Jacques van Helden

Summary

Country: Belgium

Publications

  1. pmc Machine learning techniques to identify putative genes involved in nitrogen catabolite repression in the yeast Saccharomyces cerevisiae
    Kevin Kontos
    Machine Learning Group, , , , Boulevard du Triomphe CP 212, 1050 Brussels, Belgium
    BMC Proc 2:S5. 2008
  2. pmc Regulatory sequence analysis tools
    Jacques van Helden
    Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Universite Libre de Bruxelles, Campus Plaine, CP 263, Bld du Triomphe, B 1050 Bruxelles, Belgium
    Nucleic Acids Res 31:3593-6. 2003
  3. pmc Unraveling networks of co-regulated genes on the sole basis of genome sequences
    Sylvain Brohée
    Lab Bioinformatique des Génomes et des Réseaux BiGRe, Universite Libre de Bruxelles ULB, CP 263, Campus Plaine, Bld du Triomphe, 1050 Brussels, Belgium
    Nucleic Acids Res 39:6340-58. 2011
  4. doi request reprint Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules
    Jean Valery Turatsinze
    Laboratoire de Bioinformatique des Génomes et des Réseaux BiGRe, Université Libre de Bruxelles CP 263, Campus Plaine, Boulevard du Triomphe, Bruxelles, Belgium
    Nat Protoc 3:1578-88. 2008
  5. pmc NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways
    Sylvain Brohée
    Laboratoire de Bioinformatique des Génomes et Réseaux BiGRE, Universite Libre de Bruxelles ULB, Boulevard du Triomphe, CP263, B 1050 Bruxelles, Belgium
    Nucleic Acids Res 36:W444-51. 2008
  6. doi request reprint Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences
    Matthieu Defrance
    Laboratoire de Bioinformatique des Génomes et des Réseaux BiGRe, Universite Libre de Bruxelles, Campus Plaine, CP 263, Boulevard du Triomphe, Bruxelles, Belgium
    Nat Protoc 3:1589-603. 2008
  7. doi request reprint Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services: an example with ChIP-chip data
    Olivier Sand
    Laboratoire de Bioinformatique des Génomes et des Réseaux BiGRe, Universite Libre de Bruxelles, Campus Plaine, CP 263, Boulevard du Triomphe, Bruxelles, Belgium
    Nat Protoc 3:1604-15. 2008
  8. doi request reprint Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl
    Olivier Sand
    Laboratoire de Bioinformatique des Génomes et des Réseaux BiGRe, Université Libre de Bruxelles CP 263, Campus Plaine, Boulevard du Triomphe, B 1050 Bruxelles, Belgium
    Bioinformatics 25:2739-40. 2009
  9. pmc Pathway discovery in metabolic networks by subgraph extraction
    Karoline Faust
    Laboratoire de Bioinformatique des Génomes et des Réseaux BiGRe, Universite Libre de Bruxelles, Bruxelles, Belgium
    Bioinformatics 26:1211-8. 2010
  10. doi request reprint Network Analysis Tools: from biological networks to clusters and pathways
    Sylvain Brohée
    Laboratoire de Bioinformatique des Génomes et des Réseaux BiGRe, Universite Libre de Bruxelles, Campus Plaine, CP 263, Boulevard du Triomphe, Bruxelles, Belgium
    Nat Protoc 3:1616-29. 2008

Detail Information

Publications35

  1. pmc Machine learning techniques to identify putative genes involved in nitrogen catabolite repression in the yeast Saccharomyces cerevisiae
    Kevin Kontos
    Machine Learning Group, , , , Boulevard du Triomphe CP 212, 1050 Brussels, Belgium
    BMC Proc 2:S5. 2008
    ..CONCLUSION : These results suggest that our approach can successfully identify potential NCR genes. Hence, the dimensionality of the problem of identifying all genes involved in NCR is drastically reduced...
  2. pmc Regulatory sequence analysis tools
    Jacques van Helden
    Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Universite Libre de Bruxelles, Campus Plaine, CP 263, Bld du Triomphe, B 1050 Bruxelles, Belgium
    Nucleic Acids Res 31:3593-6. 2003
    ..RSAT currently holds >100 fully sequenced genomes and these data are regularly updated from GenBank...
  3. pmc Unraveling networks of co-regulated genes on the sole basis of genome sequences
    Sylvain Brohée
    Lab Bioinformatique des Génomes et des Réseaux BiGRe, Universite Libre de Bruxelles ULB, CP 263, Campus Plaine, Bld du Triomphe, 1050 Brussels, Belgium
    Nucleic Acids Res 39:6340-58. 2011
    ..Long-term benefits can easily be perceived when considering the exponential increase of new genome sequences...
  4. doi request reprint Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules
    Jean Valery Turatsinze
    Laboratoire de Bioinformatique des Génomes et des Réseaux BiGRe, Université Libre de Bruxelles CP 263, Campus Plaine, Boulevard du Triomphe, Bruxelles, Belgium
    Nat Protoc 3:1578-88. 2008
    ..This protocol is also tested on random control sequences to evaluate the reliability of the predictions. Each task requires a few minutes of computation time on the server. The complete protocol can be executed in about one hour...
  5. pmc NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways
    Sylvain Brohée
    Laboratoire de Bioinformatique des Génomes et Réseaux BiGRE, Universite Libre de Bruxelles ULB, Boulevard du Triomphe, CP263, B 1050 Bruxelles, Belgium
    Nucleic Acids Res 36:W444-51. 2008
    ..NeAT can also be used as web services (SOAP/WSDL interface), in order to design programmatic workflows and integrate them with other available resources...
  6. doi request reprint Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences
    Matthieu Defrance
    Laboratoire de Bioinformatique des Génomes et des Réseaux BiGRe, Universite Libre de Bruxelles, Campus Plaine, CP 263, Boulevard du Triomphe, Bruxelles, Belgium
    Nat Protoc 3:1589-603. 2008
    ..Computation times vary from seconds (gene clusters) to minutes (whole genomes). The execution of the whole protocol should take approximately 1 h...
  7. doi request reprint Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services: an example with ChIP-chip data
    Olivier Sand
    Laboratoire de Bioinformatique des Génomes et des Réseaux BiGRe, Universite Libre de Bruxelles, Campus Plaine, CP 263, Boulevard du Triomphe, Bruxelles, Belgium
    Nat Protoc 3:1604-15. 2008
    ..This protocol is addressed to bioinformaticians and biologists with programming skills (notions of Perl). Running time is approximately 6 min on the example data set...
  8. doi request reprint Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl
    Olivier Sand
    Laboratoire de Bioinformatique des Génomes et des Réseaux BiGRe, Université Libre de Bruxelles CP 263, Campus Plaine, Boulevard du Triomphe, B 1050 Bruxelles, Belgium
    Bioinformatics 25:2739-40. 2009
    ..The complete manual, a convenient tutorial and demos are available from the RSAT website. Additional help can be found on the RSAT public forum...
  9. pmc Pathway discovery in metabolic networks by subgraph extraction
    Karoline Faust
    Laboratoire de Bioinformatique des Génomes et des Réseaux BiGRe, Universite Libre de Bruxelles, Bruxelles, Belgium
    Bioinformatics 26:1211-8. 2010
    ..Although these approaches have been adapted to metabolic networks, they are generic enough to be adjusted to other biological networks as well...
  10. doi request reprint Network Analysis Tools: from biological networks to clusters and pathways
    Sylvain Brohée
    Laboratoire de Bioinformatique des Génomes et des Réseaux BiGRe, Universite Libre de Bruxelles, Campus Plaine, CP 263, Boulevard du Triomphe, Bruxelles, Belgium
    Nat Protoc 3:1616-29. 2008
    ..e., clusters or paths) or tables displaying statistics. Typical networks comprising several thousands of nodes and arcs can be analyzed within a few minutes. The complete protocol can be read and executed in approximately 1 h...
  11. doi request reprint Prophinder: a computational tool for prophage prediction in prokaryotic genomes
    Gipsi Lima-Mendez
    Laboratoire de Bioinformatique des Génomes et des Réseaux BiGRe, Universite Libre de Bruxelles, 1050 Bruxelles, Belgium
    Bioinformatics 24:863-5. 2008
    ..Systematic and reliable predictions will enable further studies of prophages contribution to the bacteriophage gene pool and to better understand gene shuffling between prophages and phages infecting the same host...
  12. doi request reprint info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling
    Matthieu Defrance
    Laboratoire de Bioinformatique des Génomes et des Réseaux BiGRe, Université Libre de Bruxelles CP 263, Campus Plaine, Boulevard du Triomphe, B 1050 Bruxelles, Belgium
    Bioinformatics 25:2715-22. 2009
    ..However, these information-based metrics are usually used as a posteriori statistics rather than during the motif search process itself...
  13. pmc RSAT: regulatory sequence analysis tools
    Morgane Thomas-Chollier
    Laboratoire de Bioinformatique des Génomes et des Réseaux BiGRe, Universite Libre de Bruxelles, Campus Plaine, CP 263 Bld du Triomphe, B 1050 Bruxelles, Belgium
    Nucleic Acids Res 36:W119-27. 2008
    ..Since 1998, the tools have been used by several hundreds of researchers from all over the world. Several predictions made with RSAT were validated experimentally and published...
  14. ncbi request reprint Modularity of the transcriptional response of protein complexes in yeast
    Nicolas Simonis
    Service de Conformation des Macromolécules Biologiques, Centre de Biologie Structurale et Bioinformatique, CP 263, Universite Libre de Bruxelles, Bld du Triomphe B 1050 Bruxelles, Belgium
    J Mol Biol 363:589-610. 2006
    ..Together these findings suggest that transcriptional modules may represent basic functional and evolutionary building blocs of protein complexes...
  15. pmc Evaluation of clustering algorithms for protein-protein interaction networks
    Sylvain Brohée
    Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Universite Libre de Bruxelles, CP 263, Campus Plaine, Bd, du Triomphe, B 1050 Bruxelles, Belgium
    BMC Bioinformatics 7:488. 2006
    ..In this paper we present a comparative assessment of four algorithms: Markov Clustering (MCL), Restricted Neighborhood Search Clustering (RNSC), Super Paramagnetic Clustering (SPC), and Molecular Complex Detection (MCODE)...
  16. pmc Effect of 21 different nitrogen sources on global gene expression in the yeast Saccharomyces cerevisiae
    Patrice Godard
    Physiologie Moléculaire de la Cellule, IBMM, Universite Libre de Bruxelles, Rue des Pr Jeener et Brachet 12, 6041 Gosselies, Belgium
    Mol Cell Biol 27:3065-86. 2007
    ..Similar studies conducted for other nutrients should provide a more complete view of alternative metabolic pathways in yeast and contribute to the attribution of functions to many other orphan genes...
  17. pmc In silico identification of NF-kappaB-regulated genes in pancreatic beta-cells
    Najib Naamane
    Laboratory of Experimental Medicine, Universite Libre de Bruxelles, Route de Lennik, 808, CP 618, B 1070 Brussels, Belgium
    BMC Bioinformatics 8:55. 2007
    ..To identify NF-kappaB-regulated gene networks in beta-cells we presently used a discriminant analysis-based approach to predict NF-kappaB responding genes on the basis of putative regulatory elements...
  18. doi request reprint Bacterial molecular networks: bridging the gap between functional genomics and dynamical modelling
    Jacques van Helden
    Laboratoire de Bioinformatique des Génomes et des Réseaux, Universite Libre de Bruxelles, Bruxelles, Belgium
    Methods Mol Biol 804:1-11. 2012
    ..Altogether, the chapters provide a representative overview of state-of-the-art methods for data integration and retrieval, network visualization, graph analysis, and dynamical modelling...
  19. pmc Metabolic PathFinding: inferring relevant pathways in biochemical networks
    Didier Croes
    SCMBB, Universite Libre de Bruxelles, Campus Plaine, CP 263, Boulevard du Triomphe, B 1050 Bruxelles, Belgium
    Nucleic Acids Res 33:W326-30. 2005
    ..Multiple requests can be submitted in a queue. Results are returned by email, in textual as well as graphical formats (available in http://www.scmbb.ulb.ac.be/pathfinding/)...
  20. ncbi request reprint Discovery of motifs in promoters of coregulated genes
    Olivier Sand
    Service de Conformation des Macromolécules, Biologiques et de Bioinformatiques, Universite Libre de Bruxelles, Belgium
    Methods Mol Biol 395:329-48. 2007
    ..It can be used with higher organisms as well, but with a loss in reliability of the predictions. A web interface is available at the Regulatory Sequence Analysis Tools site (http://rsat.scmbb.ulb.ac.be/rsat/)...
  21. doi request reprint Reticulate representation of evolutionary and functional relationships between phage genomes
    Gipsi Lima-Mendez
    Service de Bioinformatique des Génomes et des Réseaux BiGRe, Universite Libre de Bruxelles, Bruxelles, Belgium
    Mol Biol Evol 25:762-77. 2008
    ..These 2 classification schemes provide an automatic and dynamic way of representing the relationships within the phage population and can be extended to include newly sequenced phage genomes, as well as other types of genetic elements...
  22. doi request reprint Metabolic pathfinding using RPAIR annotation
    Karoline Faust
    Laboratoire de Bioinformatique des Génomes et des Réseaux BiGRe, Universite Libre de Bruxelles, Campus Plaine, CP 263, Bld du Triomphe, B 1050 Bruxelles, Belgium
    J Mol Biol 388:390-414. 2009
    ..Our pathfinding approach is available as part of the Network Analysis Tools...
  23. pmc RSAT 2011: regulatory sequence analysis tools
    Morgane Thomas-Chollier
    Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
    Nucleic Acids Res 39:W86-91. 2011
    ..Availability (web site, stand-alone programs and SOAP/WSDL (Simple Object Access Protocol/Web Services Description Language) web services): http://rsat.ulb.ac.be/rsat/...
  24. pmc Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution
    Rekin s Janky
    Laboratoire de Bioinformatique des Génomes et des Réseaux, Universite Libre de Bruxelles ULB, Campus Plaine, CP 263, Boulevard du Triomphe, 1050 Bruxelles, Belgium
    BMC Bioinformatics 9:37. 2008
    ..However, these tools are generally used as black boxes, with default parameters. A systematic evaluation of optimal parameters for a footprint discovery strategy can bring a sizeable improvement to the predictions...
  25. ncbi request reprint Inferring meaningful pathways in weighted metabolic networks
    Didier Croes
    SCMBB Université Libre de Bruxelles, Campus Plaine, CP 263, Boulevard du Triomphe, 1050 Bruxelles, Belgium
    J Mol Biol 356:222-36. 2006
    ..We expect our approach to find useful applications in inferring metabolic pathways in newly sequenced genomes...
  26. ncbi request reprint Metrics for comparing regulatory sequences on the basis of pattern counts
    Jacques van Helden
    SCMBB, Universite Libre de Bruxelles, Campus Plaine CP 263, Boulevard du Triomphe, B 1050 Bruxelles, Belgium
    Bioinformatics 20:399-406. 2004
    ..A pattern count-based (dis)similarity metric between sequences could thus be used to classify genes according to their putative regulatory properties...
  27. doi request reprint The powerful law of the power law and other myths in network biology
    Gipsi Lima-Mendez
    Bioinformatique des Génomes et des Réseaux BiGRe, Universite Libre de Bruxelles, Campus Plaine, CP 263, Boulevard du Triomphe, B 1050 Bruxelles, Belgium
    Mol Biosyst 5:1482-93. 2009
    ....
  28. ncbi request reprint Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs
    Didier Gonze
    Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Universite Libre de Bruxelles, CP 263, Campus Plaine, Blvd du Triomphe, B 1050 Bruxelles, Belgium
    Bioinformatics 21:3490-500. 2005
    ..We evaluate our capability to discriminate phosphate- and methionine-responding genes on the basis of putative regulatory elements, despite the similarity between Met4p/Met28p/Cbf1p and Pho4p consensus...
  29. pmc Transcriptional regulation of protein complexes in yeast
    Nicolas Simonis
    Service de Conformation des Macromolécules Biologiques, Centre de Biologie Structurale et Bioinformatique, CP 263, Universite Libre de Bruxelles, Bld du Triomphe, B 1050 Bruxelles, Belgium
    Genome Biol 5:R33. 2004
    ..Second, putative regulatory sequence motifs were identified in the upstream regions of the genes involved in individual complexes and regulons were predicted on the basis of these motifs...
  30. ncbi request reprint Assessing computational tools for the discovery of transcription factor binding sites
    Martin Tompa
    Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195 2350, USA
    Nat Biotechnol 23:137-44. 2005
    ..The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools...
  31. pmc Fine-tuning enhancer models to predict transcriptional targets across multiple genomes
    Stein Aerts
    Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, Vlaams Instituut voor Biotechnologie VIB, Leuven, Belgium
    PLoS ONE 2:e1115. 2007
    ..The ability to model known TF-TG relations, together with the use of multiple genomes, results in a significant step forward in solving the architecture of gene regulatory networks...
  32. ncbi request reprint Discovery of conserved motifs in promoters of orthologous genes in prokaryotes
    Jacques van Helden
    Universite Libre de Bruxelles
    Methods Mol Biol 395:293-308. 2007
    ..The method has been used successfully to detect regulatory elements at various taxonomical levels in prokaryotes. A web interface is available at the Regulatory Sequence Analysis Tools site (http://rsat.scmbb.ulb.ac.be/rsat/)...
  33. pmc Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
    Alexander Stark
    The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02140, USA
    Nature 450:219-32. 2007
    ..We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies...
  34. ncbi request reprint An overview of data models for the analysis of biochemical pathways
    Yves Deville
    Computing Science and Engineering Department, Universite Catholique de Louvain, Louvain la Neuve, Belgium
    Brief Bioinform 4:246-59. 2003
    ..This enables us to underline the strengths and weaknesses of the different approaches, as well as to highlight relevant future research directions...
  35. pmc Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns
    Elisabeth Bon
    Laboratoire de Génétique Moléculaire et Cellulaire CNRS INRA, Institut National Agronomique Paris Grignon, F 78850 Thiverval Grignon, France
    Nucleic Acids Res 31:1121-35. 2003
    ....