Jacques van Helden

Publication Activity (10 Years)

Years Active: 1999-2022
Publications (10 Years): 3

Top Topics

Changing Environment

Sequence Analysis

Information Retrieval Systems

Graphical Interface

Top Venues

Nucleic Acids Res.

Publications

Walter Santana-Garcia, Jaime Abraham Castro-Mondragón, Mónica Padilla-Gálvez, Nga Thi Thuy Nguyen, Ana Elizondo-Salas, Najla Ksouri, François Gerbes, Denis Thieffry, Pierre Vincens, Bruno Contreras-Moreira, Jacques van Helden, Morgane Thomas-Chollier, Alejandra Medina-Rivera
RSAT 2022: regulatory sequence analysis tools. Nucleic Acids Res. 50 (W1) (2022)
Nga Thi Thuy Nguyen, Bruno Contreras-Moreira, Jaime Abraham Castro-Mondragón, Walter Santana-Garcia, Raul Ossio, Carla Daniela Robles-Espinoza, Mathieu Bahin, Samuel Collombet, Pierre Vincens, Denis Thieffry, Jacques van Helden, Alejandra Medina-Rivera, Morgane Thomas-Chollier
RSAT 2018: regulatory sequence analysis tools 20th anniversary. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Dimitri Desvillechabrol, Rachel Legendre, Claire Rioualen, Christiane Bouchier, Jacques van Helden, Sean Kennedy, Thomas Cokelaer
Sequanix: a dynamic graphical interface for Snakemake workflows. Bioinform. 34 (11) (2018)
Alejandra Medina-Rivera, Matthieu Defrance, Olivier Sand, Carl Herrmann, Jaime Abraham Castro-Mondragón, Jeremy Delerce, Sébastien Jaeger, Christophe Blanchet, Pierre Vincens, Christophe Caron, Daniel M. Staines, Bruno Contreras-Moreira, Marie Artufel, Lucie Charbonnier-Khamvongsa, Céline Hernandez, Denis Thieffry, Morgane Thomas-Chollier, Jacques van Helden
RSAT 2015: Regulatory Sequence Analysis Tools. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
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)
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 Res. 39 (Web-Server-Issue) (2011)
Karoline Faust, Didier Croes, Jacques van Helden
Prediction of metabolic pathways from genome-scale metabolic networks. Biosyst. 105 (2) (2011)
Karoline Faust, Pierre Dupont, Jérôme Callut, Jacques van Helden
Pathway discovery in metabolic networks by subgraph extraction. Bioinform. 26 (9) (2010)
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)
Karoline Faust, Didier Croes, Jacques van Helden
In response to 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'. Bioinform. 25 (23) (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. Bioinform. 25 (20) (2009)
Matthieu Defrance, Jacques van Helden
info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling. Bioinform. 25 (20) (2009)
Gipsi Lima-Mendez, Jacques van Helden, Ariane Toussaint, Raphaël Leplae
Prophinder: a computational tool for prophage prediction in prokaryotic genomes. Bioinform. 24 (6) (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 Res. 36 (Web-Server-Issue) (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 Res. 36 (Web-Server-Issue) (2008)
Rekin's Janky, Jacques van Helden
Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution. BMC Bioinform. 9 (2008)
Najib Naamane, Jacques van Helden, Decio L. Eizirik
identification of NF-kappaB-regulated genes in pancreatic beta-cells. BMC Bioinform. 8 (2007)
Sylvain Brohée, Jacques van Helden
Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinform. 7 (2006)
Ulrich Güldener, Martin Münsterkötter, Gabi Kastenmüller, Normann Strack, Jacques van Helden, Christian Lemer, J. Richelles, Shoshana J. Wodak, J. García-Martínez, José 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 Res. 33 (Database-Issue) (2005)
Didier Croes, Fabian Couche, Shoshana J. Wodak, Jacques van Helden
Metabolic PathFinding: inferring relevant pathways in biochemical networks. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
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. Bioinform. 21 (17) (2005)
N. Simonis, Shoshana J. Wodak, G. N. Cohen, Jacques van Helden
Combining pattern discovery and discriminant analysis to predict gene co-regulation. Bioinform. 20 (15) (2004)
Jacques van Helden
Metrics for comparing regulatory sequences on the basis of pattern counts. Bioinform. 20 (3) (2004)
Yves Deville, David R. Gilbert, Jacques van Helden, Shoshana J. Wodak
An overview of data models for the analysis of biochemical pathways. Briefings Bioinform. 4 (3) (2003)
Yves Deville, David R. Gilbert, Jacques van Helden, Shoshana J. Wodak
An Overview of Data Models for the Analysis of Biochemical Pathways. CMSB (2003)
Jacques van Helden
Regulatory Sequence Analysis Tools. Nucleic Acids Res. 31 (13) (2003)
Michael Schroeder, David R. Gilbert, Jacques van Helden, Penny Noy
Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer. Inf. Sci. 139 (1-2) (2001)
Jacques van Helden, Avi Naim, Christian Lemer, Renato Mancuso, Matthew D. Eldridge, Shoshana J. Wodak
From Molecular Activities and Processes to Biological Function. Briefings Bioinform. 2 (1) (2001)
Jacques van Helden, David R. 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)
Jacques van Helden, David R. Gilbert, Lorenz Wernisch, Renato Mancuso, Matthew D. Eldridge, Kirill Degtyarenko, Shoshana J. Wodak
Logical Tools for Quering and Assisting Annotation of a Biochemical Pathway Database. German Conference on Bioinformatics (1999)
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 Res. 27 (1) (1999)