Jacques van Helden

According to our database, Jacques van Helden authored at least 30 papers between 1999 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2022

RSAT 2022: regulatory sequence analysis tools.

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

Nucleic Acids Res., 2022

2018

RSAT 2018: regulatory sequence analysis tools 20th anniversary.

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

Nucleic Acids Res., 2018

Sequanix: a dynamic graphical interface for Snakemake workflows.

Dimitri Desvillechabrol, Rachel Legendre, Claire Rioualen, Christiane Bouchier, Jacques van Helden, Sean Kennedy, Thomas Cokelaer

Bioinform., 2018

2015

RSAT 2015: Regulatory Sequence Analysis Tools.

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

Nucleic Acids Res., 2015

2012

eBiomics - A Website Promoting Good Practices and Specific Methods for using Bioinformatics Resources.

Frédérique Lisacek, Patrick Koks, Pascale Berthault, Grégoire Rossier, Guy Bottu, Jacques van Helden, Jean Sylvestre, Jean-Pierre Kraehenbuhl, Jack A. M. Leunissen

Proceedings of the BIOINFORMATICS 2012 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Vilamoura, Algarve, Portugal, 1, 2012

2011

RSAT 2011: regulatory sequence analysis tools.

Morgane Thomas-Chollier, Matthieu Defrance, Alejandra Medina-Rivera, Olivier Sand, Carl Herrmann, Denis Thieffry, Jacques van Helden

Nucleic Acids Res., 2011

Prediction of metabolic pathways from genome-scale metabolic networks.

Karoline Faust, Didier Croes, Jacques van Helden

Biosyst., 2011

2010

Pathway discovery in metabolic networks by subgraph extraction.

Karoline Faust, Pierre Dupont, Jérôme Callut, Jacques van Helden

Bioinform., 2010

2009

Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl.

Olivier Sand, Morgane Thomas-Chollier, Jacques van Helden

Bioinform., 2009

In response to 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'.

Karoline Faust, Didier Croes, Jacques van Helden

Bioinform., 2009

info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling.

Matthieu Defrance, Jacques van Helden

Bioinform., 2009

Gaussian Graphical Models to Infer Putative Genes Involved in Nitrogen Catabolite Repression in S. cerevisiae.

Kevin Kontos, Bruno André, Jacques van Helden, Gianluca Bontempi

Proceedings of the Evolutionary Computation, 2009

2008

RSAT: regulatory sequence analysis tools.

Morgane Thomas-Chollier, Olivier Sand, Jean-Valéry Turatsinze, Rekin's Janky, Matthieu Defrance, Eric Vervisch, Sylvain Brohée, Jacques van Helden

Nucleic Acids Res., 2008

NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways.

Sylvain Brohée, Karoline Faust, Gipsi Lima-Mendez, Olivier Sand, Rekin's Janky, Gilles Vanderstocken, Yves Deville, Jacques van Helden

Nucleic Acids Res., 2008

Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution.

Rekin's Janky, Jacques van Helden

BMC Bioinform., 2008

Prophinder: a computational tool for prophage prediction in prokaryotic genomes.

Gipsi Lima-Mendez, Jacques van Helden, Ariane Toussaint, Raphaël Leplae

Bioinform., 2008

2007

<i>In silico </i>identification of NF-kappaB-regulated genes in pancreatic beta-cells.

Najib Naamane, Jacques van Helden, Decio L. Eizirik

BMC Bioinform., 2007

2006

Evaluation of clustering algorithms for protein-protein interaction networks.

Sylvain Brohée, Jacques van Helden

BMC Bioinform., 2006

2005

CYGD: the Comprehensive Yeast Genome Database.

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

Nucleic Acids Res., 2005

Metabolic PathFinding: inferring relevant pathways in biochemical networks.

Didier Croes, Fabian Couche, Shoshana J. Wodak, Jacques van Helden

Nucleic Acids Res., 2005

Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs.

Didier Gonze, Sylvie Pinloche, Olivier Gascuel, Jacques van Helden

Bioinform., 2005

2004

Combining pattern discovery and discriminant analysis to predict gene co-regulation.

N. Simonis, Shoshana J. Wodak, G. N. Cohen, Jacques van Helden

Bioinform., 2004

Metrics for comparing regulatory sequences on the basis of pattern counts.

Jacques van Helden

Bioinform., 2004

2003

Regulatory Sequence Analysis Tools.

Jacques van Helden

Nucleic Acids Res., 2003

An overview of data models for the analysis of biochemical pathways.

Yves Deville, David R. Gilbert, Jacques van Helden, Shoshana J. Wodak

Briefings Bioinform., 2003

2001

Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer.

Michael Schroeder, David R. Gilbert, Jacques van Helden, Penny Noy

Inf. Sci., 2001

From Molecular Activities and Processes to Biological Function.

Jacques van Helden, Avi Naim, Christian Lemer, Renato Mancuso, Matthew D. Eldridge, Shoshana J. Wodak

Briefings Bioinform., 2001

2000

Application of Regulatory Sequence Analysis and Metabolic Network Analysis to the Interpretation of Gene Expression Data.

Jacques van Helden, David R. Gilbert, Lorenz Wernisch, Michael Schroeder, Shoshana J. Wodak

Proceedings of the Computational Biology, 2000

1999

RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli.

Heladia Salgado, Alberto Santos-Zavaleta, Ulises Garza-Ramos, Jacques van Helden, Edgar Díaz-Peredo, Julio Collado-Vides

Nucleic Acids Res., 1999

Logical Tools for Quering and Assisting Annotation of a Biochemical Pathway Database.

Jacques van Helden, David R. Gilbert, Lorenz Wernisch, Renato Mancuso, Matthew D. Eldridge, Kirill Degtyarenko, Shoshana J. Wodak

Proceedings of the German Conference on Bioinformatics, 1999