Guy Baele

Postdoc
(Group member from 2003 until 2011)


+32 (0) 9 33 13 692

VIB / Ghent University
Bioinformatics & Systems Biology
Technologiepark 927
B-9052 Gent
BELGIUM

CV

Date of birth: February 11th, 1980.
Place of birth: Zottegem, Belgium.

  • February 2009 - now: Post-doctoral researcher for the Symbrion FP7 project in the Bioinformatics and Evolutionary Genomics Group of Yves Van de Peer, Department of Plant Systems Biology, VIB, University Ghent, Belgium.
  • February 2004 - January 2009: Teaching Assistant in the department of Applied Mathematics and Computer Science.
  • October 2003 - January 2009: PhD. studies 'Detecting complex substitution patterns in non-coding sequences'. Promotor: Prof. Dr. Stijn Vansteelandt (Department of Applied Mathematics and Computer Science); co-promotor: Prof. Dr. Yves Van de Peer (Department of Plant Systems Biology).
  • October 2001 - September 2003: Licentiate of Informatics: Application-oriented Informatics (M. Sc.).
  • October 1999 - September 2001: Candidate of Informatics (B. Sc.).


Reviewer for: BMC Evolutionary Biology, Journal of Molecular Evolution, Molecular Biology and Evolution, Recomb Conference Proceedings.

Research

Modelling the covarion/heterotachy hypothesis

Phylogenetics plays an important role in many areas of biology. Placing model organisms, as well as the genes they house, in the appropriate phylogenetic context allows for a better understanding of both patterns and processes of evolution. Over the past years different evolutionary models have been designed to infer phylogenetic trees. A "covarion" model for nucleotide substitution which allows sites to turn "on" and "off" with time was proposed many years ago by Fitch and Markowitz and several approaches to model heterotachy have been developed recently. It has been argued recently that evidence supports such models over later, alternative models which postulate a static distribution of rates across sites. Advanced covarion/heterotachy models are needed to allow for the correct reconstruction of phylogenetic trees. Using these models it should also be possible to detect functional divergence.

Modelling context-dependent evolution

While many phylogenetic analyses in the past have assumed independent evolution of the sites in alignment, the trend is shifting towards using more realistic assumptions when inferring phylogenetic trees. In the past, nucleotide models have been improved and continue to improved by codon models and models assuming a known secondary (or even tertiary) structure. In regions where there is few information concerning the structure, it can be assumed that dependencies upon other sites in the alignment can lead to improvements in explaining the data. It remains to be seen which assumptions will actually lead to different, and better supported, tree topologies and whether such complex models are actually preferred over independent models. To assess this a reliable method is needed to compare (non-nested) models, keeping the error margins at a low.

Evolutionary robotics

Evolutionary robotcs is a method for automatically generating artificial brains and morphologies of autonomous robots. The Symbrion project is a large-scale integrating project (FP7) with the main focus of investigating and developing novel principles of adaptation and evolution for symbiotic multi-robot organisms based on bio-inspired approaches and modern computing paradigms. The bio-inspired evolutionary paradigms combined with robot embodiment and swarm-emergent phenomena, enable the organisms to autonomously manage their own hardware and software organization.

Papers

(14) Vanneste, K., Baele, G., Maere, S., Van de Peer, Y. (2014) Analysis of 41 plant genomes supports a wave of successful genome duplications at the Cretaceous-Tertiary boundary. Genome Res. 24(8):1334-1347 .
(13) Grbic, M., Van Leeuwen, T., Clark, T. G., Rombauts, S., Rouzé, P., Grbic, V., Osborne, E., Dermauw, W., Thi Ngoc Cao, P., Ortego, F., Hernandez-Crespo, P., Diaz, I., Martinez, N.J., Navajas, M., Sucena, E., Magalhaes, S., Nagy, L., Pace, N.R., Djuranovic, S., Smagghe, G., Iga, M., Christiaens, M., Veenstra, J., Ewer, J., Mancilla Villalobos, R., Hutter, J., Hudson, A., Velez, M., Yi, S., Zeng, Q., Pires-daSilva, A., Roch, F., Cazaux, M., Navarro, M., Zhurov, V., Acevedo, G., Bjelica, A., Fawcett, J., Bonnet, E., Martens, C., Baele, G., Wissler, L., Sanchez-Rodriguez, A., Tirry, L., Blais, C., Demeestere, K., Henz, SR., Gregory, 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.
(12) 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.
(11) Yao, Y., Baele, G., Van de Peer, Y. (2011) A bio-inspired agent-based system for controlling robot behaviour. Proceedings of the IA - 2011 IEEE Symposium on Intelligent Agents organized in IEEE Symposium Series in Computational Intelligence 2011 Paris, France.
(10) 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.
(9) 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.
(8) 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(10):1127-32.
(7) Kernbach, S., Hamann, K., Stradner, J., Thenius, R., Schmickl, T., van Rossum, A. C., Sebag, M., Bredeche, N., Yao, Y., Baele, G., Van de Peer, Y., Timmis, K.N., 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.
(6) 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. Anal. 1(5):209-13.
(5) 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.
(4) 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.
(3) Deventer, K., Baele, G., Van Eenoo, P., Pozo, J., Delbeke, T. (2008) Stability of selected chlorinated thiazide diuretics. J. Pharm. Biomed. Anal. 49(2):519-24.
(2) 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.
(1) Baele, G., Raes, J., Van de Peer, Y., Vansteelandt, S. (2006) An improved statistical method for detecting heterotachy in nucleotidesequences. . Mol. Biol. Evol. 23(7):1397-405.








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