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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: fraser c. Mol Biol Evol. 2018 Mar 1;35(3):719-733. doi: 10.1093/molbev/msx304. Mol Biol Evol. 2018. PMID: 29186559 Free PMC article.
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: fraser c. 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.
Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis.
Bezemer D, Cori A, Ratmann O, van Sighem A, Hermanides HS, Dutilh BE, Gras L, Rodrigues Faria N, van den Hengel R, Duits AJ, Reiss P, de Wolf F, Fraser C; ATHENA observational cohort. Bezemer D, et al. Among authors: fraser c. PLoS Med. 2015 Nov 3;12(11):e1001898; discussion e1001898. doi: 10.1371/journal.pmed.1001898. eCollection 2015 Nov. PLoS Med. 2015. PMID: 26529093 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: fraser c. 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.
From clinical sample to complete genome: Comparing methods for the extraction of HIV-1 RNA for high-throughput deep sequencing.
Cornelissen M, Gall A, Vink M, Zorgdrager F, Binter Š, Edwards S, Jurriaans S, Bakker M, Ong SH, Gras L, van Sighem A, Bezemer D, de Wolf F, Reiss P, Kellam P, Berkhout B, Fraser C, van der Kuyl AC; BEEHIVE Consortium. Cornelissen M, et al. Among authors: fraser c. Virus Res. 2017 Jul 15;239:10-16. doi: 10.1016/j.virusres.2016.08.004. Epub 2016 Aug 4. Virus Res. 2017. PMID: 27497916 Free 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. Among authors: fraser c. 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.
HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences.
Ratmann O, Wymant C, Colijn C, Danaviah S, Essex M, Frost SDW, Gall A, Gaiseitsiwe S, Grabowski M, Gray R, Guindon S, von Haeseler A, Kaleebu P, Kendall M, Kozlov A, Manasa J, Minh BQ, Moyo S, Novitsky V, Nsubuga R, Pillay S, Quinn TC, Serwadda D, Ssemwanga D, Stamatakis A, Trifinopoulos J, Wawer M, Leigh Brown A, de Oliveira T, Kellam P, Pillay D, Fraser C. Ratmann O, et al. Among authors: fraser c. AIDS Res Hum Retroviruses. 2017 Nov;33(11):1083-1098. doi: 10.1089/AID.2017.0061. Epub 2017 May 25. AIDS Res Hum Retroviruses. 2017. PMID: 28540766 Free PMC article.
2,487 results