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Evaluating methods for identifying and quantifying Streptococcus pneumoniae co-colonization using next-generation sequencing data.
Hackman J, Hibberd ML, Swarthout TD, Hinds J, Ashall J, Sheppard C, Tonkin-Hill G, Gould K, Brown C, Msefula J, Mataya AA, Toizumi M, Yoshida L-M, French N, Heyderman RS, Flasche S, Kwambana B, Hué S. Hackman J, et al. Among authors: tonkin hill g. Microbiol Spectr. 2024 Nov 5;12(12):e0364323. doi: 10.1128/spectrum.03643-23. Online ahead of print. Microbiol Spectr. 2024. PMID: 39499074 Free PMC article.
Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study.
Thorpe HA, Pesonen M, Corbella M, Pesonen H, Gaiarsa S, Boinett CJ, Tonkin-Hill G, Mäklin T, Pöntinen AK, MacAlasdair N, Gladstone RA, Arredondo-Alonso S, Kallonen T, Jamrozy D, Lo SW, Chaguza C, Blackwell GA, Honkela A, Schürch AC, Willems RJL, Merla C, Petazzoni G, Feil EJ, Cambieri P, Thomson NR, Bentley SD, Sassera D, Corander J. Thorpe HA, et al. Among authors: tonkin hill g. Lancet Microbe. 2024 Oct;5(10):100890. doi: 10.1016/S2666-5247(24)00113-7. Epub 2024 Aug 20. Lancet Microbe. 2024. PMID: 39178869 Free article.
Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs.
Kuronen J, Horsfield ST, Pöntinen AK, Mallawaarachchi S, Arredondo-Alonso S, Thorpe H, Gladstone RA, Willems RJL, Bentley SD, Croucher NJ, Pensar J, Lees JA, Tonkin-Hill G, Corander J. Kuronen J, et al. Among authors: tonkin hill g. Genome Res. 2024 Aug 20;34(7):1081-1088. doi: 10.1101/gr.278485.123. Genome Res. 2024. PMID: 39134411 Free PMC article.
Geographical migration and fitness dynamics of Streptococcus pneumoniae.
Belman S, Lefrancq N, Nzenze S, Downs S, du Plessis M, Lo SW; Global Pneumococcal Sequencing Consortium; McGee L, Madhi SA, von Gottberg A, Bentley SD, Salje H. Belman S, et al. Nature. 2024 Jul;631(8020):386-392. doi: 10.1038/s41586-024-07626-3. Epub 2024 Jul 3. Nature. 2024. PMID: 38961295 Free PMC article.
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: tonkin hill g. 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.
Overlapping Streptococcus pyogenes and Streptococcus dysgalactiae subspecies equisimilis household transmission and mobile genetic element exchange.
Xie O, Zachreson C, Tonkin-Hill G, Price DJ, Lacey JA, Morris JM, McDonald MI, Bowen AC, Giffard PM, Currie BJ, Carapetis JR, Holt DC, Bentley SD, Davies MR, Tong SYC. Xie O, et al. Among authors: tonkin hill g. Nat Commun. 2024 Apr 24;15(1):3477. doi: 10.1038/s41467-024-47816-1. Nat Commun. 2024. PMID: 38658529 Free PMC article.
Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis.
Xie O, Morris JM, Hayes AJ, Towers RJ, Jespersen MG, Lees JA, Ben Zakour NL, Berking O, Baines SL, Carter GP, Tonkin-Hill G, Schrieber L, McIntyre L, Lacey JA, James TB, Sriprakash KS, Beatson SA, Hasegawa T, Giffard P, Steer AC, Batzloff MR, Beall BW, Pinho MD, Ramirez M, Bessen DE, Dougan G, Bentley SD, Walker MJ, Currie BJ, Tong SYC, McMillan DJ, Davies MR. Xie O, et al. Among authors: tonkin hill g. Nat Commun. 2024 Mar 13;15(1):2286. doi: 10.1038/s41467-024-46530-2. Nat Commun. 2024. PMID: 38480728 Free PMC article.
Mutational spectra are associated with bacterial niche.
Ruis C, Weimann A, Tonkin-Hill G, Pandurangan AP, Matuszewska M, Murray GGR, Lévesque RC, Blundell TL, Floto RA, Parkhill J. Ruis C, et al. Among authors: tonkin hill g. Nat Commun. 2023 Nov 4;14(1):7091. doi: 10.1038/s41467-023-42916-w. Nat Commun. 2023. PMID: 37925514 Free PMC article.
66 results