Searching journal content for articles similar to Lees et al. 29 (2): 304.

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  1. 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
    ..., Antonescu C, Salzberg SL. 2004. 568 Versatile and open software for comparing large s. Genome Biol 5: R12. 569 26 Lees JA, Harris SR, Tonkin-Hill G, Gladstone RA, Lo SW, Weiser JN, Corander J, Bentley 570 SD, Croucher NJ. 2019. Fast and flexible bacterial genomic epidemiology with 571 PopPUNK. Genome Res 29...
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  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
    ...of bacterial meningitis, taken from the largest PopPUNK cluster, were used for testing and comparison with SKA1 (Kremer et al. 2017; Lees et al. 2018, 2019). The 288 E. coli assemblies used for the online analyses were extracted from the GenomeTrackr database (Allard et al. 2016), and all correspond...
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  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
    ...genomic epidemiology with PopPUNK. Genome Res 29: 304–316. doi:10.1101/gr.241455.118 ↵Lees JA, Mai TT, Galardini M, Wheeler NE, Horsfield ST, Parkhill J, Corander J. 2020. Improved prediction of bacterial genotype-phenotype associations using interpretable pan-spanning regressions. mBio 11: e01344-20. doi...
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  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
    ...resistance in Streptococcus pneumoniae, identifying key resistance determinants that were missed when using only a single reference . ggCaller is a novel bacterial analysis tool with applications in bacterial evolution and epidemiology.Accurate representation of a population's genomic diversity, known...
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  5. 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
    ...-free whole- clustering using Population Partitioning Using Nucleotide K-mers (Pop-PUNK) v.1.2.2 (Lees et al. 2019). Phylogenies of the resulting clades were then constructed using RAxML v8.2.8 with the GTR+ Gamma rate model after removing recombination using Gubbins v2.4.0. Pans for both data sets were...
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  6. 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
    ...recombination affects the evolution of the population.ResultsPopulation structureThe PopPUNK clustering of the successfully sequenced Burkina Faso collection of 2838 carriage isolates returned 17 clusters, five of which were single isolate and three that had fewer than 10 isolates. These eight clusters were...
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