Jacques van Helden

Summary

Country: Belgium

Publications

  1. pmc Transcriptional and epigenetic signatures of zygotic genome activation during early Drosophila embryogenesis
    Elodie Darbo
    Technological Advances for Genomics and Clinics TAGC, INSERM U1090, Universite de la Mediterranee, Campus de Luminy, 13288 Marseille Cedex 9, France
    BMC Genomics 14:226. 2013
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. doi request reprint Predicting metabolic pathways by sub-network extraction
    Karoline Faust
    Department of Applied Biological Sciences DBIT, Vrije Universiteit Brussel, Bruxelles, Belgium
    Methods Mol Biol 804:107-30. 2012

Collaborators

Detail Information

Publications18

  1. pmc Transcriptional and epigenetic signatures of zygotic genome activation during early Drosophila embryogenesis
    Elodie Darbo
    Technological Advances for Genomics and Clinics TAGC, INSERM U1090, Universite de la Mediterranee, Campus de Luminy, 13288 Marseille Cedex 9, France
    BMC Genomics 14:226. 2013
    ..The regulatory mechanisms underlying these drastic transcriptional changes remain largely unknown...
  2. 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...
  3. 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...
  4. 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...
  5. 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...
  6. 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...
  7. 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...
  8. 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...
  9. 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...
  10. doi request reprint Predicting metabolic pathways by sub-network extraction
    Karoline Faust
    Department of Applied Biological Sciences DBIT, Vrije Universiteit Brussel, Bruxelles, Belgium
    Methods Mol Biol 804:107-30. 2012
    ....
  11. 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...
  12. 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...
  13. 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...
  14. 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
    ....
  15. 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/)...
  16. 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...
  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. 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)...