Searching journal content for articles similar to Zhou et al. 28 (9): 1395.

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  1. Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
    • Nora Zidane,
    • Carla Rodrigues,
    • Valérie Bouchez,
    • Martin Rethoret-Pasty,
    • Virginie Passet,
    • Sylvain Brisse,
    • and Chiara Crestani
    Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
    ...Z, Alikhan NF, Sergeant MJ, Luhmann N, Vaz C, Francisco AP, Carriço JA, Achtman M. 2018. GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Res 28: 1395–1404. doi:10.1101/gr.232397.117 ↵Zhou Z, Alikhan NF, Mohamed K, Yulei F, the Agama Study Group...
  2. Method: Accurate reconstruction of bacterial pan- and core genomes with PEPPAN
    • Zhemin Zhou,
    • Jane Charlesworth,
    • and Mark Achtman
    Genome Res. November 2020 30: 1667-1679; Published in Advance October 14, 2020, doi:10.1101/gr.260828.120
    ...of a bacterial species or set of strains (Tettelin et al. 2005). Bacterial pans can be divided into the core , which consists of the subset of genes that are present in all s, and the accessory , which consists of genes that are variably present among individual s. The core often contains phylogenetic signals...
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  3. 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
    ...Phandango (Hadfield et al. 2018), the browser-based viewer GrapeTree (Zhou et al. 2018), network analysis tool Cytoscape (Shannon et al. 2003), and the online epidemiology platform Microreact (Argimón et al. 2016). Microreact allows interactive views of a neighbor joining tree of core distances on the left...
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  4. Resource: The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity
    • Zhemin Zhou,
    • Nabil-Fareed Alikhan,
    • Khaled Mohamed,
    • Yulei Fan,
    • the Agama Study Group,
    • and Mark Achtman
    Genome Res. January 2020 30: 138-152; Published in Advance December 6, 2019, doi:10.1101/gr.251678.119
    ....g., NCBI Sequence Read Archive [SRA]) of short-read sequences of bacterial pathogens that have been deposited since the recent drop in price of high-throughput sequencing (https://www..gov/sequencingcostsdata/). In October 2019, SRA contained genomic sequence reads from 430,417 Salmonella, Escherichia...
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