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Producing polished prokaryotic pangenomes with the Panaroo pipeline.
Tonkin-Hill G, MacAlasdair N, Ruis C, Weimann A, Horesh G, Lees JA, Gladstone RA, Lo S, Beaudoin C, Floto RA, Frost SDW, Corander J, Bentley SD, Parkhill J. Tonkin-Hill G, et al. Genome Biol. 2020 Jul 22;21(1):180. doi: 10.1186/s13059-020-02090-4. Genome Biol. 2020. PMID: 32698896 Free PMC article.
Stronger together.
Lees JA, Tonkin-Hill G, Bentley SD. Lees JA, et al. Nat Rev Microbiol. 2017 Sep;15(9):516. doi: 10.1038/nrmicro.2017.95. Epub 2017 Aug 7. Nat Rev Microbiol. 2017. PMID: 28781366 No abstract available.
Fast and flexible bacterial genomic epidemiology with PopPUNK.
Lees JA, Harris SR, Tonkin-Hill G, Gladstone RA, Lo SW, Weiser JN, Corander J, Bentley SD, Croucher NJ. Lees JA, et al. Genome Res. 2019 Feb;29(2):304-316. doi: 10.1101/gr.241455.118. Epub 2019 Jan 24. Genome Res. 2019. PMID: 30679308 Free PMC article.
Fast hierarchical Bayesian analysis of population structure.
Tonkin-Hill G, Lees JA, Bentley SD, Frost SDW, Corander J. Tonkin-Hill G, et al. Nucleic Acids Res. 2019 Jun 20;47(11):5539-5549. doi: 10.1093/nar/gkz361. Nucleic Acids Res. 2019. PMID: 31076776 Free PMC article.
Genome-wide epistasis and co-selection study using mutual information.
Pensar J, Puranen S, Arnold B, MacAlasdair N, Kuronen J, Tonkin-Hill G, Pesonen M, Xu Y, Sipola A, Sánchez-Busó L, Lees JA, Chewapreecha C, Bentley SD, Harris SR, Parkhill J, Croucher NJ, Corander J. Pensar J, et al. Nucleic Acids Res. 2019 Oct 10;47(18):e112. doi: 10.1093/nar/gkz656. Nucleic Acids Res. 2019. PMID: 31361894 Free PMC article.
Bacterial genome-wide association study of hyper-virulent pneumococcal serotype 1 identifies genetic variation associated with neurotropism.
Chaguza C, Yang M, Cornick JE, du Plessis M, Gladstone RA, Kwambana-Adams BA, Lo SW, Ebruke C, Tonkin-Hill G, Peno C, Senghore M, Obaro SK, Ousmane S, Pluschke G, Collard JM, Sigaùque B, French N, Klugman KP, Heyderman RS, McGee L, Antonio M, Breiman RF, von Gottberg A, Everett DB, Kadioglu A, Bentley SD. Chaguza C, et al. Commun Biol. 2020 Oct 8;3(1):559. doi: 10.1038/s42003-020-01290-9. Commun Biol. 2020. PMID: 33033372 Free PMC article.
Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era.
Pöntinen AK, Top J, Arredondo-Alonso S, Tonkin-Hill G, Freitas AR, Novais C, Gladstone RA, Pesonen M, Meneses R, Pesonen H, Lees JA, Jamrozy D, Bentley SD, Lanza VF, Torres C, Peixe L, Coque TM, Parkhill J, Schürch AC, Willems RJL, Corander J. Pöntinen AK, et al. Nat Commun. 2021 Mar 9;12(1):1523. doi: 10.1038/s41467-021-21749-5. Nat Commun. 2021. PMID: 33750782 Free PMC article.
59 results