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Items: 27

1.

HIV-1 Transmission Patterns in Men Who Have Sex with Men: Insights from Genetic Source Attribution Analysis.

Le Vu S, Ratmann O, Delpech V, Brown AE, Gill ON, Tostevin A, Dunn D, Fraser C, Volz EM.

AIDS Res Hum Retroviruses. 2019 Sep;35(9):805-813. doi: 10.1089/AID.2018.0236.

2.

Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.

Ratmann O, Grabowski MK, Hall M, Golubchik T, Wymant C, Abeler-Dörner L, Bonsall D, Hoppe A, Brown AL, de Oliveira T, Gall A, Kellam P, Pillay D, Kagaayi J, Kigozi G, Quinn TC, Wawer MJ, Laeyendecker O, Serwadda D, Gray RH, Fraser C; PANGEA Consortium and Rakai Health Sciences Program.

Nat Commun. 2019 Mar 29;10(1):1411. doi: 10.1038/s41467-019-09139-4.

3.

Phylogenies from dynamic networks.

Metzig C, Ratmann O, Bezemer D, Colijn C.

PLoS Comput Biol. 2019 Feb 26;15(2):e1006761. doi: 10.1371/journal.pcbi.1006761. eCollection 2019 Feb.

4.

Cultural conformity generates extremely stable traditions in bird song.

Lachlan RF, Ratmann O, Nowicki S.

Nat Commun. 2018 Jun 20;9(1):2417. doi: 10.1038/s41467-018-04728-1.

5.

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.

Virus Evol. 2018 May 18;4(1):vey007. doi: 10.1093/ve/vey007. eCollection 2018 Jan.

6.

Molecular Epidemiology of HIV-1 Subtype B Reveals Heterogeneous Transmission Risk: Implications for Intervention and Control.

Volz EM, Le Vu S, Ratmann O, Tostevin A, Dunn D, Orkin C, O'Shea S, Delpech V, Brown A, Gill N, Fraser C; UK HIV Drug Resistance Database.

J Infect Dis. 2018 Apr 23;217(10):1522-1529. doi: 10.1093/infdis/jiy044.

7.

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.

Mol Biol Evol. 2017 Nov 23. doi: 10.1093/molbev/msx304. [Epub ahead of print]

8.

Comparison of cluster-based and source-attribution methods for estimating transmission risk using large HIV sequence databases.

Le Vu S, Ratmann O, Delpech V, Brown AE, Gill ON, Tostevin A, Fraser C, Volz EM.

Epidemics. 2018 Jun;23:1-10. doi: 10.1016/j.epidem.2017.10.001. Epub 2017 Oct 20.

9.

Improved Algorithmic Complexity for the 3SEQ Recombination Detection Algorithm.

Lam HM, Ratmann O, Boni MF.

Mol Biol Evol. 2018 Jan 1;35(1):247-251. doi: 10.1093/molbev/msx263.

10.

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.

AIDS Res Hum Retroviruses. 2017 Nov;33(11):1083-1098. doi: 10.1089/AID.2017.0061. Epub 2017 May 25.

11.

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.

Mol Biol Evol. 2017 Jan;34(1):185-203. doi: 10.1093/molbev/msw217. Epub 2016 Oct 7.

12.

Origin, imports and exports of HIV-1 subtype C in South Africa: A historical perspective.

Wilkinson E, Rasmussen D, Ratmann O, Stadler T, Engelbrecht S, de Oliveira T.

Infect Genet Evol. 2016 Dec;46:200-208. doi: 10.1016/j.meegid.2016.07.008. Epub 2016 Jul 12.

13.

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.

AIDS Res Hum Retroviruses. 2016 Sep;32(9):904-8. doi: 10.1089/AID.2016.0079. Epub 2016 Aug 2.

14.

Sources of HIV infection among men having sex with men and implications for prevention.

Ratmann O, van Sighem A, Bezemer D, Gavryushkina A, Jurriaans S, Wensing A, de Wolf F, Reiss P, Fraser C; ATHENA observational cohort.

Sci Transl Med. 2016 Jan 6;8(320):320ra2. doi: 10.1126/scitranslmed.aad1863.

15.

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.

Epidemiology. 2016 Mar;27(2):247-56. doi: 10.1097/EDE.0000000000000423. Erratum in: Epidemiology. 2016 May;27(3):e24.

16.

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.

PLoS Med. 2015 Nov 3;12(11):e1001898; discussion e1001898. doi: 10.1371/journal.pmed.1001898. eCollection 2015 Nov.

17.

PANGEA-HIV: phylogenetics for generalised epidemics in Africa.

Pillay D, Herbeck J, Cohen MS, de Oliveira T, Fraser C, Ratmann O, Brown AL, Kellam P; PANGEA-HIV Consortium.

Lancet Infect Dis. 2015 Mar;15(3):259-61. doi: 10.1016/S1473-3099(15)70036-8. No abstract available.

18.

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.

Epidemics. 2014 Jun;7:28-34. doi: 10.1016/j.epidem.2014.04.003. Epub 2014 Apr 18.

19.

Phylodynamic inference and model assessment with approximate bayesian computation: influenza as a case study.

Ratmann O, Donker G, Meijer A, Fraser C, Koelle K.

PLoS Comput Biol. 2012;8(12):e1002835. doi: 10.1371/journal.pcbi.1002835. Epub 2012 Dec 27.

20.

Impact of cross-protective vaccines on epidemiological and evolutionary dynamics of influenza.

Arinaminpathy N, Ratmann O, Koelle K, Epstein SL, Price GE, Viboud C, Miller MA, Grenfell BT.

Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):3173-7. doi: 10.1073/pnas.1113342109. Epub 2012 Feb 7.

21.

Inference for nonlinear epidemiological models using genealogies and time series.

Rasmussen DA, Ratmann O, Koelle K.

PLoS Comput Biol. 2011 Aug;7(8):e1002136. doi: 10.1371/journal.pcbi.1002136. Epub 2011 Aug 25.

22.

A dimensionless number for understanding the evolutionary dynamics of antigenically variable RNA viruses.

Koelle K, Ratmann O, Rasmussen DA, Pasour V, Mattingly J.

Proc Biol Sci. 2011 Dec 22;278(1725):3723-30. doi: 10.1098/rspb.2011.0435. Epub 2011 May 4.

23.

Explaining rapid reinfections in multiple-wave influenza outbreaks: Tristan da Cunha 1971 epidemic as a case study.

Camacho A, Ballesteros S, Graham AL, Carrat F, Ratmann O, Cazelles B.

Proc Biol Sci. 2011 Dec 22;278(1725):3635-43. doi: 10.1098/rspb.2011.0300. Epub 2011 Apr 27.

24.

From evidence to inference: probing the evolution of protein interaction networks.

Ratmann O, Wiuf C, Pinney JW.

HFSP J. 2009 Oct;3(5):290-306. doi: 10.2976/1.3167215. Epub 2009 Oct 19.

25.

Model criticism based on likelihood-free inference, with an application to protein network evolution.

Ratmann O, Andrieu C, Wiuf C, Richardson S.

Proc Natl Acad Sci U S A. 2009 Jun 30;106(26):10576-81. doi: 10.1073/pnas.0807882106. Epub 2009 Jun 12.

26.

FunCat functional inference with belief propagation and feature integration.

Surmeli D, Ratmann O, Mewes HW, Tetko IV.

Comput Biol Chem. 2008 Oct;32(5):375-7. doi: 10.1016/j.compbiolchem.2008.06.004. Epub 2008 Jul 3.

PMID:
18684672
27.

Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum.

Ratmann O, Jørgensen O, Hinkley T, Stumpf M, Richardson S, Wiuf C.

PLoS Comput Biol. 2007 Nov;3(11):e230. Epub 2007 Oct 9.

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