Searching journal content for Stephen D Bentley in author.

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  1. Method: Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs
    • Juri Kuronen,
    • Samuel T. Horsfield,
    • Anna K. Pöntinen,
    • Sudaraka Mallawaarachchi,
    • Sergio Arredondo-Alonso,
    • Harry Thorpe,
    • Rebecca A. Gladstone,
    • Rob J.L. Willems,
    • Stephen D. Bentley,
    • Nicholas J. Croucher,
    • Johan Pensar,
    • John A. Lees,
    • Gerry Tonkin-Hill,
    • and Jukka Corander
    Genome Res. July 2024 34: 1081-1088; Published in Advance August 12, 2024, doi:10.1101/gr.278485.123
    OPEN ACCESS ARTICLE
  2. Method: Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe
    • Gerry Tonkin-Hill,
    • Rebecca A. Gladstone,
    • Anna K. Pöntinen,
    • Sergio Arredondo-Alonso,
    • Stephen D. Bentley,
    • and Jukka Corander
    Genome Res. January 2023 33: 129-140; Published in Advance January 20, 2023, doi:10.1101/gr.277340.122
    OPEN ACCESS ARTICLE
  3. Research: The effect of recombination on the evolution of a population of Neisseria meningitidis
    • Neil MacAlasdair,
    • Maiju Pesonen,
    • Ola Brynildsrud,
    • Vegard Eldholm,
    • Paul A. Kristiansen,
    • Jukka Corander,
    • Dominique A. Caugant,
    • and Stephen D. Bentley
    Genome Res. July 2021 31: 1258-1268; Published in Advance June 9, 2021, doi:10.1101/gr.264465.120
    OPEN ACCESS ARTICLE
  4. Method: Fast and flexible bacterial genomic epidemiology with PopPUNK
    • John A. Lees,
    • Simon R. Harris,
    • Gerry Tonkin-Hill,
    • Rebecca A. Gladstone,
    • Stephanie W. Lo,
    • Jeffrey N. Weiser,
    • Jukka Corander,
    • Stephen D. Bentley,
    • and Nicholas J. Croucher
    Genome Res. February 2019 29: 304-316; Published in Advance January 24, 2019, doi:10.1101/gr.241455.118
    OPEN ACCESS ARTICLE
  5. Corrigendum: Corrigendum: Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland
    • Sandra Reuter,
    • M. Estée Török,
    • Matthew T.G. Holden,
    • Rosy Reynolds,
    • Kathy E. Raven,
    • Beth Blane,
    • Tjibbe Donker,
    • Stephen D. Bentley,
    • David M. Aanensen,
    • Hajo Grundmann,
    • Edward J. Feil,
    • Brian G. Spratt,
    • Julian Parkhill,
    • and Sharon J. Peacock
    Genome Res. September 2017 27: 1622; doi:10.1101/gr.228155.117
    OPEN ACCESS ARTICLE
  6. Resource: Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland
    • Sandra Reuter,
    • M. Estée Török,
    • Matthew T.G. Holden,
    • Rosy Reynolds,
    • Kathy E. Raven,
    • Beth Blane,
    • Tjibbe Donker,
    • Stephen D. Bentley,
    • David M. Aanensen,
    • Hajo Grundmann,
    • Edward J. Feil,
    • Brian G. Spratt,
    • Julian Parkhill,
    • and Sharon J. Peacock
    Genome Res. February 2016 26: 263-270; Published in Advance December 15, 2015, doi:10.1101/gr.196709.115
    OPEN ACCESS ARTICLE
  7. Research: A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic
    • Matthew T.G. Holden,
    • Li-Yang Hsu,
    • Kevin Kurt,
    • Lucy A. Weinert,
    • Alison E. Mather,
    • Simon R. Harris,
    • Birgit Strommenger,
    • Franziska Layer,
    • Wolfgang Witte,
    • Herminia de Lencastre,
    • Robert Skov,
    • Henrik Westh,
    • Helena Žemličková,
    • Geoffrey Coombs,
    • Angela M. Kearns,
    • Robert L.R. Hill,
    • Jonathan Edgeworth,
    • Ian Gould,
    • Vanya Gant,
    • Jonathan Cooke,
    • Giles F. Edwards,
    • Paul R. McAdam,
    • Kate E. Templeton,
    • Angela McCann,
    • Zhemin Zhou,
    • Santiago Castillo-Ramírez,
    • Edward J. Feil,
    • Lyndsey O. Hudson,
    • Mark C. Enright,
    • Francois Balloux,
    • David M. Aanensen,
    • Brian G. Spratt,
    • J. Ross Fitzgerald,
    • Julian Parkhill,
    • Mark Achtman,
    • Stephen D. Bentley,
    • and Ulrich Nübel
    Genome Res. April 2013 23: 653-664; Published in Advance January 8, 2013, doi:10.1101/gr.147710.112
    OPEN ACCESS ARTICLE
  8. Research: Microevolution of extensively drug-resistant tuberculosis in Russia
    • Nicola Casali,
    • Vladyslav Nikolayevskyy,
    • Yanina Balabanova,
    • Olga Ignatyeva,
    • Irina Kontsevaya,
    • Simon R. Harris,
    • Stephen D. Bentley,
    • Julian Parkhill,
    • Sergey Nejentsev,
    • Sven E. Hoffner,
    • Rolf D. Horstmann,
    • Timothy Brown,
    • and Francis Drobniewski
    Genome Res. April 2012 22: 735-745; Published in Advance January 31, 2012, doi:10.1101/gr.128678.111
  9. LETTER: Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes
    • Mohammed Sebaihia,
    • Michael W. Peck,
    • Nigel P. Minton,
    • Nicholas R. Thomson,
    • Matthew T.G. Holden,
    • Wilfrid J. Mitchell,
    • Andrew T. Carter,
    • Stephen D. Bentley,
    • David R. Mason,
    • Lisa Crossman,
    • Catherine J. Paul,
    • Alasdair Ivens,
    • Marjon H.J. Wells-Bennik,
    • Ian J. Davis,
    • Ana M. Cerdeño-Tárraga,
    • Carol Churcher,
    • Michael A. Quail,
    • Tracey Chillingworth,
    • Theresa Feltwell,
    • Audrey Fraser,
    • Ian Goodhead,
    • Zahra Hance,
    • Kay Jagels,
    • Natasha Larke,
    • Mark Maddison,
    • Sharon Moule,
    • Karen Mungall,
    • Halina Norbertczak,
    • Ester Rabbinowitsch,
    • Mandy Sanders,
    • Mark Simmonds,
    • Brian White,
    • Sally Whithead,
    • and Julian Parkhill
    Genome Res. July 2007 17: 1082-1092; Published in Advance May 22, 2007, doi:10.1101/gr.6282807
    OPEN ACCESS ARTICLE
  10. ARTICLE: The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation
    • Nicholas R. Thomson,
    • Corin Yeats,
    • Kenneth Bell,
    • Matthew T.G. Holden,
    • Stephen D. Bentley,
    • Morag Livingstone,
    • Ana M. Cerdeño-Tárraga,
    • Barbara Harris,
    • Jon Doggett,
    • Doug Ormond,
    • Karen Mungall,
    • Kay Clarke,
    • Theresa Feltwell,
    • Zahra Hance,
    • Mandy Sanders,
    • Michael A. Quail,
    • Claire Price,
    • Bart G. Barrell,
    • Julian Parkhill,
    • and David Longbottom
    Genome Res. May 2005 15: 629-640; Published in Advance April 18, 2005, doi:10.1101/gr.3684805
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