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Items: 1 to 20 of 191

1.

Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak.

Dellicour S, Baele G, Dudas G, Faria NR, Pybus OG, Suchard MA, Rambaut A, Lemey P.

Nat Commun. 2018 Jun 8;9(1):2222. doi: 10.1038/s41467-018-03763-2.

2.

Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.

Ibrahim B, Arkhipova K, Andeweg AC, Posada-Céspedes S, Enault F, Gruber A, Koonin EV, Kupczok A, Lemey P, McHardy AC, McMahon DP, Pickett BE, Robertson DL, Scheuermann RH, Zhernakova A, Zwart MP, Schönhuth A, Dutilh BE, Marz M.

Viruses. 2018 May 14;10(5). pii: E256. doi: 10.3390/v10050256.

3.

Viral Characteristics Associated with the Clinical Nonprogressor Phenotype Are Inherited by Viruses from a Cluster of HIV-1 Elite Controllers.

Casado C, Marrero-Hernández S, Márquez-Arce D, Pernas M, Marfil S, Borràs-Grañana F, Olivares I, Cabrera-Rodríguez R, Valera MS, de Armas-Rillo L, Lemey P, Blanco J, Valenzuela-Fernández A, Lopez-Galíndez C.

MBio. 2018 Apr 10;9(2). pii: e02338-17. doi: 10.1128/mBio.02338-17.

4.

Proposal for a new subtype of the zoonotic genotype 3 Hepatitis E virus: HEV-3l.

De Sabato L, Lemey P, Vrancken B, Bonfanti L, Ceglie L, Vaccari G, Di Bartolo I.

Virus Res. 2018 Mar 15;248:1-4. doi: 10.1016/j.virusres.2018.02.010. Epub 2018 Feb 13.

PMID:
29452164
5.

A novel hepatitis B virus species discovered in capuchin monkeys sheds new light on the evolution of primate hepadnaviruses.

de Carvalho Dominguez Souza BF, König A, Rasche A, de Oliveira Carneiro I, Stephan N, Corman VM, Roppert PL, Goldmann N, Kepper R, Müller SF, Völker C, de Souza AJS, Gomes-Gouvêa MS, Moreira-Soto A, Stöcker A, Nassal M, Franke CR, Rebello Pinho JR, Soares MDCP, Geyer J, Lemey P, Drosten C, Netto EM, Glebe D, Drexler JF.

J Hepatol. 2018 Jun;68(6):1114-1122. doi: 10.1016/j.jhep.2018.01.029. Epub 2018 Feb 8.

6.

Landscape attributes governing local transmission of an endemic zoonosis: Rabies virus in domestic dogs.

Brunker K, Lemey P, Marston DA, Fooks AR, Lugelo A, Ngeleja C, Hampson K, Biek R.

Mol Ecol. 2018 Feb;27(3):773-788. doi: 10.1111/mec.14470. Epub 2018 Jan 29.

7.

Host Genetic Variation Does Not Determine Spatio-Temporal Patterns of European Bat 1 Lyssavirus.

Troupin C, Picard-Meyer E, Dellicour S, Casademont I, Kergoat L, Lepelletier A, Dacheux L, Baele G, Monchâtre-Leroy E, Cliquet F, Lemey P, Bourhy H.

Genome Biol Evol. 2017 Nov 1;9(11):3202-3213. doi: 10.1093/gbe/evx236.

8.

Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling.

Vrancken B, Suchard MA, Lemey P.

Virus Evol. 2017 Oct 6;3(2):vex028. doi: 10.1093/ve/vex028. eCollection 2017 Jul.

9.

Phylogenetic Factor Analysis.

Tolkoff MR, Alfaro ME, Baele G, Lemey P, Suchard MA.

Syst Biol. 2018 May 1;67(3):384-399. doi: 10.1093/sysbio/syx066.

PMID:
28950376
10.

A21 HIV-1 sub-subtype F1 outbreak among MSM in Belgium.

Vinken L, Fransen K, Pineda-Peña AC, Alexiev I, Balotta C, Debaisieux L, Devaux C, García Ribas S, Gomes P, Incardona F, Kaiser R, Ruelle J, Sayan M, Paraschiv S, Paredes R, Peeters M, Sonnerborg A, Vancutsem E, Van den Wijngaert S, Van Ranst M, Verhofstede C, Vandamme AM, Lemey P, Van Laethem K.

Virus Evol. 2017 Mar 5;3(Suppl 1). pii: vew036.020. doi: 10.1093/ve/vew036.020. eCollection 2017 Mar. No abstract available.

11.

Genetic Diversity of Highly Pathogenic Avian Influenza A(H5N8/H5N5) Viruses in Italy, 2016-17.

Fusaro A, Monne I, Mulatti P, Zecchin B, Bonfanti L, Ormelli S, Milani A, Cecchettin K, Lemey P, Moreno A, Massi P, Dorotea T, Marangon S, Terregino C.

Emerg Infect Dis. 2017 Sep;23(9):1543-1547. doi: 10.3201/eid2309.170539. Epub 2017 Sep 17.

12.

Using Viral Gene Sequences to Compare and Explain the Heterogeneous Spatial Dynamics of Virus Epidemics.

Dellicour S, Rose R, Faria NR, Vieira LFP, Bourhy H, Gilbert M, Lemey P, Pybus OG.

Mol Biol Evol. 2017 Oct 1;34(10):2563-2571. doi: 10.1093/molbev/msx176.

PMID:
28651357
13.

The multi-faceted dynamics of HIV-1 transmission in Northern Alberta: A combined analysis of virus genetic and public health data.

Vrancken B, Adachi D, Benedet M, Singh A, Read R, Shafran S, Taylor GD, Simmonds K, Sikora C, Lemey P, Charlton CL, Tang JW.

Infect Genet Evol. 2017 Aug;52:100-105. doi: 10.1016/j.meegid.2017.04.005. Epub 2017 Apr 18.

PMID:
28427935
14.

Virus genomes reveal factors that spread and sustained the Ebola epidemic.

Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F, Caddy SL, Cotten M, D'Ambrozio J, Dellicour S, Di Caro A, Diclaro JW, Duraffour S, Elmore MJ, Fakoli LS, Faye O, Gilbert ML, Gevao SM, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans BL, Hiscox JA, Jah U, Kugelman JR, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith LW, Qu J, Quick J, Pas SD, Phan MVT, Pollakis G, Reusken CB, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Wölfel R, Yozwiak NL, Andersen KG, Blyden SO, Bolay F, Carroll MW, Dahn B, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Günther S, Happi CT, Holmes EC, Kargbo B, Keïta S, Kellam P, Koopmans MPG, Kuhn JH, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti PC, Sall A, Ströher U, Wurie I, Suchard MA, Lemey P, Rambaut A.

Nature. 2017 Apr 20;544(7650):309-315. doi: 10.1038/nature22040. Epub 2017 Apr 12.

15.

Bayesian codon substitution modelling to identify sources of pathogen evolutionary rate variation.

Baele G, Suchard MA, Bielejec F, Lemey P.

Microb Genom. 2016 Jun 24;2(6):e000057. doi: 10.1099/mgen.0.000057. eCollection 2016 Jun.

16.

The epidemic dynamics of hepatitis C virus subtypes 4a and 4d in Saudi Arabia.

Al-Qahtani AA, Baele G, Khalaf N, Suchard MA, Al-Anazi MR, Abdo AA, Sanai FM, Al-Ashgar HI, Khan MQ, Al-Ahdal MN, Lemey P, Vrancken B.

Sci Rep. 2017 Mar 21;7:44947. doi: 10.1038/srep44947.

17.

Phylogenetic relationships of the HA and NA genes between vaccine and seasonal influenza A(H3N2) strains in Korea.

Kim JI, Lee I, Park S, Bae JY, Yoo K, Cheong HJ, Noh JY, Hong KW, Lemey P, Vrancken B, Kim J, Nam M, Yun SH, Cho WI, Song JY, Kim WJ, Park MS, Song JW, Kee SH, Song KJ, Park MS.

PLoS One. 2017 Mar 3;12(3):e0172059. doi: 10.1371/journal.pone.0172059. eCollection 2017.

18.

Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST.

Baele G, Lemey P, Rambaut A, Suchard MA.

Bioinformatics. 2017 Jun 15;33(12):1798-1805. doi: 10.1093/bioinformatics/btx088.

PMID:
28200071
19.

Emerging Concepts of Data Integration in Pathogen Phylodynamics.

Baele G, Suchard MA, Rambaut A, Lemey P.

Syst Biol. 2017 Jan 1;66(1):e47-e65. doi: 10.1093/sysbio/syw054. Review.

20.

Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza.

Cybis GB, Sinsheimer JS, Bedford T, Rambaut A, Lemey P, Suchard MA.

Stat Med. 2018 Jan 30;37(2):195-206. doi: 10.1002/sim.7196. Epub 2017 Jan 18.

PMID:
28098392

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