BioSapiens 9th European School of Bioinformatics

1. BioSapiens 9th European School of Bioinformatics Biochemical networks and pathwaysSylvain Brohée & Jacques van Helden(with the help of Gipsi Lima-Mendez) 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/

2. Bioinformatique des Génomes et des Réseaux (BiGRe)Université Libre de Bruxelles 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) Jean-Valéry Turatsinze PhD student Olivier Sand Postdoc Rekin’s Janky Ex-PhD student Morgane Thomas-Chollier Postdoc Didier Gonze Premier assistant Matthieu Defrance Postdoc Eric Vervisch Ex-Research fellow Myriam Loubriat Secretary Jacques van Helden Chargé de cours Karoline Faust PhD student Sylvain Brohée Postdoc Raphaël Leplae Postdoc Gipsi Lima Postdoc Ariane Toussaint Professor Jean Valéry Turatsinze PhD student 2

3. Graph-based analysis of biochemical networks

4. Links and references • Network Analysis Tools (NeAT) • http://rsat.ulb.ac.be/neat/ • Publications • 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. • 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. • 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. • 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. • 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. • 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. • 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. • Brohee, S. & van Helden, J. (2006). Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 7, 488. • 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. • 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.