Jacques van Helden

Frédérique Lisacek, Patrick Koks, Pascale Berthault, Grégoire Rossier, Guy Bottu, Jacques van Helden, Jean Sylvestre, Jean-Pierre Kraehenbuhl, Jack A. M. Leunissen: eBiomics - A Website Promoting Good Practices and Specific Methods for using Bioinformatics Resources. BIOINFORMATICS 2012: 386-391

Karoline Faust, Didier Croes, Jacques van Helden: Prediction of metabolic pathways from genome-scale metabolic networks. Biosystems 105(2): 109-121 (2011)

Morgane Thomas-Chollier, Matthieu Defrance, Alejandra Medina-Rivera, Olivier Sand, Carl Herrmann, Denis Thieffry, Jacques van Helden: RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Research 39(Web-Server-Issue): 86-91 (2011)

Karoline Faust, Pierre Dupont, Jérôme Callut, Jacques van Helden: Pathway discovery in metabolic networks by subgraph extraction. Bioinformatics 26(9): 1211-1218 (2010)

Matthieu Defrance, Jacques van Helden: info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling. Bioinformatics 25(20): 2715-2722 (2009)

Olivier Sand, Morgane Thomas-Chollier, Jacques van Helden: Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl. Bioinformatics 25(20): 2739-2740 (2009)

Karoline Faust, Didier Croes, Jacques van Helden: In response to 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'. Bioinformatics 25(23): 3202-3205 (2009)

Kevin Kontos, Bruno André, Jacques van Helden, Gianluca Bontempi: Gaussian Graphical Models to Infer Putative Genes Involved in Nitrogen Catabolite Repression in S. cerevisiae. EvoBIO 2009: 13-24

Gipsi Lima-Mendez, Jacques van Helden, Ariane Toussaint, Raphaël Leplae: Prophinder: a computational tool for prophage prediction in prokaryotic genomes. Bioinformatics 24(6): 863-865 (2008)

Rekin's Janky, Jacques van Helden: Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution. BMC Bioinformatics 9 (2008)

Morgane Thomas-Chollier, Olivier Sand, Jean-Valéry Turatsinze, Rekin's Janky, Matthieu Defrance, Eric Vervisch, Sylvain Brohée, Jacques van Helden: RSAT: regulatory sequence analysis tools. Nucleic Acids Research 36(Web-Server-Issue): 119-127 (2008)

Sylvain Brohée, Karoline Faust, Gipsi Lima-Mendez, Olivier Sand, Rekin's Janky, Gilles Vanderstocken, Yves Deville, Jacques van Helden: NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways. Nucleic Acids Research 36(Web-Server-Issue): 444-451 (2008)

Najib Naamane, Jacques van Helden, Decio L. Eizirik: In silico identification of NF-kappaB-regulated genes in pancreatic beta-cells. BMC Bioinformatics 8 (2007)

Sylvain Brohée, Jacques van Helden: Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 7: 488 (2006)

Didier Gonze, Sylvie Pinloche, Olivier Gascuel, Jacques van Helden: Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs. Bioinformatics 21(17): 3490-3500 (2005)

Ulrich Güldener, Martin Münsterkötter, Gabi Kastenmüller, Normann Strack, Jacques van Helden, Christian Lemer, J. Richelles, Shoshana J. Wodak, J. García-Martínez, J. E. Pérez-Ortín, Holger Michael, Andreas Kaps, E. Talla, Bernard Dujon, Bruno André, J. L. Souciet, J. De Montigny, E. Bon, C. Gaillardin, Hans-Werner Mewes: CYGD: the Comprehensive Yeast Genome Database. Nucleic Acids Research 33(Database-Issue): 364-368 (2005)

Didier Croes, Fabian Couche, Shoshana J. Wodak, Jacques van Helden: Metabolic PathFinding: inferring relevant pathways in biochemical networks. Nucleic Acids Research 33(Web-Server-Issue): 326-330 (2005)

Jacques van Helden: Metrics for comparing regulatory sequences on the basis of pattern counts. Bioinformatics 20(3): 399-406 (2004)

N. Simonis, Shoshana J. Wodak, G. N. Cohen, Jacques van Helden: Combining pattern discovery and discriminant analysis to predict gene co-regulation. Bioinformatics 20(15): 2370-2379 (2004)

Yves Deville, David Gilbert, Jacques van Helden, Shoshana J. Wodak: An overview of data models for the analysis of biochemical pathways. Briefings in Bioinformatics 4(3): 246-259 (2003)

Jacques van Helden: Regulatory Sequence Analysis Tools. Nucleic Acids Research 31(13): 3593-3596 (2003)

Yves Deville, David Gilbert, Jacques van Helden, Shoshana J. Wodak: An Overview of Data Models for the Analysis of Biochemical Pathways. CMSB 2003: 174

Jacques van Helden, Avi Naim, Christian Lemer, Renato Mancuso, Matthew Eldridge, Shoshana J. Wodak: From Molecular Activities and Processes to Biological Function. Briefings in Bioinformatics 2(1): 81-107 (2001)

Michael Schroeder, David Gilbert, Jacques van Helden, Penny Noy: Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer. Inf. Sci. 139(1-2): 19-57 (2001)

Jacques van Helden, David Gilbert, Lorenz Wernisch, Michael Schroeder, Shoshana J. Wodak: Application of Regulatory Sequence Analysis and Metabolic Network Analysis to the Interpretation of Gene Expression Data. JOBIM 2000: 147-164

Heladia Salgado, Alberto Santos-Zavaleta, Ulises Garza-Ramos, Jacques van Helden, Edgar Díaz-Peredo, Julio Collado-Vides: RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli. Nucleic Acids Research 27(1): 59-60 (1999)

Jacques van Helden, David Gilbert, Lorenz Wernisch, Renato Mancuso, Matthew Eldridge, Kirill Degtyarenko, Shoshana J. Wodak: Logical Tools for Quering and Assisting Annotation of a Biochemical Pathway Database. German Conference on Bioinformatics 1999: 227-229