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Items: 40

1.

Accounting for population structure reveals ambiguity in the Zaire Ebolavirus reservoir dynamics.

Vrancken B, Wawina-Bokalanga T, Vanmechelen B, Martí-Carreras J, Carroll MW, Nsio J, Kapetshi J, Makiala-Mandanda S, Muyembe-Tamfum JJ, Baele G, Vermeire K, Vergote V, Ahuka-Mundeke S, Maes P.

PLoS Negl Trop Dis. 2020 Mar 4;14(3):e0008117. doi: 10.1371/journal.pntd.0008117. eCollection 2020 Mar.

2.

Evaluating predictive markers for viral rebound and safety assessment in blood and lumbar fluid during HIV-1 treatment interruption.

De Scheerder MA, Van Hecke C, Zetterberg H, Fuchs D, De Langhe N, Rutsaert S, Vrancken B, Trypsteen W, Noppe Y, Van Der Gucht B, Pelgrom J, Van Wanzeele F, Palmer S, Lemey P, Gisslén M, Vandekerckhove L.

J Antimicrob Chemother. 2020 Feb 13. pii: dkaa003. doi: 10.1093/jac/dkaa003. [Epub ahead of print]

PMID:
32053203
3.

In Search of Covariates of HIV-1 Subtype B Spread in the United States-A Cautionary Tale of Large-Scale Bayesian Phylogeography.

Hong SL, Dellicour S, Vrancken B, Suchard MA, Pyne MT, Hillyard DR, Lemey P, Baele G.

Viruses. 2020 Feb 5;12(2). pii: E182. doi: 10.3390/v12020182.

4.

HIV persists throughout deep tissues with repopulation from multiple anatomical sources.

Chaillon A, Gianella S, Dellicour S, Rawlings SA, Schlub TE, De Oliveira MF, Ignacio C, Porrachia M, Vrancken B, Smith DM.

J Clin Invest. 2020 Apr 1;130(4):1699-1712. doi: 10.1172/JCI134815.

5.

Limited evolution of the yellow fever virus 17d in a mouse infection model.

Kum DB, Mishra N, Vrancken B, Thibaut HJ, Wilder-Smith A, Lemey P, Neyts J, Dallmeier K.

Emerg Microbes Infect. 2019;8(1):1734-1746. doi: 10.1080/22221751.2019.1694394.

6.

Disentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza.

Fusaro A, Zecchin B, Vrancken B, Abolnik C, Ademun R, Alassane A, Arafa A, Awuni JA, Couacy-Hymann E, Coulibaly M'B, Gaidet N, Go-Maro E, Joannis T, Jumbo SD, Minoungou G, Meseko C, Souley MM, Ndumu DB, Shittu I, Twabela A, Wade A, Wiersma L, Akpeli YP, Zamperin G, Milani A, Lemey P, Monne I.

Nat Commun. 2019 Nov 22;10(1):5310. doi: 10.1038/s41467-019-13287-y.

7.

Divergence dating using mixed effects clock modelling: An application to HIV-1.

Bletsa M, Suchard MA, Ji X, Gryseels S, Vrancken B, Baele G, Worobey M, Lemey P.

Virus Evol. 2019 Sep 5;5(2):vez036. doi: 10.1093/ve/vez036. eCollection 2019 Jul.

8.

Cross-country migration linked to people who inject drugs challenges the long-term impact of national HCV elimination programmes.

Vrancken B, Cuypers L, Pérez AB, Chueca N, Anton-Basantas J, de la Iglesia A, Fuentes J, Pineda JA, Téllez F, Bernal E, Rincón P, Von Wichman MA, Fuentes A, Vera F, Rivero-Juárez A, Jiménez M, Vandamme AM, García F.

J Hepatol. 2019 Dec;71(6):1270-1272. doi: 10.1016/j.jhep.2019.08.010. Epub 2019 Oct 1. No abstract available.

PMID:
31585736
9.

Drivers of HIV-1 transmission: The Portuguese case.

Pineda-Peña AC, Pingarilho M, Li G, Vrancken B, Libin P, Gomes P, Camacho RJ, Theys K, Barroso Abecasis A; Portuguese HIV-1 Resistance Study Group.

PLoS One. 2019 Sep 30;14(9):e0218226. doi: 10.1371/journal.pone.0218226. eCollection 2019.

10.

HIV Rebound Is Predominantly Fueled by Genetically Identical Viral Expansions from Diverse Reservoirs.

De Scheerder MA, Vrancken B, Dellicour S, Schlub T, Lee E, Shao W, Rutsaert S, Verhofstede C, Kerre T, Malfait T, Hemelsoet D, Coppens M, Dhondt A, De Looze D, Vermassen F, Lemey P, Palmer S, Vandekerckhove L.

Cell Host Microbe. 2019 Sep 11;26(3):347-358.e7. doi: 10.1016/j.chom.2019.08.003. Epub 2019 Aug 27.

PMID:
31471273
11.

Comparing patterns and scales of plant virus phylogeography: Rice yellow mottle virus in Madagascar and in continental Africa.

Rakotomalala M, Vrancken B, Pinel-Galzi A, Ramavovololona P, Hébrard E, Randrianangaly JS, Dellicour S, Lemey P, Fargette D.

Virus Evol. 2019 Aug 1;5(2):vez023. doi: 10.1093/ve/vez023. eCollection 2019 Jul.

12.

New evidence for the east-west spread of the highly pathogenic avian influenza H5N1 virus between Central Asian and east Asian-Australasian flyways in China.

Meng W, Yang Q, Vrancken B, Chen Z, Liu D, Chen L, Zhao X, François S, Ma T, Gao R, Ru W, Li Y, He H, Zhang G, Tian H, Lu J.

Emerg Microbes Infect. 2019;8(1):823-826. doi: 10.1080/22221751.2019.1623719.

13.

Identifying the patterns and drivers of Puumala hantavirus enzootic dynamics using reservoir sampling.

Laenen L, Vergote V, Vanmechelen B, Tersago K, Baele G, Lemey P, Leirs H, Dellicour S, Vrancken B, Maes P.

Virus Evol. 2019 Apr 22;5(1):vez009. doi: 10.1093/ve/vez009. eCollection 2019 Jan.

14.

Increasing importance of European lineages in seeding the hepatitis C virus subtype 1a epidemic in Spain.

Pérez AB, Vrancken B, Chueca N, Aguilera A, Reina G, García-Del Toro M, Vera F, Von Wichman MA, Arenas JI, Téllez F, Pineda JA, Omar M, Bernal E, Rivero-Juárez A, Fernández-Fuertes E, de la Iglesia A, Pascasio JM, Lemey P, Garcia F, Cuypers L.

Euro Surveill. 2019 Feb;24(9). doi: 10.2807/1560-7917.ES.2019.24.9.1800227.

15.

Transmission dynamics of re-emerging rabies in domestic dogs of rural China.

Tian H, Feng Y, Vrancken B, Cazelles B, Tan H, Gill MS, Yang Q, Li Y, Yang W, Zhang Y, Zhang Y, Lemey P, Pybus OG, Stenseth NC, Zhang H, Dellicour S.

PLoS Pathog. 2018 Dec 6;14(12):e1007392. doi: 10.1371/journal.ppat.1007392. eCollection 2018 Dec.

16.

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
17.

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.

18.

Why comprehensive datasets matter when inferring epidemic links or subgenotyping.

Vrancken B, Alavian SM, Aminy A, Amini-Bavil-Olyaee S, Pourkarim MR.

Infect Genet Evol. 2018 Nov;65:350-351. doi: 10.1016/j.meegid.2018.08.012. Epub 2018 Aug 16. No abstract available.

PMID:
30118874
19.

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.

20.

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
21.

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.

22.

A18 Random amplification with next-generation sequencing to cover HIV and HCV full-length genomes.

Cuypers L, Conceição-Neto N, Dierickx T, Schrooten Y, Vrancken B, Van Wijngaerden E, Nevens F, Vandamme AM, Matthijnssens J, Van Laethem K.

Virus Evol. 2017 Mar 5;3(Suppl 1). pii: vew036.017. doi: 10.1093/ve/vew036.017. eCollection 2017 Mar. No abstract available.

23.

Cross-border spread, lineage displacement and evolutionary rate estimation of rabies virus in Yunnan Province, China.

Zhang Y, Vrancken B, Feng Y, Dellicour S, Yang Q, Yang W, Zhang Y, Dong L, Pybus OG, Zhang H, Tian H.

Virol J. 2017 Jun 3;14(1):102. doi: 10.1186/s12985-017-0769-6.

24.

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
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.

Implications of hepatitis C virus subtype 1a migration patterns for virus genetic sequencing policies in Italy.

Cuypers L, Vrancken B, Fabeni L, Marascio N, Cento V, Di Maio VC, Aragri M, Pineda-Peña AC, Schrooten Y, Van Laethem K, Balog D, Focà A, Torti C, Nevens F, Perno CF, Vandamme AM, Ceccherini-Silberstein F.

BMC Evol Biol. 2017 Mar 7;17(1):70. doi: 10.1186/s12862-017-0913-3.

27.

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.

28.

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.

29.

Detection of Natural Resistance-Associated Substitutions by Ion Semiconductor Technology in HCV1b Positive, Direct-Acting Antiviral Agents-Naïve Patients.

Marascio N, Pavia G, Strazzulla A, Dierckx T, Cuypers L, Vrancken B, Barreca GS, Mirante T, Malanga D, Oliveira DM, Vandamme AM, Torti C, Liberto MC, Focà A; The SINERGIE-UMG Study Group.

Int J Mol Sci. 2016 Aug 27;17(9). pii: E1416. doi: 10.3390/ijms17091416.

30.

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.

31.

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.

32.

Fatigue of Ti6Al4V Structural Health Monitoring Systems Produced by Selective Laser Melting.

Strantza M, Vafadari R, de Baere D, Vrancken B, van Paepegem W, Vandendael I, Terryn H, Guillaume P, van Hemelrijck D.

Materials (Basel). 2016 Feb 11;9(2). pii: E106. doi: 10.3390/ma9020106.

33.

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.

34.

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.

35.

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.

36.

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.

37.

A near-full length genotypic assay for HCV1b.

Cuypers L, Snoeck J, Vrancken B, Kerremans L, Vuagniaux G, Verbeeck J, Nevens F, Camacho RJ, Vandamme AM, Van Dooren S.

J Virol Methods. 2014 Dec;209:126-35. doi: 10.1016/j.jviromet.2014.09.009. Epub 2014 Sep 22.

PMID:
25245140
38.

The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates.

Vrancken B, Rambaut A, Suchard MA, Drummond A, Baele G, Derdelinckx I, Van Wijngaerden E, Vandamme AM, Van Laethem K, Lemey P.

PLoS Comput Biol. 2014 Apr 3;10(4):e1003505. doi: 10.1371/journal.pcbi.1003505. eCollection 2014 Apr.

39.

HIV-1 evolution in patients undergoing immunotherapy with Tat, Rev, and Nef expressing dendritic cells followed by treatment interruption.

de Goede AL, van Deutekom HW, Vrancken B, Schutten M, Allard SD, van Baalen CA, Osterhaus AD, Thielemans K, Aerts JL, Keşmir C, Lemey P, Gruters RA.

AIDS. 2013 Nov 13;27(17):2679-89. doi: 10.1097/01.aids.0000433813.67662.92.

PMID:
24149085
40.

Covering all bases in HIV research: unveiling a hidden world of viral evolution.

Vrancken B, Lequime S, Theys K, Lemey P.

AIDS Rev. 2010 Apr-Jun;12(2):89-102. Review.

PMID:
20571603

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