Address

Email: Jacques.van-Helden@univ-amu.fr
Web page: http://jacques.van-helden.perso.luminy.univ-amu.fr/
Université d’Aix-Marseille (AMU)
Lab. Technological Advances for Genomics and Clinics (TAGC)
INSERM Unit U1090, 163, Avenue de Luminy, 13288 MARSEILLE cedex 09. France.
Phone: +33 4 91 82 87 49
Fax: +33 4 91 82 87 01


In brief

Born in 1965 in Brussels (Belgium), I graduated in 1987 at the Université Libre de Bruxelles (ULB), as Agronomic Engineering, orientation applied zoology. I did a PhD thesis in neurodevelopmental biology at ULB, under the direction of Alain Ghysen, where I analyzed the mutual regulation of the proneural genes achaete and scute during the development of Drosophila imaginal discs.

Since my PhD thesis, my research activities consisted in conceiving, developing, assessing and applying bioinformatics approaches to decipher regulatory sequences and networks.

In 1997, during a postdoc in Julio Collado-Vides’ lab (UNAM, Cuernavaca, Mexico), I developed bioinformatics tools for the analysis of cis-regulatory elements. Since then, analysis of genome regulation became my main research activity, giving rise to the software suite Regulatory Sequence Analysis Tools (RSAT; http://rsat.eu/), which has been up and running since 1998.

In 1998, I joined Shoshana Wodak’s group at the European Bioinformatics Institute (EBI, Hinxton, UK, 1998-1999), where I developed bioinformatics approaches relying on graph theory (path finding, subgraph extraction), to infer metabolic pathways from sets of functionally related genes (operons, co-expression clusters, …). I pursued this project in Shoshana Wodak’s group at the Université Libre de Bruxelles (ULB, Belgium, since 1999). This work was later taken over by my own PhD students, and gave rise to the Network Analysis Tools (NeAT; http://neat.rsat.eu/), a specialized software suite for the analysis of biomolecular networks (regulatory network, metabolism, interactome).

In 2003 I obtained a position of lecturer at the Université Libre de Bruxelles (ULB, Brussels, Belgium). In 2007, I became director of the Service de Bioinformatique des génomes et des Réseaux (BiGRe). Since 2011, I moved to the South of France and became Professor at Aix-Marseille Université (AMU, Marseille, France).

My teaching domains include bioinformatics, genome analysis, network analysis, analysis of regulatory sequences, biostatistics, programming, biological evolution, biology and society.


Training

  1. 1987: Ingénieur agronome (i.e.: Master of Technology in Agronomic Sciences), orientation: zoologie appliquée. Université Libre de Bruxelles - Belgium. Qualification : grande distinction (high mark).

  2. 1995: Docteur en Sciences Agronomiques (PhD Thesis in Agronomic Sciences). Université Libre de Bruxelles - Belgium. Qualification : la plus grande distinction  (highest mark).


Academic positions

  1. Since November 2011: Professor at Aix-Marseille Université (Marseille, France).

  2. 2010 - 2011: Professor at the Université Libre de Bruxelles (Brussels, Belgium).

  3. 2007-2011: Director of the Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Belgium

  4. 2003-2010: Chargé de cours (Professor) at the Université Libre de Bruxelles (Bruxelles - Belgium).

  5. 1999-2003: Researcher at the Service de Conformation des Macromolécules Biologiques, Université Libre de Bruxelles (Bruxelles - Belgium). Head: Shoshana Wodak. Research topic: development of aMAZE, a database on protein function and biochemical networks.

  6. 1998-99: Postdoc at the European Institute of Bioinformatics (Cambridge - UK). (Head: Shoshana Wodak). Research topic: development of aMAZE, a database on protein function and biochemical networks.

  7. 1997: Postdoc at the Centro de Investigación sobre la Fijacion de Nitrógeno, Universidad Nacional Autonoma de Mexico (Cuernavaca - Mexico), Laboratorio de Biologia Computacional (Head: Julio Collado-Vides). Research topic: computational analysis of regulatory sequences in the yeast Saccharomyces cerevisiae.

  8. 1995-96: Postdoctoral position at the Université de Montpellier II (Montpellier - France), Service de Neurogénétique du Développement (Heads: Christine Dambly-Chaudière & Alain Ghysen). Topic: installation of a digital imaging system and development of image analysis routines.

  9. 1989-1995: PhD Thesis at the Université Libre de Bruxelles (Belgium), Service de Neurobiologie. Supervisor: Alain Ghysen. Title: Analyse fonctionnelle du complexe génique achaete-scute chez Drosophila melanogaster [Functional analysis of the achaete-scute gene complex in Drosophila melanogaster].

  10. 1989: Research fellowship in the laboratory of Huug Schooneveld, Agricultural University (Wageningen - Netherlands). Research topic: immunocytochemical localisation of FMRF-like neuropeptides in the Colorado Beetle Leptinotarsa decemlineata.

  11. 1987: Graduate thesis (Université Libre de Bruxelles, Laboratoire de Biologie Animale et d’Histologie Comparée). Supervisor: Jacqueline Naisse. Title: Relation plante-insecte au niveau du métabolisme des phytostérols et des ecdystéroides: action de 3 inhibiteurs de la biosynthèse des stérols [Plant-insect relationship in the metabolism of phytosterols and ecdysteroids: action of 3 sterol biosynthesis inhibitors].

Mobility

  1. 2010-2011: Invited Professor

    • Ecole Normale Supérieure, Paris, France (2 months).
    • Université de Marseille-Méditerranée, Marseille, France (1 month).
  2. Since 2009: Invited lecturer at the Université Pierre et Marie Curie, Paris, France (12h course per year).

  3. September 2009 - September 2010. Sabbatical year - Université de Marseille - Méditerrannée, Unité TAGC-Technological Advances for Genomics and Clinics.

  4. Since 2005: Invited Professor in the Licenciatura en Ciencias Genomicas (Cuernavaca, Mexico). I teach every year a course on the analysis of regulatory sequences (8h course + 8h practicals).

  5. September - December 2006: sabbatical visit at the Centro de Ciencias Genomicas (Cuernavaca - Mexico). Collaboration with Julio Collado-Vides on the analysis of bacterial regulation.

  6. January - September 2003 (half-time): Researcher at the Interdisciplinary Research Institute (IRI, Lille - France). Research topic: analysis of regulatory networks.


Publications

58 publications in international reviews with referring + 9 invited book chapters + edition of 1 collective volume.

Detailed publication list: http://jacques.van-helden.perso.luminy.univ-amu.fr/publications_JvH.html


Conferences and seminars

Detailed list of conferences and seminars: http://jacques.van-helden.perso.luminy.univ-amu.fr/conferences_JvH.html


Thesis supervision

Detailed list of supervised theses: http://jacques.van-helden.perso.luminy.univ-amu.fr/thesis_supervision_JvH.html


Research projects

Collaborative networks

  1. GREEKC

  2. CHARME

  3. ORICHOICE (2014-2018). Appel à projets génériques, funded by Agence Nationale de la Recherche (France). Topics: Replication origins in the control of genomic stability and cell identity. Coordinator: Marcel Mechali.

Previous collaborative projects

  1. France Génomique WP2.6 (2014-2016). Infrastructure funded by France Génomique. Topics: Regulation of gene expression.

  2. AMIDEX (2014-2016). AMIDEX funded by Aix-Marseille Université. Topics: Hox-mediated control of autophagy : from fundamental towards biomedical. Coordinator: Yacine Graba (Aix-Marseille Université - France).

  3. SEQAHEAD (2011-2014). COST action funded by EU FP7. Topics: Next Generation Sequencing Data Analysis Network. Partners: (Institutions from 16 European countries - Europe). I am vice-chair of the Work Group 5 “Training”.

  4. ALLBIO (2011-2014). Broadening the Bioinformatics Infrastructure to unicellular, animal, and plant science. EU-funded project (Call FP7-KBBE-2011-5-CP-CSA) coordinated by Erik Bongcam-Rudloff (University Uppsala, Sweden). Partners: 10 EU countries (Institutions from 10 European countries - Europe).

  5. ALL-Net (2009-2011). Télévie funded by the Belgian Fonds National de la Recherche Scientifique - Communauté Francophone de Belgique. Topics: Perturbation of interactome networks in acute lymphoblastic leukemia. Partners: Jean-Claude Twizere (Université Catholique de Louvain - Belgique).

  6. MICROME (2009-2013). Large-scale collaborative project (EU FP7) funded by EU FP7. Topics: The Microme Project: A Knowledge-Based Bioinformatics Framework for Microbial Pathway Genomics. Partners: 14 European laboratories (14 European institutions - Europe).

  7. BioMaGNet (2006-2011). Inter-university Attraction Pole. Funding: Belgian Scientific Policy (BELSPO). Topics: Bioinformatics and Modelling — from Genomes to Networks. Partners: 6 Belgian universities.

  8. Ebiomics (2009-2011). Lifelong Learning Programme Erasmus Multilateral projects Virtual Campuses funded by EU FP7. Topics: E-training in bioinformatics for -omics applications. Partners: (Wageningen University (WUR); Swiss Institute for Bioinformatics (SIB) - Europe).

  9. ARC levures (2004-2009). Actions de Recherches Concertées. Financement Communauté Française de Belgique. Sujet: Integration d’approches exprérimentales et théoriques pour décrypter les réseaux moléculaires d’utilisation de l’azote chez la levure. Partenaires: Bruno André, Gianluca Bontempi & Marcelline Kaufman (Université Libre de Bruxelles - Belgique).

  10. BioSapiens (2004-2008). Network of Excellence (EU FP6). topics: European network of bioinformatics resources for the analysis of Human genome and model organisms. Partners: 31 laboratories (24 European institutions - 15 european countries).

  11. TransMaze (2006-2008). Réseaux II. Financement Région Wallonne de Belgique. Sujet: Outils logiciels d’analyse de transduction de signal. Partenaires: Yves Deville (Université Catholique de Louvain - Belgique).


Teaching

Teaching subjects

  • Master courses:
    • Statistical analysis of genomic data
    • Analysis of regulatory networks
    • Programming project for biology
    • Science and society
    • Tools and methods for bioinformatics
  • Bachelor courses:
    • Applied bioinformatics
    • Evolutionary biology

Referring activities

Scientific journals

  • BMC Bioinformatics
  • PLoS Computational Biology
  • Bioinformatics
  • Nucleic Acids Research
  • Journal of Molecular Biology
  • Journal of Theoretical Biology
  • Functional & Integrative Genomics
  • In silico Biology
  • Médecine-Science

Grant evaluations

  • BBSRC - UK
  • IMPG - France
  • INRIA - France
  • ADN - France
  • IWT - Belgium

Scientific committees of conferences