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Items: 1 to 20 of 157

1.

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. pii: e12217. doi: 10.7554/eLife.12217.

2.

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.

3.

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.

4.

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.

5.

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.

6.

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.

7.

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.

PMID:
26526428
8.

Contribution of Epidemiological Predictors in Unraveling the Phylogeographic History of HIV-1 Subtype C in Brazil.

Gräf T, Vrancken B, Maletich Junqueira D, de Medeiros RM, Suchard MA, Lemey P, Esteves de Matos Almeida S, Pinto AR.

J Virol. 2015 Dec;89(24):12341-8. doi: 10.1128/JVI.01681-15. Epub 2015 Sep 30.

PMID:
26423943
9.

Ecuador Paraiso Escondido Virus, a New Flavivirus Isolated from New World Sand Flies in Ecuador, Is the First Representative of a Novel Clade in the Genus Flavivirus.

Alkan C, Zapata S, Bichaud L, Moureau G, Lemey P, Firth AE, Gritsun TS, Gould EA, de Lamballerie X, Depaquit J, Charrel RN.

J Virol. 2015 Dec;89(23):11773-85. doi: 10.1128/JVI.01543-15. Epub 2015 Sep 9.

10.

Bayesian Inference Reveals Host-Specific Contributions to the Epidemic Expansion of Influenza A H5N1.

Trovão NS, Suchard MA, Baele G, Gilbert M, Lemey P.

Mol Biol Evol. 2015 Dec;32(12):3264-75. doi: 10.1093/molbev/msv185. Epub 2015 Sep 3.

PMID:
26341298
11.

Genome-Wide Evolutionary Analyses of G1P[8] Strains Isolated Before and After Rotavirus Vaccine Introduction.

Zeller M, Donato C, Trovão NS, Cowley D, Heylen E, Donker NC, McAllen JK, Akopov A, Kirkness EF, Lemey P, Van Ranst M, Matthijnssens J, Kirkwood CD.

Genome Biol Evol. 2015 Aug 8;7(9):2473-83. doi: 10.1093/gbe/evv157.

12.

Disentangling the impact of within-host evolution and transmission dynamics on the tempo of HIV-1 evolution.

Vrancken B, Baele G, Vandamme AM, van Laethem K, Suchard MA, Lemey P.

AIDS. 2015 Jul 31;29(12):1549-56. doi: 10.1097/QAD.0000000000000731.

PMID:
26244394
13.

Synonymous and nonsynonymous distances help untangle convergent evolution and recombination.

Chi PB, Chattopadhyay S, Lemey P, Sokurenko EV, Minin VN.

Stat Appl Genet Mol Biol. 2015 Aug;14(4):375-89. doi: 10.1515/sagmb-2014-0078.

PMID:
26061623
14.

Global circulation patterns of seasonal influenza viruses vary with antigenic drift.

Bedford T, Riley S, Barr IG, Broor S, Chadha M, Cox NJ, Daniels RS, Gunasekaran CP, Hurt AC, Kelso A, Klimov A, Lewis NS, Li X, McCauley JW, Odagiri T, Potdar V, Rambaut A, Shu Y, Skepner E, Smith DJ, Suchard MA, Tashiro M, Wang D, Xu X, Lemey P, Russell CA.

Nature. 2015 Jul 9;523(7559):217-20. doi: 10.1038/nature14460. Epub 2015 Jun 8.

15.

Correction: Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis.

Rhee SY, Blanco JL, Jordan MR, Taylor J, Lemey P, Varghese V, Hamers RL, Bertagnolio S, de Wit TF, Aghokeng AF, Albert J, Avi R, Avila-Rios S, Bessong PO, Brooks JI, Boucher CA, Brumme ZL, Busch MP, Bussmann H, Chaix ML, Chin BS, D'Aquin TT, De Gascun CF, Derache A, Descamps D, Deshpande AK, Djoko CF, Eshleman SH, Fleury H, Frange P, Fujisaki S, Harrigan PR, Hattori J, Holguin A, Hunt GM, Ichimura H, Kaleebu P, Katzenstein D, Kiertiburanakul S, Kim JH, Kim SS, Li Y, Lutsar I, Morris L, Ndembi N, Kee PN, Paranjape RS, Peeters M, Poljak M, Price MA, Ragonnet-Cronin ML, Reyes-Terán G, Rolland M, Sirivichayakul S, Smith DM, Soares MA, Soriano VV, Ssemwanga D, Stanojevic M, Stefani MA, Sugiura W, Sungkanuparph S, Tanuri A, Tee KK, Truong HM, van de Vijver DA, Vidal N, Yang C, Yang R, Yebra G, Ioannidis JP, Vandamme AM, Shafer RW.

PLoS Med. 2015 Jun 1;12(6):e1001845. doi: 10.1371/journal.pmed.1001845. eCollection 2015 Jun. No abstract available.

16.

Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient- and sequence-level meta-analysis.

Rhee SY, Blanco JL, Jordan MR, Taylor J, Lemey P, Varghese V, Hamers RL, Bertagnolio S, Rinke de Wit TF, Aghokeng AF, Albert J, Avi R, Avila-Rios S, Bessong PO, Brooks JI, Boucher CA, Brumme ZL, Busch MP, Bussmann H, Chaix ML, Chin BS, D'Aquin TT, De Gascun CF, Derache A, Descamps D, Deshpande AK, Djoko CF, Eshleman SH, Fleury H, Frange P, Fujisaki S, Harrigan PR, Hattori J, Holguin A, Hunt GM, Ichimura H, Kaleebu P, Katzenstein D, Kiertiburanakul S, Kim JH, Kim SS, Li Y, Lutsar I, Morris L, Ndembi N, Ng KP, Paranjape RS, Peeters M, Poljak M, Price MA, Ragonnet-Cronin ML, Reyes-Terán G, Rolland M, Sirivichayakul S, Smith DM, Soares MA, Soriano VV, Ssemwanga D, Stanojevic M, Stefani MA, Sugiura W, Sungkanuparph S, Tanuri A, Tee KK, Truong HM, van de Vijver DA, Vidal N, Yang C, Yang R, Yebra G, Ioannidis JP, Vandamme AM, Shafer RW.

PLoS Med. 2015 Apr 7;12(4):e1001810. doi: 10.1371/journal.pmed.1001810. eCollection 2015 Apr. Erratum in: PLoS Med. 2015 Jun;12(6):e1001845.

17.

Global migration of influenza A viruses in swine.

Nelson MI, Viboud C, Vincent AL, Culhane MR, Detmer SE, Wentworth DE, Rambaut A, Suchard MA, Holmes EC, Lemey P.

Nat Commun. 2015 Mar 27;6:6696. doi: 10.1038/ncomms7696.

18.

An integrated map of HIV genome-wide variation from a population perspective.

Li G, Piampongsant S, Faria NR, Voet A, Pineda-Peña AC, Khouri R, Lemey P, Vandamme AM, Theys K.

Retrovirology. 2015 Feb 15;12:18. doi: 10.1186/s12977-015-0148-6.

19.

Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: applications to viral and host phenotypic evolution.

Vrancken B, Lemey P, Rambaut A, Bedford T, Longdon B, Günthard HF, Suchard MA.

Methods Ecol Evol. 2015 Jan 1;6(1):67-82.

20.

New insights into flavivirus evolution, taxonomy and biogeographic history, extended by analysis of canonical and alternative coding sequences.

Moureau G, Cook S, Lemey P, Nougairede A, Forrester NL, Khasnatinov M, Charrel RN, Firth AE, Gould EA, de Lamballerie X.

PLoS One. 2015 Feb 26;10(2):e0117849. doi: 10.1371/journal.pone.0117849. eCollection 2015.

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