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Items: 1 to 50 of 109

1.

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics.

Ayres DL, Cummings MP, Baele G, Darling AE, Lewis PO, Swofford DL, Huelsenbeck JP, Lemey P, Rambaut A, Suchard MA.

Syst Biol. 2019 Apr 23. pii: syz020. doi: 10.1093/sysbio/syz020. [Epub ahead of print]

PMID:
31034053
2.

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.

3.

Bayesian inference of evolutionary histories under time-dependent substitution rates.

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

Mol Biol Evol. 2019 Apr 19. pii: msz094. doi: 10.1093/molbev/msz094. [Epub ahead of print]

PMID:
31004175
4.

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
5.

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
6.

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.

7.

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.

8.

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7.

Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA.

Syst Biol. 2018 Sep 1;67(5):901-904. doi: 10.1093/sysbio/syy032.

9.

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.

10.

PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context.

Libin P, Vanden Eynden E, Incardona F, Nowé A, Bezenchek A; EucoHIV Study Group, Sönnerborg A, Vandamme AM, Theys K, Baele G.

Bioinformatics. 2017 Dec 15;33(24):3993-3995. doi: 10.1093/bioinformatics/btx535.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts.

Gallone B, Steensels J, Prahl T, Soriaga L, Saels V, Herrera-Malaver B, Merlevede A, Roncoroni M, Voordeckers K, Miraglia L, Teiling C, Steffy B, Taylor M, Schwartz A, Richardson T, White C, Baele G, Maere S, Verstrepen KJ.

Cell. 2016 Sep 8;166(6):1397-1410.e16. doi: 10.1016/j.cell.2016.08.020.

21.

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.

22.

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.

23.

Sub-Epidemics Explain Localized High Prevalence of Reduced Susceptibility to Rilpivirine in Treatment-Naive HIV-1-Infected Patients: Subtype and Geographic Compartmentalization of Baseline Resistance Mutations.

Theys K, Van Laethem K, Gomes P, Baele G, Pineda-Peña AC, Vandamme AM, Camacho RJ, Abecasis AB.

AIDS Res Hum Retroviruses. 2016 May;32(5):427-33. doi: 10.1089/AID.2015.0095. Epub 2016 Jan 29.

24.

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.

25.

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.

26.

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.

27.

HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations.

Faria NR, Rambaut A, Suchard MA, Baele G, Bedford T, Ward MJ, Tatem AJ, Sousa JD, Arinaminpathy N, Pépin J, Posada D, Peeters M, Pybus OG, Lemey P.

Science. 2014 Oct 3;346(6205):56-61. doi: 10.1126/science.1256739. Epub 2014 Oct 2.

28.

πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios.

Bielejec F, Lemey P, Carvalho LM, Baele G, Rambaut A, Suchard MA.

BMC Bioinformatics. 2014 May 7;15:133. doi: 10.1186/1471-2105-15-133.

29.

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary.

Vanneste K, Baele G, Maere S, Van de Peer Y.

Genome Res. 2014 Aug;24(8):1334-47. doi: 10.1101/gr.168997.113. Epub 2014 May 16.

30.

Air travel is associated with intracontinental spread of dengue virus serotypes 1-3 in Brazil.

Nunes MR, Palacios G, Faria NR, Sousa EC Jr, Pantoja JA, Rodrigues SG, Carvalho VL, Medeiros DB, Savji N, Baele G, Suchard MA, Lemey P, Vasconcelos PF, Lipkin WI.

PLoS Negl Trop Dis. 2014 Apr 17;8(4):e2769. doi: 10.1371/journal.pntd.0002769. eCollection 2014 Apr.

31.

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.

32.

Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography.

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

Syst Biol. 2014 Jul;63(4):493-504. doi: 10.1093/sysbio/syu015. Epub 2014 Mar 12.

33.

Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2.

Lemey P, Rambaut A, Bedford T, Faria N, Bielejec F, Baele G, Russell CA, Smith DJ, Pybus OG, Brockmann D, Suchard MA.

PLoS Pathog. 2014 Feb 20;10(2):e1003932. doi: 10.1371/journal.ppat.1003932. eCollection 2014 Feb.

34.

Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency.

Baele G, Lemey P.

Bioinformatics. 2013 Aug 15;29(16):1970-9. doi: 10.1093/bioinformatics/btt340. Epub 2013 Jun 12.

PMID:
23766415
35.

Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution.

Baele G, Lemey P, Vansteelandt S.

BMC Bioinformatics. 2013 Mar 6;14:85. doi: 10.1186/1471-2105-14-85.

36.

Accurate model selection of relaxed molecular clocks in bayesian phylogenetics.

Baele G, Li WL, Drummond AJ, Suchard MA, Lemey P.

Mol Biol Evol. 2013 Feb;30(2):239-43. doi: 10.1093/molbev/mss243. Epub 2012 Oct 22.

37.

Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty.

Baele G, Lemey P, Bedford T, Rambaut A, Suchard MA, Alekseyenko AV.

Mol Biol Evol. 2012 Sep;29(9):2157-67. doi: 10.1093/molbev/mss084. Epub 2012 Mar 7.

38.

The genome of Tetranychus urticae reveals herbivorous pest adaptations.

Grbić M, Van Leeuwen T, Clark RM, Rombauts S, Rouzé P, Grbić V, Osborne EJ, Dermauw W, Ngoc PC, Ortego F, Hernández-Crespo P, Diaz I, Martinez M, Navajas M, Sucena É, Magalhães S, Nagy L, Pace RM, Djuranović S, Smagghe G, Iga M, Christiaens O, Veenstra JA, Ewer J, Villalobos RM, Hutter JL, Hudson SD, Velez M, Yi SV, Zeng J, Pires-daSilva A, Roch F, Cazaux M, Navarro M, Zhurov V, Acevedo G, Bjelica A, Fawcett JA, Bonnet E, Martens C, Baele G, Wissler L, Sanchez-Rodriguez A, Tirry L, Blais C, Demeestere K, Henz SR, Gregory TR, Mathieu J, Verdon L, Farinelli L, Schmutz J, Lindquist E, Feyereisen R, Van de Peer Y.

Nature. 2011 Nov 23;479(7374):487-92. doi: 10.1038/nature10640.

39.

Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes.

Baele G, Van de Peer Y, Vansteelandt S.

BMC Evol Biol. 2011 May 27;11:145. doi: 10.1186/1471-2148-11-145.

40.

Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences.

Baele G, Van de Peer Y, Vansteelandt S.

BMC Evol Biol. 2010 Aug 10;10:244. doi: 10.1186/1471-2148-10-244.

41.

Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding sequences.

Baele G, Van de Peer Y, Vansteelandt S.

J Mol Evol. 2010 Jul;71(1):34-50. doi: 10.1007/s00239-010-9362-y. Epub 2010 Jul 11.

PMID:
20623275
42.

A screening methodology based on Random Forests to improve the detection of gene-gene interactions.

De Lobel L, Geurts P, Baele G, Castro-Giner F, Kogevinas M, Van Steen K.

Eur J Hum Genet. 2010 Oct;18(10):1127-32. doi: 10.1038/ejhg.2010.48. Epub 2010 May 12.

43.

Interpretation of urinary concentrations of pseudoephedrine and its metabolite cathine in relation to doping control.

Deventer K, Van Eenoo P, Baele G, Pozo OJ, Van Thuyne W, Delbeke FT.

Drug Test Anal. 2009 May;1(5):209-13. doi: 10.1002/dta.31.

PMID:
20355197
44.

Efficient context-dependent model building based on clustering posterior distributions for non-coding sequences.

Baele G, Peer YV, Vansteelandt S.

BMC Evol Biol. 2009 Apr 30;9:87. doi: 10.1186/1471-2148-9-87.

45.

Stability of selected chlorinated thiazide diuretics.

Deventer K, Baele G, Van Eenoo P, Pozo OJ, Delbeke FT.

J Pharm Biomed Anal. 2009 Feb 20;49(2):519-24. doi: 10.1016/j.jpba.2008.11.001. Epub 2008 Nov 13.

PMID:
19108977
46.

A model-based approach to study nearest-neighbor influences reveals complex substitution patterns in non-coding sequences.

Baele G, Van de Peer Y, Vansteelandt S.

Syst Biol. 2008 Oct;57(5):675-92. doi: 10.1080/10635150802422324.

PMID:
18853356
47.

An improved statistical method for detecting heterotachy in nucleotide sequences.

Baele G, Raes J, Van de Peer Y, Vansteelandt S.

Mol Biol Evol. 2006 Jul;23(7):1397-405. Epub 2006 May 3.

PMID:
16672284
48.

Comparison of five different citrated tubes and their in vitro effects on platelet activation.

Philippé J, De Logi E, Baele G.

Clin Chem. 2004 Mar;50(3):656-8. No abstract available.

49.

Thromboprophylaxis in general medical patients.

Baele G, David JL, de Maeseneer M, Deneys V, Dicato MA, Gilis L, Hainaut P, Hermans C, Kristin J, Motte S, van der Plancken M, Verhaeghe R, Vermylen J, von Kemp K, Wautrecht JC, Zicot M; Thrombosis Guidelines Group of the Belgian Society on Thrombosis and Haemostasis; Belgian Working Group on Angiology.

Acta Cardiol. 2003 Feb;58(1):41-2. No abstract available.

PMID:
12625495
50.

Cyclosporine treatment of acquired hemophilia due to factor VIII antibodies.

Petrovic M, Derom E, Baele G.

Haematologica. 2000 Aug;85(8):895-6. No abstract available.

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