CV2009 - present: PhD student, Department of Plant Systems Biology and Bioinformatics, VIB - University of Ghent
2009 - present: Predoctoral Fellow of the Research Foundation - Flanders (FWO)
2004 - 2009: MSc in Biology, University of Ghent (specialization: major Research, minors Functional Biology and Evolution)
ResearchAs a traditional biologist, I always have had a strong interest in evolution. Whether talking about developmental biology, genetics, anatomy or ecology, it was always the link with evolution that fascinated me most. As a PhD student in the field of bioinformatics, I view computational biology as a tool to explore the concepts of (molecular) evolution. My main research focus is heavily concentrated around gene duplication. More and more, gene duplication appears to have been a major driving force in evolution of paramount importance. Whether we’re talking about small-scale gene duplications (SSDs) that happen constantly, or massive whole genome duplications (WGDs) that generate huge amounts of raw genetic material in one go, it seems the tinkering of evolution with these extra gene copies has played a major role in the establishment of several evolutionary innovations and complexities. My current research effort centers on the correct inference of WGDs from age distributions of duplicated genes, and the study of paranome expansion after WGD (e.g. Vanneste et al. 2012). I also have a keen interest in the study of small-scale gene duplications, which tells us more about the exact molecular mechanisms that are responsible for the establishment of new gene duplicates in the genome (e.g. Voordeckers et al. 2012). This work is done mainly on, but is not limited to, plants. These have experienced multiple, relatively recent, rounds of WGD and are therefore an ideal system to study the effects of gene duplication on both a small and a large scale.
Papers(6) De Wilde, K., De Buck, S., Vanneste, K., Depicker, A. (2013) Recombinant antibody production in Arabidopsis seeds triggers an unfolded protein response. Plant Physiololgy 161, 1021-33.
(5) Vanneste, K., Van de Peer, Y., Maere, S. (2013) Inference of genome duplications from age distributions revisited. Mol. Biol. Evol. 30, 177-90.
(4) Nystedt, B., Street, N. R., Zuccolo, A., Lin, Y.-C., Wetterbom, A., Vezzi, A., Scofield, D. G., Delhomme, N., Alexeyenko, A., Giacomello, S., Vicedomini, R., Sahlin, K., Sherwood, E., Elfstand, M., Gramzow, L., Holmberg, K., Hällman, J., Keech, O., Klasson, L., Koriabine, M., Kucukoglu, M., Käller, M., Luthman, J., Lysholm, F., Olson, A., Niittylä, T., Ritland, K., Rilakovic, N., Rosselló, J. A., Sena, J., Svensson, T., Talavera-López, C., Theißen, G., Vanneste, K., Tuominen, H., Zhang, J., Wu, Z., Zerbe, P., Bhalerao, R.P., Bohlmann, J., Arvestad, L., Bousquet, J., Garcia Gil, R., de Jong, P.J., Hvidsten, T. R., MacKay, J., Ritland, K., Morgante, M., Sundberg, B., Van de Peer, Y., Lee Thompson, S., Nilsson, O., Andersson, B., Lundeberg, J., Jansson, S. (2013) The 20 Gbp Norway spruce genome sheds light on conifer genome evolution. Nature (In Press).
(3) * Vandesteene, L., * Lopez-Galvis, L., Vanneste, K., Maere, S., Lammens, T., Rolland, F., Lunn, J., Avonce, N., Beeckman, T., Van Dijck, P. (2012) Expansive evolution of the Trehalose-6-phosphatase gene family in Arababidopsis thaliana. Plant Physiol. 160, 884-96. *contributed equally
(2) * Vekemans, D., * Proost, S., Vanneste, K., Coenen, H., Viaene, T., Ruelens, P., Maere, S., Van de Peer, Y., Geuten, K. (2012) Gamma paleohexaploidy in the stem-lineage of core eudicots: significance for MADS-box gene and species diversification. Mol. Biol. Evol. 29,3793-806. *contributed equally
(1) * Voordeckers, K., * Brown, M.T., Vanneste, K., van der Zande, E., Voet, A., Maere, S., Verstrepen, K.J. (2012) Reconstruction of ances metabolic enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplication. PloS Biolology 10, e1001446 . *contributed equally
VIB / UGent
Bioinformatics & Evolutionary Genomics
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