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
(16) Smoot, M., Ono, K., Ideker, T., Maere, S. (2011) PiNGO: a Cytoscape plugin to find candidate genes in biological networks. Bioinformatics 27:1030-1.
(15) Van Leene, J., Hollunder, J., Eeckhout, D., Persiau, G., Van De Slijke, E., Stals, H., Van Isterdael, G., Verkest, A., Neirynck, S., Buffel, Y., De Bodt, S., Maere, S., Laukens, K., Pharazyn, A., Ferreira, P.C., Eloy, N., Renne, C., Meyer, C., Faure, J.D., Steinbrenner, J., Beynon, J., Larkin, J.C., Van de Peer, Y., Hilson, P., Kuiper, M., De Veylder, L., Van Onckelen, H., Inzé, D., Witters, E., De Jaeger, G. (2010) Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Mol Syst Biol. 10:397.
(14) Van de Peer, Y., Maere, S., Meyer, A. (2010) 2R or not 2R is not the question anymore. Nat Rev Genet doi:10.1038/nrg2600-c2 (Correspondence on Nat Rev Genet 10:725-32)
(13) 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)
(12) Van de Peer, Y., Maere, S., Meyer, A. (2009) The evolutionary significance of ancient genome duplications. Nat Rev Genet 10:725-32.
(11) 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.
(10) * 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.
(9) Maere, S., Van Dijck, P., Kuiper, M. (2008) Extracting expression modules from perturbational gene expression compendia. BMC Systems Biology 2:33.
(8) * 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.
(7) 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.
(6) 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.
(5) 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.
(4) 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.
(3) * De Bodt, S., * Maere, S., Van de Peer, Y. (2005) Genome duplication and the origin of angiosperms. Trends Ecol. Evol. 20, 591-7.
(2) 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.
(1) * 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
Computational Systems Biology
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. One of our main interests is the development of methods to analyze functional genomics data and integrate them in models that reflect the regulatory wiring and modularity of biological systems, and ultimately predict their behavior. We are also developing user-friendly computational tools to assist wet-lab researchers in the interpretation of large-scale datasets and biological networks.
Evolution of Biological Systems
We are especially interested in figuring out how biological systems evolve. One particular aspect that we study intensively, in collaboration with the Van de Peer lab, is how gene and genome duplications affect the evolution of organisms. Expansion of gene families by duplication and subsequent functional diversification is considered of major importance for the development of biological novelties during evolution. However, we have only begun to elucidate the mechanisms underlying evolutionary innovation through gene duplication. Recent studies have shown that regulatory gene duplicates (transcription factors, signal transducers and developmental genes) have been retained in excess after genome duplications in A. thaliana and other organisms. More importantly, it seems that duplicates in many regulatory gene families are retained almost exclusively after genome duplication, suggesting a key role for large-scale gene duplication events in plant evolution. In addition, we found indications that genome duplications are mainly evolutionary successful under certain circumstances, e.g. after mass extinction events, raising the intriguing possibility that ecological catastrophes may ultimately lead to more complex plants.