Searching journal content for John A. Lees in author.

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  1. Method: Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm
    • Samuel T. Horsfield,
    • Basil C.T. Fok,
    • Yuhan Fu,
    • Paul Turner,
    • John A. Lees,
    • and Nicholas J. Croucher
    Genome Res. April 2025 35: 1025-1040; Published in Advance March 4, 2025, doi:10.1101/gr.279435.124
    OPEN ACCESS ARTICLE
  2. 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
  3. 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
  4. Method: Accurate and fast graph-based pangenome annotation and clustering with ggCaller
    • Samuel T. Horsfield,
    • Gerry Tonkin-Hill,
    • Nicholas J. Croucher,
    • and John A. Lees
    Genome Res. September 2023 33: 1622-1637; Published in Advance August 24, 2023, doi:10.1101/gr.277733.123
    OPEN ACCESS ARTICLE
  5. Method: Genealogical inference and more flexible sequence clustering using iterative PopPUNK
    • Bin Zhao,
    • John A. Lees,
    • Hongjin Wu,
    • Chao Yang,
    • and Daniel Falush
    Genome Res. May 30, 2023 gr.277395.122; Published in Advance May 30, 2023, doi:10.1101/gr.277395.122
    ACCEPTED MANUSCRIPT
  6. 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
  7. 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
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