Stefanie De Bodt

Postdoc
(Group member from 2000 until 2011)


+ 32 (0) 9 33 13 692

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

CV

Date of birth: March 11th, 1979
Place of birth: Ghent, Belgium

February 2006 - now: Postdoctoral position in the Bioinformatics and Evolutionary Genomics Group of Yves Van de Peer, Department of Plant Systems Biology, VIB, University Ghent, Belgium.

April 2004 - February 2006: PhD studies "Effects of gene and genome duplication on the development and evolution of angiosperms". Bioinformatics and Evolutionary Genomics Group of Yves Van de Peer, Department of Plant Systems Biology, VIB, University Ghent, Belgium.

October 2003 - March 2004: European Science Foundation (ESF) exchange grant, Program Integrated Approaches for Functional Genomics, Comparative promoter analysis of DEF- and GLO-like MADS-box genes in eudicot plants. Genetics Chair of Guenter Theissen, Friedrich-Schiller University, Jena, Germany.

October 2001 - October 2003: PhD studies "Effects of gene and genome duplication on the development and evolution of angiosperms". Bioinformatics and Evolutionary Genomics Group of Yves Van de Peer, Department of Plant Systems Biology, VIB, University Ghent, Belgium.

1999 - 2001: Biotechnology, University Ghent, Belgium.

1997 - 1999: Chemistry, University Ghent, Belgium.

Research

Evolution of duplicated genes and genomes

Studying the structure and evolution of plant MADS-box genes, I was fascinated by the enormous diversity of flowering plants (De Bodt et al. 2005b). Wondering how a wide range of floral morphologies came about, I took my first steps in bioinformatics and realized the power of computational methods and whole-genome data in exploring plant evolutionary biology. Soon, I was struck by the high number of transcription factor encoding genes and troubled by fact that we did not have a clue on the function of a high number of genes (De Bodt et al. 2003a; 2003b). Exploring all duplicated genes of the Arabidopsis genome, we investigated how and when these genes were created. We observed that genes with particular functions (such as transcription factors, signal transducers and developmental genes) had been preferentially retained after whole-genome duplication (Maere et al. 2005). This is in clear contrast with genes involved in, for instance, secondary metabolism and response to biotic stimuli, which had been preferentially retained after small-scale gene duplication or with genes that had been poorly retained overall (such as genes involved in DNA metabolism and cell cycle). Inevitably, my interest in the mechanisms underlying these evolutionary patterns grew. Functional divergence of duplicated genes could explain the retention of a high number of transcription factor encoding genes (e.g. a MADS-box gene) as this could allow for the evolution of novel features (e.g. a novel floral organ structure) (De Bodt et al. 2003; 2005). Nevertheless, studying the expression (Casneuf et al. 2006) and promoter divergence (De Bodt et al. 2006) of duplicated genes points to a considerable number of duplicated genes with redundant expression patterns. Consequently, we aim to determine the impact of factors, such as gene dosage, genomic and environmental context, on the fate of duplicated genes.

Detection of plant miRNAs and miRNA targets

Recently, a totally new level of regulatory control was discovered in higher plants and animals. MicroRNAs, tiny genome-encoded regulators, were shown to have crucial roles in, for instance, diverse developmental pathways. In plants, the activity of miRNAs relies on the recognition of a miRNA binding site in the coding part of the target gene. Upon binding, the mRNA of the target genes is cleaved by RISC. A few hundred miRNA genes have been identified in the genome of higher plants such as Arabidopsis, poplar and rice (Bonnet et al. 2004; 2006). Although some miRNA genes are conserved throughout the plant kingdom, evidence grows on the presence of lineage or species-specific miRNAs in plants. Through a comparative approach, we aim to detect highly specific miRNAs in closely related plant species. As such, we attempt to identify miRNAs, which have a regulatory role in agronomically interesting processes, specific to certain plant lineages.

Papers

(15) Szakonyi, D., Van Landeghem, S., Baerenfaller, K., Baeyens, L., Blomme, J., Casanova-Sáez, R., De Bodt, S., Esteve-Bruna, D., Fiorani, F., Gonzalez, A., Grønlund, J., G.H. Immink, R., Jover-Gil, S., Kuwabara, A., Muñoz-Nortes, T., D.J. van Dijk, A., Wilson-Sánchez, D., Buchanan-Wollaston, V., C. Angenent, G., Van de Peer, Y., Inzé, D., Luis Micol, J., Gruissem, W., Walsh, S., Hilson, P. (2015) The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining. Current Plant Biology 2:1-11.

(14) Vercruyssen, L., Verkest, A., Gonzalez, A., Heyndrickx, KS., Eeckhout, D., Han, B., Jégu, T., Archacki, R., Van Leene, J., Andriankaja, M., De Bodt, S., Abeel, T., Coppens, F., Dhondt, S., De Milde, L., Vermeersch, M., Maleux, K., Gevaert, O., Jerzmanowski, A., Benhamed, M., Wagner, D., Vandepoele, K., De Jaeger, G., Inzé, D. (2014) ANGUSTIFOLIA3 Binds to SWI/SNF Chromatin Remodeling Complexes to Regulate Transcription during Arabidopsis Leaf Development. The Plant Cell 26(1):210-29 .

(13) Van Landeghem, S., De Bodt, S., Drebert, Z. J., Inzé, D., Van de Peer, Y. (2013) The potential of text mining in data integration and network biology for plant research: a case study on Arabidopsis. The Plant Cell 25(3):794-807.

(12) Verelst, W., Bertolini, E., De Bodt, S., Vandepoele, K., Demeulenaere, M., Enrico Pe, M., Inzé, D. (2012) Molecular and physiological analysis of growth-limiting drought stress in Brachypodium distachyon leaves. Molecular Plant 6(2):311-22.

(11) De Bodt, S., Carvajal, D., Hollunder, J., Van den Cruyce, J., Movahedi, S., Inzé, D. (2010) CORNET: a user-friendly tool for data mining and integration. Plant Physiol. 152(3):1167-79.

(10) De Bodt, S., Proost, S., Vandepoele, K., Rouzé, P., Van de Peer, Y. (2009) Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. BMC Genomics 10:288.

(9) Smykal, P., Gennen, J., De Bodt, S., Ranganath, V., Melzer, S. (2007) Flowering of strict photoperiodic Nicotiana variaties in non-inductive conditions by transgenic approaches. Plant Mol. Biol. 65(3):233-42.

(8) 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 Biol. 7(2):R13.

(7) 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 Biol. 7(5):R43.

(6) De Bodt, S., Theissen, G., Van de Peer, Y. (2006) Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting. Mol. Biol. Evol. 23(6):1293-303.

(5) * 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(15):5454-9. *contributed equally

(4) * De Bodt, S., * Maere, S., Van de Peer, Y. (2005) Genome duplication and the origin of angiosperms. Trends Ecol. Evol. 20(11):591-7. *contributed equally

(3) Trindade, G.S., Da Fonseca, F.G., Marques, J.T., Diniz, S., Leite, J.A., De Bodt, S., Van de Peer, Y., Bonjardim, C.A., Ferreira, P.C.P., Kroon, E.G. (2004) The Belo Horizonte virus: a vaccinia-like virus lacking the A-type inclusion body gene isolated from infected mice. J. Gen. Virol. 85(Pt 7):2015-21.

(2) De Bodt, S., Raes, J., Van de Peer, Y., Theissen, G. (2003) And then there were many: MADS goes genomic. Trends Plant Science 8(10):475-83.

(1) De Bodt, S., Raes, J., Florquin, K., Rombauts, S., Rouzé, P., Theissen, G., Van de Peer, Y. (2003) Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants. J. Mol. Evol. 56(5):573-86.











Contact:
VIB / UGent
Bioinformatics & Evolutionary Genomics
Technologiepark 927
B-9052 Gent
BELGIUM
+32 (0) 9 33 13807 (phone)
+32 (0) 9 33 13809 (fax)

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