Searching journal content for Simon R. Harris in author.

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  1. Method: Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis
    • Romain Derelle,
    • Johanna von Wachsmann,
    • Tommi Mäklin,
    • Joel Hellewell,
    • Timothy Russell,
    • Ajit Lalvani,
    • Leonid Chindelevitch,
    • Nicholas J. Croucher,
    • Simon R. Harris,
    • and John A. Lees
    Genome Res. October 2024 34: 1661-1673; Published in Advance October 15, 2024, doi:10.1101/gr.279449.124
    OPEN ACCESS ARTICLE
  2. 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
  3. Research: Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131
    • Teemu Kallonen,
    • Hayley J. Brodrick,
    • Simon R. Harris,
    • Jukka Corander,
    • Nicholas M. Brown,
    • Veronique Martin,
    • Sharon J. Peacock,
    • and Julian Parkhill
    Genome Res. August 2017 27: 1437-1449; Published in Advance July 18, 2017, doi:10.1101/gr.216606.116
    OPEN ACCESS ARTICLE
  4. Research: Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion
    • James Hadfield,
    • Simon R. Harris,
    • Helena M.B. Seth-Smith,
    • Surendra Parmar,
    • Patiyan Andersson,
    • Philip M. Giffard,
    • Julius Schachter,
    • Jeanne Moncada,
    • Louise Ellison,
    • María Lucía Gallo Vaulet,
    • Marcelo Rodríguez Fermepin,
    • Frans Radebe,
    • Suyapa Mendoza,
    • Sander Ouburg,
    • Servaas A. Morré,
    • Konrad Sachse,
    • Mirja Puolakkainen,
    • Suvi J. Korhonen,
    • Chris Sonnex,
    • Rebecca Wiggins,
    • Hamid Jalal,
    • Tamara Brunelli,
    • Patrizia Casprini,
    • Rachel Pitt,
    • Cathy Ison,
    • Alevtina Savicheva,
    • Elena Shipitsyna,
    • Ronza Hadad,
    • Laszlo Kari,
    • Matthew J. Burton,
    • David Mabey,
    • Anthony W. Solomon,
    • David Lewis,
    • Peter Marsh,
    • Magnus Unemo,
    • Ian N. Clarke,
    • Julian Parkhill,
    • and Nicholas R. Thomson
    Genome Res. July 2017 27: 1220-1229; Published in Advance June 6, 2017, doi:10.1101/gr.212647.116
    OPEN ACCESS ARTICLE
  5. Research: Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently
    • Sophia David,
    • Christophe Rusniok,
    • Massimo Mentasti,
    • Laura Gomez-Valero,
    • Simon R. Harris,
    • Pierre Lechat,
    • John Lees,
    • Christophe Ginevra,
    • Philippe Glaser,
    • Laurence Ma,
    • Christiane Bouchier,
    • Anthony Underwood,
    • Sophie Jarraud,
    • Timothy G. Harrison,
    • Julian Parkhill,
    • and Carmen Buchrieser
    Genome Res. November 2016 26: 1555-1564; Published in Advance September 23, 2016, doi:10.1101/gr.209536.116
    OPEN ACCESS ARTICLE
  6. Research: Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection
    • Simon R. Harris,
    • Carl Robinson,
    • Karen F. Steward,
    • Katy S. Webb,
    • Romain Paillot,
    • Julian Parkhill,
    • Matthew T.G. Holden,
    • and Andrew S. Waller
    Genome Res. September 2015 25: 1360-1371; Published in Advance July 9, 2015, doi:10.1101/gr.189803.115
    OPEN ACCESS ARTICLE
  7. Method: Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture
    • Helena M.B. Seth-Smith,
    • Simon R. Harris,
    • Rachel J. Skilton,
    • Frans M. Radebe,
    • Daniel Golparian,
    • Elena Shipitsyna,
    • Pham Thanh Duy,
    • Paul Scott,
    • Lesley T. Cutcliffe,
    • Colette O’Neill,
    • Surendra Parmar,
    • Rachel Pitt,
    • Stephen Baker,
    • Catherine A. Ison,
    • Peter Marsh,
    • Hamid Jalal,
    • David A. Lewis,
    • Magnus Unemo,
    • Ian N. Clarke,
    • Julian Parkhill,
    • and Nicholas R. Thomson
    Genome Res. May 2013 23: 855-866; Published in Advance March 22, 2013, doi:10.1101/gr.150037.112
  8. 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
  9. 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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