectively constrained, even when known regulatory elements are excluded
Author / Creator:Thorpe, Harry A ; Bayliss, Sion C ; Hurst, Laurence D ; Feil, Edward J
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2016-08
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Genome evolution and the emergence of pathogenicity in avian Escherichia coli

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Rapid geographical source attribution of Salmonella enterica serovar Enteritidis genomes using hierarchical machine learning

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Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages

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Patterns of cross‐resistance and collateral sensitivity between clinical antibiotics and natural antimicrobials

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Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter

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Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon

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Author Correction: Genome evolution and the emergence of pathogenicity in avian Escherichia coli

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Campylobacter jejuni genotypes are associated with post-infection irritable bowel syndrome in humans

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Comparative Analyses of Selection Operating on Nontranslated Intergenic Regions of Diverse Bacterial Species

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Agricultural intensification and the evolution of host specialism in the enteric pathogen Campylobacter jejuni

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Draft Genome Sequences of Salinivibrio proteolyticus, Salinivibrio sharmensis, Salinivibrio siamensis, Salinivibrio costicola subsp. alcaliphilus, Salinivibrio costicola subsp. vallismortis, and 29 Ne...

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Quantifying bacterial evolution in the wild: a birthday problem for Campylobacter lineages

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PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

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Gene composition as a potential barrier to large recombinations in the bacterial pathogen Klebsiella pneumoniae

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Piggy: A Rapid, Large-Scale Pan-Genome Analysis Tool for Intergenic Regions in Bacteria

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Rapid statistical methods for inferring intra- and inter-hospital transmission of nosocomial pathogens from whole genome sequence data

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The large majority of intergenic sites in bacteria are selectively constrained, even when known regulatory elements are excluded

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