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Guy Baele

Principal investigator

 

 

"Statistical and computational phylogenetics"

guy.baele@kuleuven.be
 

tel. +32 16 321287

Rega Institute
Evolutionary and Computational Virology Section
Herestraat 49
3000 Leuven
BELGIUM



Guy Baele Photo

 

Current research topics

Pathogen phylodynamics

To identify the causal mechanisms leading to disease emergence, endemic maintenance and epidemic expansion, epidemiologists would benefit tremendously from a full characterization of pathogen spread in space and time. The extensive sequencing efforts for recent epidemics, such as the West African Ebola epidemic, testify that analyses of pathogen genetic data are becoming increasingly important sources of information in epidemiology. The new era of metagenomics promises to harvest such data in unprecedented quantities with remarkable rapidity. With the objective to assist in designing effective intervention and prevention strategies, we are continuing the development of a comprehensive statistical framework for uncovering the spatial and temporal dynamics of pathogen genomes. To this aim, we will design and extend a series of computationally tractable models that use the rapidly proliferating viral genome data to their full potential, connect molecular evolution to underlying spatial processes, and pave the path to rigorous and powerful phylogeographic hypothesis testing. Armed with these tools, we investigate how genetic variation within important viral pathogens, such as influenza, rabies and HIV, arises and persists across a diverse range of hosts and environments.

Bayesian model selection & Bayesian model averaging

Marginal likelihood estimates to compare models using Bayes factors frequently accompany Bayesian phylogenetic inference. Approaches to estimate marginal likelihoods have garnered increased attention over the past decade. In particular, the introduction of path sampling and stepping-stone sampling into Bayesian phylogenetics has tremendously improved the accuracy of model selection. These sampling techniques are now used to evaluate complex evolutionary and population genetic models on empirical data sets, but considerable computational demands still hamper their widespread adoption. We have recently adapted generalized SS (GSS) for use in coalescent-based phylogenetics, employing the concept of “working distributions” to facilitate - or shorten - the integration process that underlies marginal likelihood estimation. Despite the improvements brought about by our method, while still incorporating phylogenetic uncertainty, Bayesian model selection remains computationally demanding. As such, we plan to further develop Bayesian model averaging approaches to test their performance and avoid a potentially time-consuming model selection exercise. 

TEACHING

  • Introduction to Object-Oriented Programming (B-KUL-I0D41A & B-KUL-I0S75A) (2019 - present)
  • Bioinformatics and Systems Biology: Sequence, Structure and Evolution (B-KUL-E02N3A) (2017 - present)
  • Evolutionary and Quantitative Genetics (B-KUL-I0D53A) (2016 - 2020)

  • Applied Biostatistics: Exercise Sessions (B-KUL-E04N1a) (2017)

  • Introduction to Biostatistics: Exercise Sessions (B-KUL-E07C0a) (2017)

Publications

  1. Brito, A. F., Baele, G., Nahata, K. D., Grubaugh, N. D., Pinney, J. W. (2021) Intrahost speciations and host switches shaped the evolution of herpesviruses. Virus Evol. (in press).
  2. Kalkauskas, A., Perron, U., Sun, Y., Goldman, N., Baele, G., Guindon, S., De Maio, N. (2020) Sampling bias and model choice in continuous phylogeography: getting lost on a random walk. PLoS Comp. Biol. (in press).
  3. Bastide, P., Ho, L. S. T., Baele, G., Lemey, P., Suchard, M. A. (2020) Efficient Bayesian inference of general Gaussian models on large phylogenetic trees. Ann. Appl. Stat. (in press).
  4. Dellicour, S., Durkin, K., Hong, S. L., Vanmechelen, B., Martí-Carreras, J., Gill, M. S., Meex, C., Bontems, S., André, E., Gilbert, M., Walker, C., De Maio, N., Faria, N. R., Hadfield, J., Hayette, M.-P., Bours, V., Wawina-Bokalanga, T., Artesi, M., Baele, G.*, Maes, P.* (2020) A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages. Mol. Biol. Evol. (in press). (*authors contributed equally)
  5. Lemey, P., Hong, S. L., Hill, V., Baele, G., Poletto, C., Colizza, V., O'Toole, A., McCrone, J. T., Andersen, K., Worobey, M., Nelson, M., Rambaut, A., Suchard, M. A. (2020) Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2. Nature Comms. (in press).
  6. Fountain-Jones, N. M., Kraberger, S., Gagne, R., Trumbo, D. R., Salerno, P. E., Funk, W. C., Crooks, K., Biek, R., Alldredge, M., Logan, K., Baele, G., Dellicour, S., Ernest, H. B., VandeWoude, S., Carver, S., Craft, M. E. (2020) Host relatedness and landscape connectivity shape pathogen spread in the puma, a large secretive carnivore. Commun. Biol. (in press).
  7. Wawina-Bokalanga, T., Vanmechelen, B., Lhermitte, V., Martí-Carreras, J., Vergote, V., Raymond Koundouno, F., Akoi-Boré, J., Thom, R., Tipton, T., Steeds, K., Balla Moussa, K., Amento, A., Laenen, L., Duraffour, S., Gabriel, M., Ruibal, P., Hall, Y., Kader-Kondé, M., Günther, S., Baele, G., Muñoz-Fontela, C., Van Weyenbergh, J., Carroll, M. W., Maes, P. (2020) Human diversity of Killer cell Immunoglobulin-like Receptors (KIRs) and HLA class I alleles, and their impact on Ebola virus disease outcome. Emerg. Infect. Dis. (in press).
  8. Baele, G., Gill, M. S., Lemey, P., Suchard, M. A. (2020) Hamiltonian Monte Carlo sampling to estimate past population dynamics using the skygrid coalescent model in a Bayesian phylogenetics framework. Wellcome Open Res. 2020, 5: 53.
  9. Duchêne, S., Featherstone, L., Haritopoulou-Sinanidou, M., Rambaut, A., Lemey, P., Baele, G. (2020) Temporal signal and the phylodynamic threshold of SARS-CoV-2. Virus Evol. (in press).
  10. Duchêne, S., Lemey, P., Stadler, T., Ho, S. Y. W., Duchene, D. A., Dhanasekaran, V., Baele, G. (2020) Bayesian evaluation of temporal signal in measurably evolving populations. Mol. Biol. Evol. (in press).
  11. Lequime, S., Bastide, P., Dellicour, S., Lemey, P., Baele, G. (2020) nosoi: a stochastic agent-based transmission chain simulation framework in R. Methods. Ecol. Evol. 11: 1002-1007.
  12. Ji, X., Zhang, Z., Holbrook, A., Nishimura, A., Baele, G., Rambaut, A., Lemey, P., Suchard, M. A. (2020) Gradients do grow on trees: a linear-time O(N)-dimensional gradient for statistical phylogenetics. Mol. Biol. Evol. (in press).
  13. He, W.-T., Ji, X., He, W., Dellicour, S., Wang, S., Li, G., Zhang, L., Gilbert, M., Zhu, H., Xing, G., Veit, M., Huang, Z., Han, G.-Z., Huang, Y., Suchard, M. A., Baele, G., Lemey, P., Su, S. (2020) Genomic epidemiology, evolutionary, and transmission dynamics of porcine deltacoronavirus. Mol. Biol. Evol. (in press).
  14. Mavian, C., Kosakovsky Pond, S., Marini, S., Rife Magalis, B., Vandamme, A.-M., Dellicour, S., Scarpino, S. V., Houldcroft, C., Villabona-Arenas, J., Paisie, T. K., Trovão, N. S., Boucher, C., Zhang, Y., Scheuermann, R. H., Gascuel, O., Tsan-Yuk Lam, T., Suchard, M. A., Abecasis, A., Wilkinson, E., de Oliveira, T., Bento, A. I., Schmidt, H. A., Martin, D., Hadfield, J., Faria, N., Grubaugh, N. D., Neher, R. A., Baele, G., Lemey, P., Stadler, T., Albert, J., Crandall, K. A., Leitner, T., Stamatakis, A., Prosperi, M., Salemi, M. (2020) Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-CoV-2 infections unreliable. Proc. Natl. Acad. Sci. USA 117(23): 12522-12523.
  15. Baele, G., Gill, M. S., Bastide, P., Lemey, P., Suchard, M. A. (2020) Markov-modulated continuous-time Markov chains to identify site- and branch-specific evolutionary variation in BEAST. Syst. Biol. (in press).
  16. Holbrook, A. J., Lemey, P., Baele, G., Dellicour, S., Brockmann, D., Rambaut, A., Suchard, M. A. (2020) Massive parallelization boosts big Bayesian multidimensional scaling. J. Comp. Graph. Stat. (in press).
  17. Peña, V., Vieira, C., Braga, J. C., Aguirre, J., Rösler, A., Baele, G., De Clerck, O., Le Gall, L. (2020) Radiation of the coralline red algae (Corallinophycidae, Rhodophyta) crown group as inferred from a multilocus time-calibrated phylogeny. Mol. Phyl. Evol. 150: 106845.
  18. Gill, M. S., Lemey, P., Rambaut, A., Suchard, M. A., Baele, G. (2020) Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction. Mol. Biol. Evol. 37(6): 1832-1842.
  19. Vrancken, B., Wawina-Bokalanga, T., Vanmechelen, B., Martí-Carreras, J., Carroll, M. W., Nsio, J., Kapetshi, J., Makiala-Mandanda, S., Muyembe-Tamfum, J., Baele, G., Vermeire, K., Vergote, V., Ahuka-Mundeke, S., Maes, P. (2020) Accounting for population structure reveals ambiguity in the Zaire Ebolavirus reservoir dynamics. Plos. Negl. Trop. Dis. 14(3): e0008117.
  20. Hong, S. L., Dellicour, S., Vrancken, B., Suchard, M. A., Pyne, M. T., Hillyard, D. R., Lemey, P., Baele, G. (2020) In search of covariates of HIV-1 subtype B spread in the United States - A cautionary tale of large-scale Bayesian phylogeography. Viruses 12(2), 182.
  21. Leone, A., Puncher, G. N., Ferretti, F., Sperone, E., Tripepi, S., Micarelli, P., Gambarelli, A., Sarà, M., Arculeo, M., Doria, G., Garibaldi, F., Dall’Asta, A., Minelli, D., Cilli, E., Vanni, S., Serena, F., Díaz-Jaimes, P., Baele, G., Tinti, F., Cariani, A. (2019) Pliocene colonization of the Mediterranean by Great White Shark inferred from fossil records, historical jaws, phylogeographic and divergence time analyses. J. Biogeogr. 47(5): 1119-1129.
  22. Dellicour, S., Lemey, P., Artois, J., Lam, T. T., Fusaro, A., Monne, I., Cattoli, G., Kuznetsov, D., Xenarios, I., Dauphin, G., Kalpravidh, W., Von Dobschuetz, S., Claes, F., Newman, S. H., Suchard, M. A., Baele, G.*, Gilbert, M.* (2019) Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference – application to H5N1 spread in the Mekong region. Bioinformatics. (in press) (*authors contributed equally)
  23. Gallone, B., Steensels, J., Mertens, S., Dzialo, M. C., Gordon, J. L., Wauters, R., Theßeling, F. A., Bellinazzo, F., Saels, V., Herrera-Malaver, B., Prahl, T., White, C., Hutzler, M., Meußdoerffer, F., Malcorps, P., Souffriau, B., Daenen, L., Baele, G., Maere, S., Verstrepen, K. J. (2019) Interspecific hybridization facilitates niche adaptation in beer yeast. Nature Ecol. Evol. 3:1562–1575.
  24. Grubaugh, N. D., Saraf, S., Gangavarapu, K., Watts, A., Tan, A. L., Oidtman, R. J., Ladner, J. T., Oliveira, G., Matteson, N. L., Kraemer, M. U. G., Vogels, C. B. F., Hentoff, A., Batia, D., Stanek, D., Scott, B., Landis, V., Stryker, I., Cone, M. R., Kopp IV, E. W., Cannons, A. C., Heberlein-Larson, L., White, S., Gillis, L. D., Ricciardi, M. J., Kwal, J., Lichtenberger, P. K., Magnani, D. M., Watkins, D. I., Palacios, G., Hamer, D. H., GeoSentinel Surveillance Network, Gardner, L. M., Perkins, T. A., Baele, G., Khan, K., Morrison, A., Isern, S., Michael, S. F., Andersen, K. G. (2019) Travel surveillance and genomics uncover a hidden Zika outbreak during the waning epidemic. Cell 178(5):1057–1071.
    Journal cover ; Video abstract
  25. Faria, N. R., Vidal, N., Lourenco, J., Raghwani, J., Sigaloff, K. C. E., Tatem, A. J., van de Vijver, D. A. M. C., Pineda, A. C., Rose, R., Wallis, C. L., Ahuka-Mundeke, S., Muyembe-Tamfum, J. J., Muwonga, J., Suchard, M. A., Rinke de Wit, T. F., Hamers, R. L., Ndembi, N., Baele, G., Peeters, M., Pybus, O. G., Lemey, P., Dellicour, S. (2019). Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa. PLoS Path. (in press).
  26. Dellicour, S., Troupin, C., Jahanbakhsh, F., Salama, A., Massoudi, S., Moghaddam, M., Baele, G., Lemey, P., Gholami, A., Bourhy, H. (2019) Using phylogeographic approaches to analyse the dispersal history, velocity, and direction of viral lineages – application to rabies virus spread in Iran. Mol. Ecol. 28(18):4335–4350.
  27. Bletsa, M., Suchard, M. A., Ji, X., Gryseels, S., Vrancken, B., Baele, G., Worobey, M., Lemey, P. (2019) Divergence dating using mixed effects clock modelling: an application to HIV-1. Virus Evol. 5(2): vez036.
  28. Hill, V., Baele, G. (2019) Bayesian estimation of past population dynamics in BEAST 1.10 using the Skygrid coalescent model. Mol. Biol. Evol. 36(11): 2620–2628.
  29. Theys, K., Vandamme, A.-M., Lemey, P., Baele, G. (2019) Advances in visualisation tools for phylogenomic and phylodynamic studies of viral diseases. Front. Public Health 7:208.
  30. Membrebe, J. V., Suchard, M. A., Rambaut, A., Baele, G., Lemey, P. (2019) Bayesian inference of evolutionary histories under time-dependent substitution rates. Mol. Biol. Evol. 36(8):1793–1803.
  31. Ayres, D. L., Cummings, M. P., Baele, G., Darling, A. E., Lewis, P. O., Swofford, D. L., Huelsenbeck, J. P., Lemey, P., Rambaut, A., Suchard, M. A. (2019) BEAGLE 3: Improved performance, scaling, and usability for a high-performance computing library for statistical phylogenetics. Syst. Biol. 68(6): 1052–1061.
  32. Laenen, L., Vergote, V., Vanmechelen, B., Tersago, K., Baele, G., Lemey, P., Leirs, H., Dellicour, S., Vrancken, B., Maes, P. (2019) Identifying the patterns and drivers of Puumala hantavirus enzootic dynamics using reservoir sampling. Virus Evol. 5(1): vez009.
  33. Baele, G., Dellicour, S., Suchard, M. A., Lemey, P., Vrancken, B. (2018) Recent advances in computational phylodynamics. Curr. Opin. Virol. 31: 24-32.
  34. Faria, N. R., Kraemer, M. U. G., Hill, S., Goes de Jesus, J., Aguiar, R. S., Iani, F. C. M., Xavier, J., Quick, J., du Plessis, L., Dellicour, S., Theze, J., Carvalho, R. D. O., Baele, G., Wu, C.-H., Silveira, P. P., Arruda, M. B., Pereira, M. A., Pereira, G. C., Lourenco, J., Obolski, U., Abade, L., Vasylyeva, T., Giovanetti, M., Li, D., Weiss, D. J., Wint, W. G. R., Shearer, F. M., Funk, S., Nikolay, B., Adelino, T. E. R., Oliveira, M. A. A., Silva, M. V. F., Sacchetto, L., Figueiredo, P. O., de Rezende, I. M., Mello, E. M., Said, R. F. C., Santos, D. A., Ferraz, M. L., Brito, M. G., Santana, L. F., Menezes, M. T., Brindeiro, R. M., Tanuri, A., dos Santos, F. C. P., Cunha, M. S., Nogueira, J. S., Rocco, I. M., da Costa, A. C., Komninakis, S. C. V., Azevedo, V., Chieppe, A. O., Araujo, E. S. M., Mendonca, M. C. L., dos Santos, C. C., dos Santos, C. D., Mares-Guia, M. A., Nogueira, R. M. R., Sequeira, P. C., Abreu, R. G., Garcia, M. H. O., Abreu, A. L., Okumoto, O., Kroon, E. G., de Albuquerque, C. F. C., Lewandowski, K., Pullan, S. T., Carroll, M., Sabino, E. C., Souza, R. P., Suchard, M. A., Lemey, P., Trindade, G. S., Drumond, B. P., Filippis, A. M. B., Loman, N., Cauchemez, S., Alcantara, L. C. Jr., Pybus, O. G. (2018) Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science 31(361): 894-899.
  35. Suchard, M. A., Lemey, P., Baele, G., Ayres, D. L., Drummond, A. J., Rambaut, A. (2018) Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 4(1): vey016.
  36. Rambaut, A., Drummond, A. J., Xie, D., Baele, G., Suchard, M. A. (2018) Posterior summarisation in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67(5): 901-904.
  37. Dellicour, S., Baele, G., Dudas, G., Faria, N. R., Pybus, O. G., Suchard, M. A., Rambaut, A., Lemey, P. (2018) Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak. Nature Comms. 9: 2222.
  38. Tolkoff, M. R., Alfaro, M. E., Baele, G., Lemey, P., Suchard, M. A. (2018) Phylogenetic factor analysis. Syst. Biol. 67(3): 384-399.
  39. 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. (2017). Host genetic variation does not determine spatio-temporal patterns of European bat 1 lyssavirus. Genome Biol. Evol. 9(11): 3202-3213.
  40. Libin, P., Vanden Eynden, E., Incardona, F., Nowé, A., Bezenchek, A., EucoHIV study group, Sönnerborg, A., Vandamme A.-M., Theys, K., Baele, G. (2017) PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context. Bioinformatics. 33(24): 3993-3995.
  41. Al-Qahtani, A. A., Baele, G., Khalaf, N., Suchard, M. A., Al-Anazi, M. R., Abdo, A. A., Sanai, F. M., Al-Ashgar, H. I., Khan, M. Q., Al-Ahdal, M. N., Lemey, P., Vrancken, B. (2017) The epidemic dynamics of hepatitis C virus subtypes 4a and 4d in Saudi Arabia. Sci. Rep. 7:44947.
  42. Dudas, G., Carvalho, L. M., Bedford, T., Tatem, A. J., Baele, G., Faria, N., Park, D., Ladner, J., Arias, A., Asogun, D., Bielejec, F., Caddy, S., Cotten, M., Dambrozio, J., Dellicour, S., Di Caro, A., Diclaro, J., Duraffour, S., Elmore, M., Fakoli, L., Gilbert, M., Gevao, S. M., Gire, S., Gladden-Young, A., Gnirke, A., Goba, A., Grant, D., Haagmans, B., Hiscox, J., Jah, U., Kargbo, B., Kugelman, J., Liu, D., Lu, J., Malboeuf, C., Mate, S., Matthews, D., Matranga, C., Meredith, L., Qu, J., Quick, J., Pas, S., Phan, M., Poliakis, G., Reusken, C., Sanchez-Lockhart, M., Schaffner, S., Schieffelin, J., Sealfon, R., Simon-Loriere, E., Smits, S., Stoecker, K., Thorne, L., Tobin, E. A., Vandi, M., Watson, S., West, K., Whitmer, S., Wiley, M., Winnicki, S., Wohl, S., Wölfel, R., Yozwiak, N., Andersen, K., Blyden, S., Bolay, F., Dahn, B., Carroll, M., Diallo, B., Formenty, P., Fraser, C., Gao, G., Garry, R., Goodfellow, I., Günther, S., Happi, C., Holmes, E., Kargbo, B., Kellam, P., Koopmans, M., Loman, N., Magassouba, N., Naidoo, D., Nichol, S., Nyenswah, T., Palacios, G., Pybus, O. G., Sabeti, P., Sall, A., Sakoba, K., Ströeher, U., Wurie, I., Suchard, M. A., Lemey, P., Rambaut, A. (2017) Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature 544(7650): 309-315.
  43. Baele, G., Lemey, P., Rambaut, A., Suchard, M. A. (2017) Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST. Bioinformatics 33(12): 1798-1805.
  44. Gill, M. S., Ho, L. S. T., Baele, G., Lemey, P., Suchard, M. A. (2017) A relaxed directional random walk model for phylogenetic trait evolution. Syst. Biol. 66(3): 299-319.
  45. Bielejec, F., Baele, G., Rodrigo, A. G., Suchard, M. A., Lemey, P. (2016) Identifying predictors of time-inhomogeneous viral evolutionary processes. Virus Evol. 2(2): vew023.
  46. Gallone, B., Steensels, J., Prahl, T., Soriaga, L., Saels, V., Herrera, 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, K. J. (2016) Domestication and divergence of Saccharomyces cerevisiae beer yeasts. Cell 166(6), 1397-1410.
  47. Baele, G., Suchard, M. A., Rambaut, A., Lemey, P. (2017) Emerging concepts of data integration in pathogen phylodynamics. Syst. Biol. 66(1):e47–e65.
  48. Bielejec, F., Baele, G., Vrancken, B., Suchard, M. A., Rambaut, A., Lemey, P. (2016) SpreaD3: interactive visualisation of spatiotemporal history and trait evolutionary processes. Mol. Biol. Evol. 33(8), 2167-2169.
  49. Baele, G., Suchard, M. A., Bielejec, F., Lemey, P. (2016) Bayesian codon substitution modeling to identify sources of pathogen evolutionary rate variation. Microb. Gen. 2(6), e000057.
  50. Vrancken, B., Trovão, N. S., Baele, G., Van Wijngaerden, E., Vandamme, A.-M., Van Laethem, K., Lemey, P. (2016) Quantifying next generation sequencing sample pre-processing bias in HIV-1 complete genome sequencing. Viruses 8(1), 12.
  51. Theys, K., Van Laethem, K., Gomes, P., Baele, G., Pineda-Peña, A.-C., Vandamme, A.-M., Camacho, R., Abecasis, A. B., on behalf of the Portuguese HIV-1 Resistance Study Group. (2016) 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. AIDS Res. Hum. Retroviruses 32(5), 427-433.
  52. Baele, G., Lemey, P., Suchard, M. A. (2016) Genealogical working distributions for Bayesian model testing with phylogenetic uncertainty. Syst. Biol. 65(2), 250-264.
  53. Trovão, N. S., Baele, G., Vrancken, B., Bielejec, F., Suchard, M. A., Fargette, D., Lemey, P. (2015) Host ecology determines the dispersal patterns of a plant virus. Virus Evol. 1(1), vev016.
  54. Trovão, N. S., Suchard, M. A., Baele, G., Gilbert, M., Lemey, P. (2015) Bayesian inference reveals host-specific contributions to the epidemic expansion of Influenza A H5N1. Mol. Biol. Evol. 32(12), 3264-3275.
  55. Vrancken, B., Baele, G., Vandamme, A.-M., Van Laethem, K., Suchard, M. A., Lemey, P. (2015) Disentangling the impact of within-host evolution and transmission dynamics on the tempo of HIV-1 evolution. AIDS 29(12), 1549-1556.
  56. Faria, N. R., Rambaut, A., Suchard, M. A., Baele, G., Bedford, T., Ward, M. J., Tatem, A. J., Sousa, J. D., Arinaminpathy, N., Pépin, J., Posada, D., Peeters, M., Pybus, O. G., Lemey, P. (2014) The early spread and epidemic ignition of HIV-1 in human populations. Science 346(6205), 56-61.
  57. Vanneste, K., Baele, G., Maere, S., Van de Peer, Y. (2014) Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary. Genome Res. 24, 1334-1347.
  58. Bielejec, F., Lemey, P., Carvalho, L. M., Baele, G., Rambaut, A., Suchard, M. A. (2014) πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios. BMC Bioinformatics 15:133.
  59. Bielejec, F., Lemey, P., Baele, G., Rambaut, A., Suchard, M. A. (2014) Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography. Syst. Biol. 63(4), 493-504.
  60. Nunes, M. R. T., Palacios, G., Faria, N. R., Costa Sousa Jr., E., Pantoja, J. A., Rodrigues, S. G., Carvalho, V. L., Medeiros, D. B. A., Savji, N., Baele, G., Suchard, M. A., Lemey, P., Vasconcelos, P. F. C., Lipkin, W. I. (2014) Air travel is associated with intracontinental spread of dengue virus serotypes 1-3 lineages in Brazil. PLoS Neglect. Trop. D. 8(4): e2769.
  61. Vrancken, B., Rambaut, A., Suchard, M. A., Drummond, A. J., Baele, G., Derdelinckx, I., Van Wijngaerden, E., Vandamme, A.-M., Van Laethem, K., Lemey, P. (2014) The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates. PLoS Comp. Biol. 10(4): e1003505.
  62. Lemey, P., Rambaut, A., Bedford, T., Faria, N. R., Bielejec, F., Baele, G., Russell, C. A., Smith, D. J., Pybus, O. G., Brockmann, D., Suchard, M. A. (2014) Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2. PLoS Pathog. 10(2), e1003932.
  63. Baele, G., Lemey, P. (2013) Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency. Bioinformatics 29(16), 1970-1979.
  64. Baele, G., Lemey, P., Vansteelandt, S. (2013) Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution. BMC Bioinformatics 14, 85.
  65. Baele, G., Li, W. L. S., Drummond, A. J., Suchard, M. A., Lemey, P. (2013) Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics. Mol. Biol. Evol. 30(2), 239-243.
  66. Baele, G., Lemey, P., Bedford, T., Rambaut, A., Suchard, M. A., Alekseyenko, A. V. (2012) Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol. Biol. Evol. 29(9), 2157-2167.
  67. Baele, G. (2012) Context-dependent evolutionary models for non-coding sequences: an overview of several decades of research and an analysis of Laurasiatheria and Primate evolution. Evol. Biol. 39(1), 61-82.
  68. Grbić, M., Van Leeuwen, T., Clark, R. M., Rombauts, S., Rouzé, P., Grbić, V., Osborne, E. J., Dermauw, W., Thi Ngoc Cao, P., Ortego, F., Hernández-Crespo, P., Diaz, I., Martinez, M., Navajes, M., Sucena, E., Magalhães, S., Nagy, L., Pace, R. M., Djuranović, S., Smagghe, G., Iga, M., Christiaens, O., Veenstra, J. A., Ewer, J., Villalobos, R. M., Hutter, J. L., Hudson, S. D., Velez, M., Yi, S. V., Zeng, J., Pires-daSilva, A., Roch, F., Cazaux, M., Navarro, M., Zhurov, V., Acevedo, G., Bjelica, A., Fawcett, J. A., Bonnet, E., Martens, C., Baele, G., Wissler, L., Sanchez-Rodriguez, A., Tirry, L., Blais, C., Demeestere, K., Henz, S. R., Gregory, T. R., Mathieu, J., Verdon, L., Farinelli, L., Schmutz, J., Lindquist, E., Feyereisen, R., Van de Peer, Y. (2011) The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature 479, 487-492.
  69. Baele, G., Van de Peer, Y., Vansteelandt, S. (2011) Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes. BMC Evol. Biol. 11, 145.
  70. Yao, Y., Baele, G., Van de Peer, Y. (2011) A bio-inspired agent-based system for controlling robot behaviour. IEEE Symposium Series in Computational Intelligence, Symposium on Intelligent Agents organized in the IEEE Symposium Series in Computational Intelligence 2011, Paris, France.
  71. Baele, G., Van de Peer, Y., Vansteelandt, S. (2010) Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences. BMC Evol. Biol. 10, 244.
  72. Baele, G., Van de Peer, Y., Vansteelandt, S. (2010) Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding sequences. J. Mol. Evol. 71(1), 34-50.
  73. De Lobel, L., Geurts, P., Baele, G., Castro-Giner, F., Kogevinas, M., Van Steen, K. (2010) A screening methodology based on Random Forests to improve the detection of gene-gene interactions. Eur. J. Hum. Genet. 18, 1127-1132.
  74. Kernbach, S., Hamann, K., Stradner, J., Thenius, R., Schmickl, T., Crailsheim, K., van Rossum, A. C., Sebag, M., Bredeche, N., Yao, Y., Baele, G., Van de Peer, Y., Timmis, J., Mokhtar, M., Tyrrell, A., Eiben, A. E., McKibbin, S. P., Liu, W., Winfield, A. F. T. (2009) On adaptive self-organization in artificial robot organisms. Computation World: Future Computing, Service Computation, Cognitive, Adaptive, Content, Patterns, 33-43.
  75. Deventer, K., Van Eenoo, P., Baele, G., Pozo, J., Van Thuyne, W., Delbeke, T. (2009) Interpretation of urinary concentrations of pseudoephedrine and its metabolite cathine in relation to doping control. Drug Test. Analysis 1(5), 209-213.
  76. Baele, G., Van de Peer, Y., Vansteelandt, S. (2009) Efficient context-dependent model building based on clustering posterior distributions for non-coding sequences. BMC Evol. Biol. 9, 87.
  77. Baele, G., Bredeche, N., Haasdijk, E., Maere, S., Michiels, N., Van de Peer, Y., Schmickl, T., Schwarzer, C., Thenius, R. (2009) Open-ended On-board Evolutionary Robotics for Robot Swarms. Proceedings of the 2009 IEEE Congress On Evolutionary Computation, 1123-1130.
  78. Deventer, K., Baele, G., Van Eenoo, P., Pozo, J., Delbeke, T. (2008) Stability of selected chlorinated thiazide diuretics. J. Pharma. Biomed. Anal. 49, 519-24.
  79. Baele, G., Van de Peer, Y., Vansteelandt, S. (2008) A model-based approach to study nearest-neighbor influences reveals complex substitution patterns in non-coding sequences. Syst. Biol. 57(5), 675-92.
  80. Baele, G., Raes, J., Van de Peer, Y., Vansteelandt, S. (2006). An improved statistical method for detecting heterotachy in nucleotide sequences. Mol. Biol. Evol. 23(7), 1397-1405.

Book chapters/contributions

  1. Zhukova, A., Gascuel, O., Duchêne, S., Ayres, D. L., Lemey, P., Baele, G. (2020) Efficiently analysing large viral data sets in computational phylogenomics. Book chapter in 'Phylogenetics in the genomic era'. Open Access, licensed under CC BY-NC-ND 4.0. Editors: C. Scornavacca, F. Delsuc, N. Galtier.
  2. Ayres, D. L., Lemey, P., Baele, G., Suchard, M. A. (2020) BEAGLE 3 high-performance computational library for phylogenetic inference. Book chapter in 'Phylogenetics in the genomic era'. Open Access, licensed under CC BY-NC-ND 4.0. Editors: C. Scornavacca, F. Delsuc, N. Galtier.
  3. Baele, G., Ayres, D. L., Rambaut, A., Suchard, M. A., Lemey, P. (2019). High-performance computing in Bayesian phylogenetics and phylodynamics using BEAGLE. Book chapter in 'Evolutionary Genomics: Statistical & Computational Methods, 2nd edition', pages 691-722. Springer. Editor: M. Anisimova.
  4. Baele, G., Lemey, P. (2014). Bayesian model selection in phylogenetics and genealogy-based population genetics. Book chapter in 'Bayesian Phylogenetics: Methods, Computational Algorithms, and Applications'. (Chapman & Hall/CRC Mathematical & Computational Biology). Editors: M.-H. Chen, L. Kuo, P. O. Lewis. ISBN-10: 1466500794. ISBN-13: 978-1466500792.
  5. Baele, G., Yao, Y., Van de Peer, Y., Winfield, A., Kernbach, S. (2010). Adaptive control mechanisms. Springer book chapter contribution in 'Symbiotic multi-robot organisms'. Editors: P. Levi, S. Kernbach. ISBN: 978-3-642-11691-9.

 

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