Steven Maere
Evolutionary Systems Biology
VIB Department of Plant Systems Biology, UGent

PhD: VIB-Ghent Univ., Ghent, Belgium, '06 Visiting postdoc: Univ California, Berkeley, USA, '08-'09 VIB Group leader as of October 2009

e-mail phone +32 9 331 37 58 ADDRESS

Current team members
Group leader: Steven Maere

Keywords
modeling - computational biology - lateral roots - genome duplication - genetic networks

Science
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.

Fawcett J, Maere S, Van de Peer Y
Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event
P NATL ACAD SCI USA 106, 5737-42, 2009



Van de Peer Y, Maere S, Meyer A
The evolutionary significance of ancient genome duplications
NAT REV GENET 10, 725-32, 2009



Maere S, Van Dijck P, Kuiper M
Extracting expression modules from perturbational gene expression compendia
BMC Syst Biol 2, 33, 2008



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
Validating module network learning algorithms using simulated data
BMC BIOINFORMATICS 8, S5, 2007



Fleury D, Himanen K, Cnops G, Nelissen H, Boccardi T, Maere S, Beemster G, Neyt P, Anami S, Robles P, Micol J, Inzé D, Van Lijsebettens M
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, 2007

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