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Emerging concepts of data integration in pathogen phylodynamics.

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

Syst Biol. 2016 Jun 10. pii: syw054. [Epub ahead of print]


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.

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