Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 200

1.

Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains.

Otieno JR, Kamau EM, Oketch JW, Ngoi JM, Gichuki AM, Binter Š, Otieno GP, Ngama M, Agoti CN, Cane PA, Kellam P, Cotten M, Lemey P, Nokes DJ.

Virus Evol. 2018 Sep 24;4(2):vey027. doi: 10.1093/ve/vey027. eCollection 2018 Jul.

2.

Iran's hepatitis elimination programme is under threat.

Pourkarim MR, Razavi H, Lemey P, Van Ranst M.

Lancet. 2018 Sep 22;392(10152):1009. doi: 10.1016/S0140-6736(18)31810-5. Epub 2018 Sep 20. No abstract available.

PMID:
30264697
3.

Recent advances in computational phylodynamics.

Baele G, Dellicour S, Suchard MA, Lemey P, Vrancken B.

Curr Opin Virol. 2018 Aug;31:24-32. doi: 10.1016/j.coviro.2018.08.009. Epub 2018 Sep 22. Review.

PMID:
30248578
4.

Phylogenetic analysis of two genotype 3 Hepatitis E viruses from wild boar, Italy.

De Sabato L, Vaccari G, Lemey P, Amoroso MG, Fusco G, Ianiro G, Di Bartolo I.

Virus Genes. 2018 Sep 10. doi: 10.1007/s11262-018-1597-5. [Epub ahead of print]

PMID:
30203361
5.

On the importance of negative controls in viral landscape phylogeography.

Dellicour S, Vrancken B, Trovão NS, Fargette D, Lemey P.

Virus Evol. 2018 Aug 16;4(2):vey023. doi: 10.1093/ve/vey023. eCollection 2018 Jul.

6.

Genomic and epidemiological monitoring of yellow fever virus transmission potential.

Faria NR, Kraemer MUG, Hill SC, Goes de Jesus J, Aguiar RS, Iani FCM, Xavier J, Quick J, du Plessis L, Dellicour S, Thézé J, Carvalho RDO, Baele G, Wu CH, Silveira PP, Arruda MB, Pereira MA, Pereira GC, Lourenço J, Obolski U, Abade L, Vasylyeva TI, Giovanetti M, Yi D, Weiss DJ, Wint GRW, Shearer FM, Funk S, Nikolay B, Fonseca V, Adelino TER, Oliveira MAA, Silva MVF, Sacchetto L, Figueiredo PO, Rezende IM, Mello EM, Said RFC, Santos DA, Ferraz ML, Brito MG, Santana LF, Menezes MT, Brindeiro RM, Tanuri A, Dos Santos FCP, Cunha MS, Nogueira JS, Rocco IM, da Costa AC, Komninakis SCV, Azevedo V, Chieppe AO, Araujo ESM, Mendonça MCL, Dos Santos CC, Dos Santos CD, Mares-Guia AM, Nogueira RMR, Sequeira PC, Abreu RG, Garcia MHO, Abreu AL, Okumoto O, Kroon EG, de Albuquerque CFC, Lewandowski K, Pullan ST, Carroll M, de Oliveira T, Sabino EC, Souza RP, Suchard MA, Lemey P, Trindade GS, Drumond BP, Filippis AMB, Loman NJ, Cauchemez S, Alcantara LCJ, Pybus OG.

Science. 2018 Aug 31;361(6405):894-899. doi: 10.1126/science.aat7115. Epub 2018 Aug 23.

PMID:
30139911
7.

Discovery and genome characterization of three new Jeilongviruses, a lineage of paramyxoviruses characterized by their unique membrane proteins.

Vanmechelen B, Bletsa M, Laenen L, Lopes AR, Vergote V, Beller L, Deboutte W, Korva M, Avšič Županc T, Goüy de Bellocq J, Gryseels S, Leirs H, Lemey P, Vrancken B, Maes P.

BMC Genomics. 2018 Aug 16;19(1):617. doi: 10.1186/s12864-018-4995-0.

8.

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10.

Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A.

Virus Evol. 2018 Jun 8;4(1):vey016. doi: 10.1093/ve/vey016. eCollection 2018 Jan.

9.

Geographical and Historical Patterns in the Emergences of Novel Highly Pathogenic Avian Influenza (HPAI) H5 and H7 Viruses in Poultry.

Dhingra MS, Artois J, Dellicour S, Lemey P, Dauphin G, Von Dobschuetz S, Van Boeckel TP, Castellan DM, Morzaria S, Gilbert M.

Front Vet Sci. 2018 Jun 5;5:84. doi: 10.3389/fvets.2018.00084. eCollection 2018.

10.

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.

11.

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.

12.

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.

13.

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
14.

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.

15.

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.

16.

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.

17.

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.

18.

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
19.

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.

20.

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.

21.

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
22.

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
23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

Spatio-temporal analysis of Nova virus, a divergent hantavirus circulating in the European mole in Belgium.

Laenen L, Dellicour S, Vergote V, Nauwelaers I, De Coster S, Verbeeck I, Vanmechelen B, Lemey P, Maes P.

Mol Ecol. 2016 Dec;25(23):5994-6008. doi: 10.1111/mec.13887. Epub 2016 Nov 9.

PMID:
27862516
31.

1970s and 'Patient 0' HIV-1 genomes illuminate early HIV/AIDS history in North America.

Worobey M, Watts TD, McKay RA, Suchard MA, Granade T, Teuwen DE, Koblin BA, Heneine W, Lemey P, Jaffe HW.

Nature. 2016 Nov 3;539(7627):98-101. doi: 10.1038/nature19827. Epub 2016 Oct 26.

32.

A Relaxed Directional Random Walk Model for Phylogenetic Trait Evolution.

Gill MS, Tung Ho LS, Baele G, Lemey P, Suchard MA.

Syst Biol. 2017 May 1;66(3):299-319. doi: 10.1093/sysbio/syw093.

33.

Differential Infection Patterns and Recent Evolutionary Origins of Equine Hepaciviruses in Donkeys.

Walter S, Rasche A, Moreira-Soto A, Pfaender S, Bletsa M, Corman VM, Aguilar-Setien A, García-Lacy F, Hans A, Todt D, Schuler G, Shnaiderman-Torban A, Steinman A, Roncoroni C, Veneziano V, Rusenova N, Sandev N, Rusenov A, Zapryanova D, García-Bocanegra I, Jores J, Carluccio A, Veronesi MC, Cavalleri JM, Drosten C, Lemey P, Steinmann E, Drexler JF.

J Virol. 2016 Dec 16;91(1). pii: e01711-16. Print 2017 Jan 1.

34.

Identifying predictors of time-inhomogeneous viral evolutionary processes.

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

Virus Evol. 2016 Sep 6;2(2):vew023. eCollection 2016 Jul.

35.

Host ecology determines the dispersal patterns of a plant virus.

Trovão NS, Baele G, Vrancken B, Bielejec F, Suchard MA, Fargette D, Lemey P.

Virus Evol. 2015 Dec 16;1(1):vev016. eCollection 2015.

36.

The global distribution of Banana bunchy top virus reveals little evidence for frequent recent, human-mediated long distance dispersal events.

Stainton D, Martin DP, Muhire BM, Lolohea S, Halafihi M, Lepoint P, Blomme G, Crew KS, Sharman M, Kraberger S, Dayaram A, Walters M, Collings DA, Mabvakure B, Lemey P, Harkins GW, Thomas JE, Varsani A.

Virus Evol. 2015 Sep 10;1(1):vev009. eCollection 2015.

37.

Exceptional Heterogeneity in Viral Evolutionary Dynamics Characterises Chronic Hepatitis C Virus Infection.

Raghwani J, Rose R, Sheridan I, Lemey P, Suchard MA, Santantonio T, Farci P, Klenerman P, Pybus OG.

PLoS Pathog. 2016 Sep 15;12(9):e1005894. doi: 10.1371/journal.ppat.1005894. eCollection 2016 Sep.

38.

Distinct Effects of T-705 (Favipiravir) and Ribavirin on Influenza Virus Replication and Viral RNA Synthesis.

Vanderlinden E, Vrancken B, Van Houdt J, Rajwanshi VK, Gillemot S, Andrei G, Lemey P, Naesens L.

Antimicrob Agents Chemother. 2016 Oct 21;60(11):6679-6691. doi: 10.1128/AAC.01156-16. Print 2016 Nov.

39.

Genetically Different Highly Pathogenic Avian Influenza A(H5N1) Viruses in West Africa, 2015.

Tassoni L, Fusaro A, Milani A, Lemey P, Awuni JA, Sedor VB, Dogbey O, Commey AN, Meseko C, Joannis T, Minoungou GL, Ouattara L, Haido AM, Cisse-Aman D, Couacy-Hymann E, Dauphin G, Cattoli G, Monne I.

Emerg Infect Dis. 2016 Dec;22(12):2132-2136. doi: 10.3201/eid2212.160578. Epub 2016 Dec 15.

40.

Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates.

Gill MS, Lemey P, Bennett SN, Biek R, Suchard MA.

Syst Biol. 2016 Nov;65(6):1041-1056. Epub 2016 Jul 1.

41.

SERAPHIM: studying environmental rasters and phylogenetically informed movements.

Dellicour S, Rose R, Faria NR, Lemey P, Pybus OG.

Bioinformatics. 2016 Oct 15;32(20):3204-3206. Epub 2016 Jun 22.

PMID:
27334476
42.

Reassortment compatibility between PB1, PB2, and HA genes of the two influenza B virus lineages in mammalian cells.

Kim JI, Lee I, Park S, Bae JY, Yoo K, Lemey P, Park MS, Song JW, Kee SH, Song KJ, Park MS.

Sci Rep. 2016 Jun 8;6:27480. doi: 10.1038/srep27480.

43.

SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes.

Bielejec F, Baele G, Vrancken B, Suchard MA, Rambaut A, Lemey P.

Mol Biol Evol. 2016 Aug;33(8):2167-9. doi: 10.1093/molbev/msw082. Epub 2016 Apr 23.

PMID:
27189542
44.

The global antigenic diversity of swine influenza A viruses.

Lewis NS, Russell CA, Langat P, Anderson TK, Berger K, Bielejec F, Burke DF, Dudas G, Fonville JM, Fouchier RA, Kellam P, Koel BF, Lemey P, Nguyen T, Nuansrichy B, Peiris JM, Saito T, Simon G, Skepner E, Takemae N; ESNIP3 consortium, Webby RJ, Van Reeth K, Brookes SM, Larsen L, Watson SJ, Brown IH, Vincent AL.

Elife. 2016 Apr 15;5:e12217. doi: 10.7554/eLife.12217.

45.

Revealing the Micro-scale Signature of Endemic Zoonotic Disease Transmission in an African Urban Setting.

Bourhy H, Nakouné E, Hall M, Nouvellet P, Lepelletier A, Talbi C, Watier L, Holmes EC, Cauchemez S, Lemey P, Donnelly CA, Rambaut A.

PLoS Pathog. 2016 Apr 8;12(4):e1005525. doi: 10.1371/journal.ppat.1005525. eCollection 2016 Apr.

46.

ASSESSING PHENOTYPIC CORRELATION THROUGH THE MULTIVARIATE PHYLOGENETIC LATENT LIABILITY MODEL.

Cybis GB, Sinsheimer JS, Bedford T, Mather AE, Lemey P, Suchard MA.

Ann Appl Stat. 2015 Jun;9(2):969-991.

47.

Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing.

Vrancken B, Trovão NS, Baele G, van Wijngaerden E, Vandamme AM, van Laethem K, Lemey P.

Viruses. 2016 Jan 7;8(1). pii: E12. doi: 10.3390/v8010012.

48.

The recent ancestry of Middle East respiratory syndrome coronavirus in Korea has been shaped by recombination.

Kim JI, Kim YJ, Lemey P, Lee I, Park S, Bae JY, Kim D, Kim H, Jang SI, Yang JS, Kim H, Kim DW, Nam JG, Kim SS, Kim K, Myun Lee J, Song MK, Song D, Chang J, Hong KJ, Bae YS, Song JW, Lee JS, Park MS.

Sci Rep. 2016 Jan 6;6:18825. doi: 10.1038/srep18825.

49.

Virus evolution and transmission in an ever more connected world.

Pybus OG, Tatem AJ, Lemey P.

Proc Biol Sci. 2015 Dec 22;282(1821):20142878. doi: 10.1098/rspb.2014.2878. Review.

50.

Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty.

Baele G, Lemey P, Suchard MA.

Syst Biol. 2016 Mar;65(2):250-64. doi: 10.1093/sysbio/syv083. Epub 2015 Nov 1.

Supplemental Content

Support Center