Searching journal content for D R 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. Method: Detection of long repeat expansions from PCR-free whole-genome sequence data
    • Egor Dolzhenko,
    • Joke J.F.A. van Vugt,
    • Richard J. Shaw,
    • Mitchell A. Bekritsky,
    • Marka van Blitterswijk,
    • Giuseppe Narzisi,
    • Subramanian S. Ajay,
    • Vani Rajan,
    • Bryan R. Lajoie,
    • Nathan H. Johnson,
    • Zoya Kingsbury,
    • Sean J. Humphray,
    • Raymond D. Schellevis,
    • William J. Brands,
    • Matt Baker,
    • Rosa Rademakers,
    • Maarten Kooyman,
    • Gijs H.P. Tazelaar,
    • Michael A. van Es,
    • Russell McLaughlin,
    • William Sproviero,
    • Aleksey Shatunov,
    • Ashley Jones,
    • Ahmad Al Khleifat,
    • Alan Pittman,
    • Sarah Morgan,
    • Orla Hardiman,
    • Ammar Al-Chalabi,
    • Chris Shaw,
    • Bradley Smith,
    • Edmund J. Neo,
    • Karen Morrison,
    • Pamela J. Shaw,
    • Catherine Reeves,
    • Lara Winterkorn,
    • Nancy S. Wexler,
    • The US–Venezuela Collaborative Research Group,
    • David E. Housman,
    • Christopher W. Ng,
    • Alina L. Li,
    • Ryan J. Taft,
    • Leonard H. van den Berg,
    • David R. Bentley,
    • Jan H. Veldink,
    • and Michael A. Eberle
    Genome Res. November 2017 27: 1895-1903; Published in Advance September 8, 2017, doi:10.1101/gr.225672.117
    OPEN ACCESS ARTICLE
  6. 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
  7. Resource: A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree
    • Michael A. Eberle,
    • Epameinondas Fritzilas,
    • Peter Krusche,
    • Morten Källberg,
    • Benjamin L. Moore,
    • Mitchell A. Bekritsky,
    • Zamin Iqbal,
    • Han-Yu Chuang,
    • Sean J. Humphray,
    • Aaron L. Halpern,
    • Semyon Kruglyak,
    • Elliott H. Margulies,
    • Gil McVean,
    • and David R. Bentley
    Genome Res. January 2017 27: 157-164; Published in Advance November 30, 2016, doi:10.1101/gr.210500.116
    OPEN ACCESS ARTICLE
  8. 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
  9. 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
  10. 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
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