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Detecting co-selection through excess linkage disequilibrium in bacterial genomes.
Mallawaarachchi S, Tonkin-Hill G, Pöntinen AK, Calland JK, Gladstone RA, Arredondo-Alonso S, MacAlasdair N, Thorpe HA, Top J, Sheppard SK, Balding D, Croucher NJ, Corander J. Mallawaarachchi S, et al. Among authors: gladstone ra. NAR Genom Bioinform. 2024 Jun 6;6(2):lqae061. doi: 10.1093/nargab/lqae061. eCollection 2024 Jun. NAR Genom Bioinform. 2024. PMID: 38846349 Free PMC article.
Response of the Io plasma torus to comet Shoemaker-Levy 9.
McGrath MA, Hall DT, Matheson PL, Weaver HA, Trauger JT, Smith TE, Thomas N, Gladstone R, Schneider NM, Harris WM, et al. McGrath MA, et al. Science. 1995 Mar 3;267(5202):1313-7. doi: 10.1126/science.7871429. Science. 1995. PMID: 7871429
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. Among authors: gladstone ra. 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.
International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact.
Gladstone RA, Lo SW, Lees JA, Croucher NJ, van Tonder AJ, Corander J, Page AJ, Marttinen P, Bentley LJ, Ochoa TJ, Ho PL, du Plessis M, Cornick JE, Kwambana-Adams B, Benisty R, Nzenze SA, Madhi SA, Hawkins PA, Everett DB, Antonio M, Dagan R, Klugman KP, von Gottberg A, McGee L, Breiman RF, Bentley SD; Global Pneumococcal Sequencing Consortium. Gladstone RA, et al. EBioMedicine. 2019 May;43:338-346. doi: 10.1016/j.ebiom.2019.04.021. Epub 2019 Apr 16. EBioMedicine. 2019. PMID: 31003929 Free PMC article.
Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis.
Lees JA, Ferwerda B, Kremer PHC, Wheeler NE, Serón MV, Croucher NJ, Gladstone RA, Bootsma HJ, Rots NY, Wijmega-Monsuur AJ, Sanders EAM, Trzciński K, Wyllie AL, Zwinderman AH, van den Berg LH, van Rheenen W, Veldink JH, Harboe ZB, Lundbo LF, de Groot LCPGM, van Schoor NM, van der Velde N, Ängquist LH, Sørensen TIA, Nohr EA, Mentzer AJ, Mills TC, Knight JC, du Plessis M, Nzenze S, Weiser JN, Parkhill J, Madhi S, Benfield T, von Gottberg A, van der Ende A, Brouwer MC, Barrett JC, Bentley SD, van de Beek D. Lees JA, et al. Among authors: gladstone ra. Nat Commun. 2019 May 15;10(1):2176. doi: 10.1038/s41467-019-09976-3. Nat Commun. 2019. PMID: 31092817 Free PMC article.
Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates.
Gladstone RA, Lo SW, Goater R, Yeats C, Taylor B, Hadfield J, Lees JA, Croucher NJ, van Tonder AJ, Bentley LJ, Quah FX, Blaschke AJ, Pershing NL, Byington CL, Balaji V, Hryniewicz W, Sigauque B, Ravikumar KL, Almeida SCG, Ochoa TJ, Ho PL, du Plessis M, Ndlangisa KM, Cornick JE, Kwambana-Adams B, Benisty R, Nzenze SA, Madhi SA, Hawkins PA, Pollard AJ, Everett DB, Antonio M, Dagan R, Klugman KP, von Gottberg A, Metcalf BJ, Li Y, Beall BW, McGee L, Breiman RF, Aanensen DM, Bentley SD, The Global Pneumococcal Sequencing Consortium. Gladstone RA, et al. Microb Genom. 2020 May;6(5):e000357. doi: 10.1099/mgen.0.000357. Epub 2020 Apr 29. Microb Genom. 2020. PMID: 32375991 Free PMC article.
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. Among authors: gladstone ra. Genome Biol. 2020 Jul 22;21(1):180. doi: 10.1186/s13059-020-02090-4. Genome Biol. 2020. PMID: 32698896 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. Among authors: gladstone ra. Commun Biol. 2020 Oct 8;3(1):559. doi: 10.1038/s42003-020-01290-9. Commun Biol. 2020. PMID: 33033372 Free PMC article.
85 results