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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: ratmann o. 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.
HIV-1 Sequence Data Coverage in Central East Africa from 1959 to 2013.
Lamers SL, Barbier AE, Ratmann O, Fraser C, Rose R, Laeyendecker O, Grabowski MK. Lamers SL, et al. Among authors: ratmann o. AIDS Res Hum Retroviruses. 2016 Sep;32(9):904-8. doi: 10.1089/AID.2016.0079. Epub 2016 Aug 2. AIDS Res Hum Retroviruses. 2016. PMID: 27353049 Free PMC article.
Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.
Ratmann O, Hodcroft EB, Pickles M, Cori A, Hall M, Lycett S, Colijn C, Dearlove B, Didelot X, Frost S, Hossain AS, Joy JB, Kendall M, Kühnert D, Leventhal GE, Liang R, Plazzotta G, Poon AF, Rasmussen DA, Stadler T, Volz E, Weis C, Leigh Brown AJ, Fraser C; PANGEA-HIV Consortium. Ratmann O, et al. Mol Biol Evol. 2017 Jan;34(1):185-203. doi: 10.1093/molbev/msw217. Epub 2016 Oct 7. Mol Biol Evol. 2017. PMID: 28053012 Free PMC article.
PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity.
Wymant C, Hall M, Ratmann O, Bonsall D, Golubchik T, de Cesare M, Gall A, Cornelissen M, Fraser C; STOP-HCV Consortium, The Maela Pneumococcal Collaboration, and The BEEHIVE Collaboration. Wymant C, et al. Among authors: ratmann o. Mol Biol Evol. 2018 Mar 1;35(3):719-733. doi: 10.1093/molbev/msx304. Mol Biol Evol. 2018. PMID: 29186559 Free PMC article.
Phylogenies from dynamic networks.
Metzig C, Ratmann O, Bezemer D, Colijn C. Metzig C, et al. Among authors: ratmann o. PLoS Comput Biol. 2019 Feb 26;15(2):e1006761. doi: 10.1371/journal.pcbi.1006761. eCollection 2019 Feb. PLoS Comput Biol. 2019. PMID: 30807578 Free PMC article.
State-level tracking of COVID-19 in the United States.
Unwin HJT, Mishra S, Bradley VC, Gandy A, Mellan TA, Coupland H, Ish-Horowicz J, Vollmer MAC, Whittaker C, Filippi SL, Xi X, Monod M, Ratmann O, Hutchinson M, Valka F, Zhu H, Hawryluk I, Milton P, Ainslie KEC, Baguelin M, Boonyasiri A, Brazeau NF, Cattarino L, Cucunuba Z, Cuomo-Dannenburg G, Dorigatti I, Eales OD, Eaton JW, van Elsland SL, FitzJohn RG, Gaythorpe KAM, Green W, Hinsley W, Jeffrey B, Knock E, Laydon DJ, Lees J, Nedjati-Gilani G, Nouvellet P, Okell L, Parag KV, Siveroni I, Thompson HA, Walker P, Walters CE, Watson OJ, Whittles LK, Ghani AC, Ferguson NM, Riley S, Donnelly CA, Bhatt S, Flaxman S. Unwin HJT, et al. Among authors: ratmann o. Nat Commun. 2020 Dec 3;11(1):6189. doi: 10.1038/s41467-020-19652-6. Nat Commun. 2020. PMID: 33273462 Free PMC article.
77 results