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Page 1
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.
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.
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: ratmann o. 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.
A Method to Estimate the Size and Characteristics of HIV-positive Populations Using an Individual-based Stochastic Simulation Model.
Nakagawa F, van Sighem A, Thiebaut R, Smith C, Ratmann O, Cambiano V, Albert J, Amato-Gauci A, Bezemer D, Campbell C, Commenges D, Donoghoe M, Ford D, Kouyos R, Lodwick R, Lundgren J, Pantazis N, Pharris A, Quinten C, Thorne C, Touloumi G, Delpech V, Phillips A; SSOPHIE project working group in EuroCoord. Nakagawa F, et al. Among authors: ratmann o. Epidemiology. 2016 Mar;27(2):247-56. doi: 10.1097/EDE.0000000000000423. Epidemiology. 2016. PMID: 26605814 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.
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. 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.
Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.
Wymant C, Blanquart F, Golubchik T, Gall A, Bakker M, Bezemer D, Croucher NJ, Hall M, Hillebregt M, Ong SH, Ratmann O, Albert J, Bannert N, Fellay J, Fransen K, Gourlay A, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Cornelissen M, Kellam P, Reiss P, Fraser C; BEEHIVE Collaboration. Wymant C, et al. Among authors: ratmann o. Virus Evol. 2018 May 18;4(1):vey007. doi: 10.1093/ve/vey007. eCollection 2018 Jan. Virus Evol. 2018. PMID: 29876136 Free PMC article.
High incidence of HCV in HIV-negative men who have sex with men using pre-exposure prophylaxis.
Hoornenborg E, Coyer L, Boyd A, Achterbergh RCA, Schim van der Loeff MF, Bruisten S, de Vries HJC, Koopsen J, van de Laar TJW, Prins M; Amsterdam PrEP Project team in the HIV Transmission Elimination AMsterdam (H-TEAM) Initiative. Hoornenborg E, et al. J Hepatol. 2020 May;72(5):855-864. doi: 10.1016/j.jhep.2019.11.022. Epub 2019 Dec 18. J Hepatol. 2020. PMID: 31862485
Decreased Time to Viral Suppression After Implementation of Targeted Testing and Immediate Initiation of Treatment of Acute Human Immunodeficiency Virus Infection Among Men Who Have Sex With Men in Amsterdam.
Dijkstra M, van Rooijen MS, Hillebregt MM, van Sighem A, Smit C, Hogewoning A, Davidovich U, Heijman T, Hoornenborg E, Reiss P, van der Valk M, Prins M, Prins JM, Schim van der Loeff MF, de Bree GJ; HIV Transmission Elimination Amsterdam (H-TEAM) Initiative. Dijkstra M, et al. Clin Infect Dis. 2021 Jun 1;72(11):1952-1960. doi: 10.1093/cid/ciaa505. Clin Infect Dis. 2021. PMID: 32369099
77 results