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OutbreakTools: a new platform for disease outbreak analysis using the R software.
Jombart T, Aanensen DM, Baguelin M, Birrell P, Cauchemez S, Camacho A, Colijn C, Collins C, Cori A, Didelot X, Fraser C, Frost S, Hens N, Hugues J, Höhle M, Opatowski L, Rambaut A, Ratmann O, Soubeyrand S, Suchard MA, Wallinga J, Ypma R, Ferguson N. Jombart T, et al. Among authors: ferguson n. Epidemics. 2014 Jun;7(100):28-34. doi: 10.1016/j.epidem.2014.04.003. Epub 2014 Apr 18. Epidemics. 2014. PMID: 24928667 Free PMC article.
The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water.
Karkey A, Jombart T, Walker AW, Thompson CN, Torres A, Dongol S, Tran Vu Thieu N, Pham Thanh D, Tran Thi Ngoc D, Voong Vinh P, Singer AC, Parkhill J, Thwaites G, Basnyat B, Ferguson N, Baker S. Karkey A, et al. Among authors: ferguson n. PLoS Negl Trop Dis. 2016 Jan 6;10(1):e0004346. doi: 10.1371/journal.pntd.0004346. eCollection 2016 Jan. PLoS Negl Trop Dis. 2016. PMID: 26735696 Free PMC article.
When are pathogen genome sequences informative of transmission events?
Campbell F, Strang C, Ferguson N, Cori A, Jombart T. Campbell F, et al. Among authors: ferguson n. PLoS Pathog. 2018 Feb 8;14(2):e1006885. doi: 10.1371/journal.ppat.1006885. eCollection 2018 Feb. PLoS Pathog. 2018. PMID: 29420641 Free PMC article.
outbreaker2: a modular platform for outbreak reconstruction.
Campbell F, Didelot X, Fitzjohn R, Ferguson N, Cori A, Jombart T. Campbell F, et al. Among authors: ferguson n. BMC Bioinformatics. 2018 Oct 22;19(Suppl 11):363. doi: 10.1186/s12859-018-2330-z. BMC Bioinformatics. 2018. PMID: 30343663 Free PMC article.
Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo'.
Lavezzo E, Franchin E, Ciavarella C, Cuomo-Dannenburg G, Barzon L, Del Vecchio C, Rossi L, Manganelli R, Loregian A, Navarin N, Abate D, Sciro M, Merigliano S, De Canale E, Vanuzzo MC, Besutti V, Saluzzo F, Onelia F, Pacenti M, Parisi SG, Carretta G, Donato D, Flor L, Cocchio S, Masi G, Sperduti A, Cattarino L, Salvador R, Nicoletti M, Caldart F, Castelli G, Nieddu E, Labella B, Fava L, Drigo M, Gaythorpe KAM; Imperial College COVID-19 Response Team; Brazzale AR, Toppo S, Trevisan M, Baldo V, Donnelly CA, Ferguson NM, Dorigatti I, Crisanti A; Imperial College COVID-19 Response Team. Lavezzo E, et al. Among authors: ferguson nm. Nature. 2020 Aug;584(7821):425-429. doi: 10.1038/s41586-020-2488-1. Epub 2020 Jun 30. Nature. 2020. PMID: 32604404
929 results