Vanessa Vermeirssen

Postdoc
(Group member since 2007)


+ 32 (0) 9 33 13 536

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

CV

  • Birth place and date: Dendermonde, January 15th 1977.
  • March 2007 - present: Postdoctoral researcher at Ghent University, VIB Department of Plant Systems Biology, Laboratory of Bioinformatics and Evolutionary Genomics. BELSPO return grant. Reverse-engineering of biological networks.
  • February 2004 - December 2006: Postdoctoral researcher at University of Massachusetts Medical School, USA, Program in Gene Function and Expression, Laboratory of A.J.M. Walhout, PhD, Functional Genomics. D. Collen Research Foundation-Belgian American Educational Foundation (BAEF) fellowship for Biomedical and Biotechnology Research in 2005. Mapping protein-DNA interaction networks in C. elegans by yeast one-hybrid.
  • May 2003: Ph.D. in Bioscience Engineering, Faculty of Bioscience Engineering, Ghent University "Release and activity of ACE inhibitory peptides from pea and whey protein: fermentation, in vitro digestion and transport", scientific promoters Prof. Dr. ir. W. Verstraete and Prof. Dr. ir. J. Van Camp.
  • October 1999 - September 2003: Predoctoral fellow at Ghent University, Faculty of Bioscience Engineering, Laboratory of Microbial Ecology and Technology and Laboratory of Food Chemistry and Nutrition. FWO aspirant (Fund for Scientific Research in Flanders). Functional foods.
  • October - December 2000: Research at University of Illinois, USA, Department of Animal Sciences (H.R. Gaskins, PhD) and Department of Food Science and Nutrition (K.A. Tappenden, PhD). Boehringer Ingelheim Fund.
  • October 1994 - June 1999: M.Sc. Bioscience Engineering Chemistry, Faculty of Bioscience Engineering, Ghent University. Master thesis: "Enzymatic and microbial activities in the simulator of the gastrointestinal tract of the baby (baby-SHIME)", scientific promoter Prof. Dr. ir. W. Verstraete.

Research

Systems biology and biological networks

In recent years, high-throughput methods have generated genome-wide datasets that enable us to study biological networks (biology at the systems level), rather than single genes, proteins or cells. As bioengineer, I am intrigued by systems biology, since it is an interdisciplinary research field that requires the knowledge of biology, mathematics, engineering, computer science and physics.

Differential gene expression is an important driving force in the development, function and pathology of multicellular organisms, plants as well as animals. Proper spatial and temporal gene expression is most importantly controlled at the initiation of transcription by regulatory transcription factors that directly bind to their genomic DNA targets, resulting in an activation or repression of target gene expression. In addition, the recently discovered miRNAs function as repressors at the posttranscriptional level. Both regulators, transcription factors and miRNAs, function in the context of intricate regulatory networks that describe gene expression as a function of inputs specified by physical and functional interactions between transcription factors, miRNAs and DNA. Deciphering these regulatory networks in eukaryotic organisms is the main challenge. How can we extract biologically relevant information from different genome-wide datasets (data-integration)? How can reverse-engineering algorithms be improved to more correctly infer the regulatory network? Once, we have the regulatory networks in hand, we are able to tackle specific biological questions. Which regulators and target genes control a specific biological process and how? This can be accomplished by studying network modules, groups of highly interconnected components in the network that together carry out particular biological functions. How is the regulatory specificity of transcription factors and miRNAs determined? Which mechanisms have shaped the specificity of these regulators during evolution?

Previously

Functional foods. Bioavailability of bioactive peptides. Gastrointestinal microbiota.

Papers

(22) Vermeirssen, V., De Clercq, I., Van Parys, T., Van Breusegem, F., Van de Peer, Y. (2014) Arabidopsis ensemble reverse-engineered gene regulatory network discloses interconnected transcription factors in oxidative stress. The Plant Cell 26(12):4656-4679.
(21) Zhurov, V., Navarro, M., Bruinsma, K.A., Arbona, V., Santamaria, M.E., Wybouw, M.C.N., Osborne, E.J., Ens, C., Rioja, C., Vermeirssen, V., Rubio-Somoza, I., Krishna, P., Diaz, I., Schmid, M., Gómez-Cadenas, A., Van de Peer, Y., Grbic, M., Clark, R.M., Van Leeuwen, T., Grbic, V. (2014) Reciprocal responses in the interaction between Arabidopsis and the cell-content feeding chelicerate herbivore Tetranychus urticae. Plant Physiol. 164(1):384-399.
(20) De Clercq, I., Vermeirssen, V., Van Aken, O., Vandepoele, K., Murcha, M., Law, S., Inzé, A., Ng, S., Ivanova, A., Rombaut, D., Van de Cotte, B., Jaspers, P., Van de Peer, Y., Kangasjarvi, J., Whelan, J., Van Breusegem, F. (2013) The membrane-bound NAC transcription factor ANAC013 is a regulator of mitochondrial retrograde regulation of the oxidative stress response in Arabidopsis. The Plant Cell 25(9):3472-90.
(19) Petrov, V., Vermeirssen, V., De Clercq, R., Van Breusegem, F., Minkov, I., * Vandepoele, K., * Gechev, T. (2012) Identification of cis-regulatory elements specific for different types of reactive oxygen species in Arabidopsis thaliana. Gene 499(1):52-60. *contributed equally
(18) Michoel, T., Joshi, A., Bonnet, E., Vermeirssen, V., Van de Peer, Y. (2010) Towards system level modeling of functional modules and regulatory pathways using genome-scale data. Proceedings of the Seventh International Workshop on Computational Systems Biology (WCSB 2010) 71-74. Luxembourg, Luxembourg.
(17) Vermeirssen, V., Joshi, A., Michoel, T., Bonnet, E., Casneuf, T., Van de Peer, Y. (2009) Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development. Molecular BioSystems 5(12):1817-30.
(16) Vermeirssen, V., Barrasa, M.I., Hidalgo, C., Babon, J.A.B., Sequerra, R., Doucette-Stam, L., Sengupta, P., Barabási, A.-L., Walhout, A.J.M. (2007) Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network. Genome Res. 17(7):1061-71.
(15) Vermeirssen, V., Deplancke, B., Barrasa, M.I., Reece-Hoyes, J.S., Arda, H.E., Grove, C.A., Martinez, N.J., Sequerra, R., Doucette-Stam, L., Brent, M.R., Walhout, A.J.M. (2007) A C. elegans transcription factor array and Steiner Triple System-based smart pools: high-performance tools for transcription regulatory network mapping. Nature Methods 4,659-664.
(14) Vermeirssen, V., Deplancke, B., Barrasa, M.I., Reece-Hoyes, J.S., Arda, H.E., Grove, C.A., Martinez, N.J., Sequerra, R., Doucette-Stam, L., Brent, M.R., Walhout, A.J.M. (2007) Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping. Nature Methods 4, 659-64.
(13) Deplancke, B., Vermeirssen, V., Chardakov, V., Martinez, N.J., Walhout, A.J.M. (2006) Gateway-compatible yeast one-hybrid screens. Cold Spring Harbor Protocols 2006(5). pii: pdb.prot4590.
(12) Vermeirssen, V., Van Camp, J., Verstraete, W. (2005) Fractionation of angiotensin I converting enzyme inhibitory activity from pea and whey protein in vitro gastrointestinal digests. J. Sci. Food Agric. 85,399-405.
(11) Vercruysse, S., Gelman, D., Van De Velde, S., Raes, J., Hooghe, B., Vermeirssen, V., Van Camp, J., Smagghe, G. (2005) ACE inhibitor captopril reduces ecdysteroids and oviposition in moths. Ann. NY. Acad. Sci. 1040:498-500.
(10) Vermeirssen, V., Augustijns, P., Morel, N., Van Camp, J., Opsomer, A., Verstraete, W. (2005) In vitro intestinal transport and antihypertensive activity of ACE inhibitory pea and whey digests. Int. J. Food Sci. Nutr. 56(6):415-30.
(9) Maes, W., Van Camp, J., Vermeirssen, V., Hemeryck, M., Ketelslegers, J.M., Schrezenmeir, J., Van Oostveldt, P., Huyghebaert, A. (2004) Influence of the lactokinin Ala-Leu-Pro-Met-His-Ile-Arg (ALPMHIR) on the release of endothelin-1 by endothelial cells. Regulatory Peptides 118(1-2):105-9.
(8) Vermeirssen, V., van der Bent, A., Van Camp, J., van Amerongen, A., Verstraete, W. (2004) A quantitative in silico analysis calculates the Angiotensin I Converting Enzyme (ACE) inhibitory activity in pea and whey protein digests. Biochimie 86(3):231-9.
(7) Vermeirssen, V., Van Camp, J., Verstraete, W. (2004) Bioavailability of angiotensin I converting enzyme inhibitory peptides. Review. Br. J. Nutr. 92,357-66.
(6) Vercruysse, S., Gelman, D., Raes, J., Hooghe, B., Vermeirssen, V., Van Camp, J., Smagghe, G. (2004) The angiotensin converting enzyme inhibitor captopril reduces oviposition and ecdysteroid levels in Lepidoptera. Arch. Insect Biochem. Physiol. 57(3):123-32.
(5) Vermeirssen, V., Decroos, K., Van Wijmelbeke, L., Van Camp, J., Verstraete, W. (2003) The impact of fermentation and in vitro digestion on the formation of ACE inhibitory activity from pea and whey protein. J. Dairy Sci. 86(2), 429-438.
(4) Vermeirssen, V., Van Camp, J., Devos, J, Verstraete, W. (2003) Release of Angiotensin I Converting Enzyme (ACE) inhibitory activity during in vitro gastrointestinal digestion: from batch experiment to semi-continuous model. J. Agric. Food Chem. 51(19), 5680-5687.
(3) Vermeirssen, V., Van Camp, J., Verstraete, W. (2002) Optimisation and validation of an angiotensin-converting enzyme inhibition assay for the screening of bioactive peptides. Journal of Biochemical and Biophysical Methods 51(1):75-87.
(2) Vermeirssen, V., Deplancke, B., Tappenden, K.A., Van Camp, J., Gaskins, H.R., Verstraete, W. (2002) Intestinal transport of the lactokinin Ala-Leu-Pro-Met-His-Ile-Arg through a Caco-2 Bbe monolayer. J. Pept. Sci. 8(3):95-100.
(1) De Boever, P., Wouters, R., Vermeirssen, V., Boon, N., Verstraete, W. (2001) Development of a six-stage culture system for simulating the gastrointestinal microbiota of weaned infants. Microbial Ecology in Health and Disease 13(2), 111-123.








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Bioinformatics & Evolutionary Genomics
Technologiepark 927
B-9052 Gent
BELGIUM
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