1. Jacques.van.Helden@ulb.ac.be Université Libre de Bruxelles, Belgique Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) http://www.bigre.ulb.ac.be/ Biochemical networks and pathways Sylvain Brohée & Jacques van Helden (with the help of Gipsi Lima-Mendez) BioSapiens 9th European School of Bioinformatics

2. Bioinformatique des Génomes et des Réseaux (BiGRe) Université Libre de Bruxelles 2  Development and application of bioinformatics methods for the analysis of genome function, regulation and evolution.  Regulatory sequences  Pattern discovery algorithms • Olivier Sand (Postdoc) • Matthieu Defrance (Postdoc) • Maud Vidick (Master thesis)  Evolution of cis-acting elements in Bacteria • Rekin’s Janky (PhD student)  Regulation of development in Drosophila • Jean Valéry Turatsinze (PhD student)  Hox regulation in Vertebrates • Morgane Thomas-Chollier (PhD student)  Regulation of phages and prophages • Rossy Gabin Nkoubouala (Master student)  Work flows on transcriptional regulation • Eric Vervisch (Research fellow)  Molecular networks  Analysis of regulatory networks • Rekin’s Janky (PhD student),Sylvain Brohée (PhD student)  Interactions between membrane-associated proteins • Sylvain Brohée (PhD student)  Inference of metabolic pathways • Karoline Faust (PhD student)  Signal transduction pathways • Olivier Sand (Postdoc)  Mobile genetic elements in prokaryotes • Raphaël Leplae (Postdoc) • Gipsi Lima (PhD student) • Ariane Toussaint (Professor)  Modelling of dynamical systems • Didier Gonze (Premier assistant) Gipsi Lima Postdoc Ariane Toussaint Professor Raphaël Leplae Postdoc Jean Valéry Turatsinze PhD student Rekin’s Janky Ex-PhD student Morgane Thomas-Chollier Postdoc Olivier Sand Postdoc Jacques van Helden Chargé de cours Matthieu Defrance Postdoc Sylvain Brohée Postdoc Karoline Faust PhD student Didier Gonze Premier assistant Eric Vervisch Ex-Research fellow Myriam Loubriat Secretary Jean-Valéry Turatsinze PhD student

3. Graph-based analysis of biochemical networks

4. Links and references  Network Analysis Tools (NeAT)  http://rsat.ulb.ac.be/neat/ http://rsat.ulb.ac.be/neat/  Publications 1.van Helden, J., Naim, A., Mancuso, R., Eldridge, M., Wernisch, L., Gilbert, D. & Wodak, S. (2000). Representing and analyzing molecular and cellular function in the computer. Biological Chemistry 381, 921-935. 2.van Helden, J., Naim, A., Lemer, C., Mancuso, R., Eldridge, M. & Wodak, S. (2001). From molecular activities and processes to biological function. Briefings in Bioinformatics 2(1), 81-93. 3.van Helden, J., Gilbert, D., Wernisch, L., Schroeder, M. & Wodak, S. (2001). Applications of regulatory sequence analysis and metabolic network analysis to the interpretation of gene expression data. Lecture Notes in Computer Sciences 2066, 155-172. 4.van Helden, J., Wernisch, L., Gilbert, D. & Wodak, S. (2002). Graph-based analysis of metabolic networks. In Bioinformatics and Genome Analysis (Mewes, H.-W., Weiss, B. & Seidel, H., eds.), Vol. 38. Springer-Verlag, Berlin Heidelberg. 5.Deville, Y., D. Gilbert, J. van Helden, and S.J. Wodak (2003). An overview of data models for the analysis of biochemical pathways. Brief Bioinform 4: 246-259. 6.Croes, D., F. Couche, S.J. Wodak, and J. van Helden (2005). Metabolic PathFinding: inferring relevant pathways in biochemical networks. Nucleic Acids Res 33: W326-330. 7.Croes, D., F. Couche, S.J. Wodak, and J. van Helden (2006). Inferring meaningful pathways in weighted metabolic networks. J Mol Biol 356: 222-236. 8.Brohee, S. & van Helden, J. (2006). Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 7, 488. 9.Brohee, S., Faust, K., Lima-Mendez, G., Vanderstocken, G. and van Helden, J. (2008). Network Analysis Tools: from biological networks to clusters and pathways. Nat Protoc 3, 1616-29. 10.Brohee, S., Faust, K., Lima-Mendez, G., Sand, O., Janky, R., Vanderstocken, G., Deville, Y. and van Helden, J. (2008). NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways. Nucleic Acids Res.