Maere Lab | Evolutionary Systems Biology
Steven Maere
1999 : M.Sc. Engineering Physics, Ghent University
2001 : M.Sc. Biotechnology, Ghent University
2002-2006: Predoctoral Fellow of the Research Foundation - Flanders (FWO)
2006 : PhD in Computational Biology
2006-now: Postdoctoral Fellow of the Research Foundation - Flanders (FWO)
2008-2009 : Visiting postdoc UC Berkeley (Eisen lab), sponsored by FWO, Fulbright and BAEF
2009-now : PI, Plant Systems Biology dept, VIB
Research
Group Leader
VIB / Ghent University
Evolutionary Systems Biology
Technologiepark 927
B-9052 Gent
BELGIUM
Publications
Maere, S., Van de Peer, Y. (2009) Duplicate retention after small‐ and large‐scale duplications. In: Evolution after gene duplication, Liberles, D.A. and Dittmar, K., eds., Wiley (in press)
Van de Peer, Y., Maere, S., Meyer, A. (2009) The evolutionary significance of ancient genome duplications. Nat Rev Genet (in press).
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 (CEC 2009), 1123-30.
* Fawcett, J., * Maere, S., Van de Peer, Y. (2009) Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc Natl Acad Sci 106, 5737-42.
Maere, S., Van Dijck, P., Kuiper, M. (2008) Extracting expression modules from perturbational gene expression compendia. BMC Systems Biology 2:33.
* Michoel, T., * Maere, S., Bonnet, E., Joshi, A., Saeys, Y., Van den Bulcke, T., Van Leemput, K., van Remortel, P., Kuiper, M., Marchal, K., Van de Peer, Y. (2007) Validating module networks learning algorithms using simulated data. BMC Bioinformatics 8, S5.
Fleury, D., Himanen, K., Cnops, G., Nelissen, B., Boccardi, T.M., Maere, S., Beemster, G.T.S., Neyt, P., Anami, S., Robles, P., Micol, J.S., Inzé, D., Van Lijsebettens, M. (2007) The Arabidopsis thaliana homolog of yeast BRE1 has a function in cell cycle regulation during early leaf and root growth. Plant Cell 19, 417-32.
Cline, M.S., Smoot, M., Cerami, E., Kuchinsky, A., Landys, N., Workman, C., Christmas, R., Avila-Campilo, I., Creech, M., Gross, B., Hanspers, K., Isserlin, R., Kelley, R., Killcoyne, S., Lotia, S., Maere, S., Morris, J., Ono, K., Pavlovic, V., Pico, A.R., Vailaya, A., Wang, X., Adler, A., Conklin, B.R., Hood, L., Kuiper, M., Sander, C., Schmulevich, I., Schwikowski, B., Warner, G.J., Ideker, T., Bader, G.D. (2007) Integration of biological networks and gene expression data using Cytoscape. Nature Protocols 2, 2366 - 2382.
Casneuf, T., De Bodt, S., Raes, J., Maere, S., Van de Peer, Y. (2006) Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biology 7, R13.
Blomme, T., Vandepoele, K., De Bodt, S., Simillion, C., Maere, S., Van de Peer, Y. (2006) The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biology 7, R43.
* De Bodt, S., * Maere, S., Van de Peer, Y. (2005) Genome duplication and the origin of angiosperms. Trends Ecol. Evol. 20, 591-7.
Maere, S., Heymans, K., Kuiper, M. (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. Bioinformatics 21, 3448-9.
* Maere, S., * De Bodt, S., Raes, J., Casneuf, T., Van Montagu, M., Kuiper, M., Van de Peer, Y. (2005) Modeling gene and genome duplications in eukaryotes. Proc. Natl. Acad. Sci. USA 102, 5454-9.
*contributed equally
Modeling Biological Systems
With the availability of fully sequenced genomes and the development of high-throughput functional genomics technologies, we now have the tools to look at the molecular biology of an organism from a systemic viewpoint. Systems biology is a dynamic and highly interdisciplinary field, requiring input from biology as well as engineering, physics and mathematics. Our main interest is to develop computational methods to analyze functional genomics data and build mathematical models that reflect the regulatory wiring of biological systems. We currently focus on modeling the development of lateral roots in the model plant Arabidopsis thaliana.
Evolution of Biological Systems
Expansion of gene families by duplication and subsequent functional diversification is considered to be of major importance for the development of biological novelties during evolution. However, we have only begun to elucidate the mechanisms underlying evolutionary innovation through gen(om)e duplication. Particularly, expansion and functional diversification of regulatory gene families is considered necessary to bring about an increase in morphological complexity. Recent studies in A. thaliana have found that transcription factors, signal transducers and developmental genes have been retained in excess after genome duplications. More importantly, it seems that the majority of these genes could have been retained only because they were created through genome duplication, suggesting a key role for large-scale gene duplication events in plant evolution (see Maere et al. PNAS 2005, De Bodt et al. TREE 2005, Fawcett et al. PNAS 2009).
We are studying the impact of small- and large-scale gene duplications in the evolution of plant complexity and developmental processes (evo-devo) from a systems biology perspective. Morphological evolution reflects the evolution of the underlying developmental networks, and it is therefore necessary to study the evolution of genetic networks in order to comprehend the evolution of organisms. We currently study the impact of duplication and functional diversification of AUX/IAAs and ARFs on the evolution of developmental processes in plants.