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A pluralistic account of homology: adapting the models to the data.
Haggerty LS, Jachiet PA, Hanage WP, Fitzpatrick DA, Lopez P, O'Connell MJ, Pisani D, Wilkinson M, Bapteste E, McInerney JO. Haggerty LS, et al. Among authors: hanage wp. Mol Biol Evol. 2014 Mar;31(3):501-16. doi: 10.1093/molbev/mst228. Epub 2013 Nov 22. Mol Biol Evol. 2014. PMID: 24273322 Free PMC article. Review.
Evidence for soft selective sweeps in the evolution of pneumococcal multidrug resistance and vaccine escape.
Croucher NJ, Chewapreecha C, Hanage WP, Harris SR, McGee L, van der Linden M, Song JH, Ko KS, de Lencastre H, Turner C, Yang F, Sá-Leão R, Beall B, Klugman KP, Parkhill J, Turner P, Bentley SD. Croucher NJ, et al. Among authors: hanage wp. Genome Biol Evol. 2014 Jun 10;6(7):1589-602. doi: 10.1093/gbe/evu120. Genome Biol Evol. 2014. PMID: 24916661 Free PMC article.
Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis.
Méric G, Miragaia M, de Been M, Yahara K, Pascoe B, Mageiros L, Mikhail J, Harris LG, Wilkinson TS, Rolo J, Lamble S, Bray JE, Jolley KA, Hanage WP, Bowden R, Maiden MC, Mack D, de Lencastre H, Feil EJ, Corander J, Sheppard SK. Méric G, et al. Among authors: hanage wp. Genome Biol Evol. 2015 Apr 16;7(5):1313-28. doi: 10.1093/gbe/evv066. Genome Biol Evol. 2015. PMID: 25888688 Free PMC article.
Methods for data analysis.
Hanage WP, Aanensen DM. Hanage WP, et al. Methods Mol Biol. 2009;551:287-304. doi: 10.1007/978-1-60327-999-4_20. Methods Mol Biol. 2009. PMID: 19521881 Review.
Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages.
Hilty M, Wüthrich D, Salter SJ, Engel H, Campbell S, Sá-Leão R, de Lencastre H, Hermans P, Sadowy E, Turner P, Chewapreecha C, Diggle M, Pluschke G, McGee L, Eser ÖK, Low DE, Smith-Vaughan H, Endimiani A, Küffer M, Dupasquier M, Beaudoing E, Weber J, Bruggmann R, Hanage WP, Parkhill J, Hathaway LJ, Mühlemann K, Bentley SD. Hilty M, et al. Among authors: hanage wp. Genome Biol Evol. 2014 Dec 4;6(12):3281-94. doi: 10.1093/gbe/evu263. Genome Biol Evol. 2014. PMID: 25480686 Free PMC article.
Rapid pneumococcal evolution in response to clinical interventions.
Croucher NJ, Harris SR, Fraser C, Quail MA, Burton J, van der Linden M, McGee L, von Gottberg A, Song JH, Ko KS, Pichon B, Baker S, Parry CM, Lambertsen LM, Shahinas D, Pillai DR, Mitchell TJ, Dougan G, Tomasz A, Klugman KP, Parkhill J, Hanage WP, Bentley SD. Croucher NJ, et al. Among authors: hanage wp. Science. 2011 Jan 28;331(6016):430-4. doi: 10.1126/science.1198545. Science. 2011. PMID: 21273480 Free PMC article.
Population genomics of post-vaccine changes in pneumococcal epidemiology.
Croucher NJ, Finkelstein JA, Pelton SI, Mitchell PK, Lee GM, Parkhill J, Bentley SD, Hanage WP, Lipsitch M. Croucher NJ, et al. Among authors: hanage wp. Nat Genet. 2013 Jun;45(6):656-63. doi: 10.1038/ng.2625. Epub 2013 May 5. Nat Genet. 2013. PMID: 23644493 Free PMC article.
222 results