Jacques van Helden - curriculum vitae

Address Email: Jacques.van-Helden@univ-amu.fr Web page: http://jacques.van-helden.perso.luminy.univmed.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 14 Fax: +33 4 91 82 87 01

In brief

Born: 07 January 1965, Brussels (Belgium).
Citizenship: Belgian.
Training: Agronomic Engineer, PhD thesis in developmental genetics of Drosophila. Postdocs in bioinformatics.
Current position: Professor at the Université Libre de Bruxelles.
Director of the Service de Bioinformatique des Génomes et des Réseaux (BiGRe).
Research interest: development, evaluation and application of bioinformatics approaches for the analysis of genomes (especially regulatory sequences) and biomolecular networks (regulatory, metabolic, protein interactions).
Teaching: bioinformatics, genome analysis, network analysis, analysis of regulatory sequences, @biostatistics, biology and society.
Languages: French, English, Spanish, Dutch.

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. From 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

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

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

Conferences and seminars

• 28 oral presentations at scientific conferences (3 as keynote speaker, 19 as invited speaker).
• 11 oral presentations at workshops (invited speaker).
• 19 invited seminars.

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

Thesis supervision

• 12 PhD theses (6 directions among which 1 ongoing + 5 co-directions, among which 1 ongoing).
• 21 Master theses (18 directions + 3 co-directions).

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

Ongoing research projects

1. BioMaGNet (2006-2011). Inter-university Attraction Pole. Funding: Belgian Scientific Policy (BELSPO). Topics: Bioinformatics and Modelling — from Genomes to Networks. Partners: 6 Belgian universities.
2. 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).
3. 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).
4. 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).
5. 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".
6. ALLBIO (2011-2015). 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).

Teaching

Teaching subjects

• Master courses: Genomic, proteomic and evolution; Statistics for bioinformatics; Analysis of biomolecular interaction networks; Bioinformatics applied to food production; Bioinformatics approaches to regulation (analysis of cis-regulatory sequences, analysis of transcriptome data); Introduction to bioinformatics.
• Bachelor courses: Biology and society (social and ecologicla issues of biological research and applications).

Courses currently taught

Previous courses

List of previously taught courses http://jacques.van-helden.perso.luminy.univmed.fr/teaching.html

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 submissions

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

Scientific committees of conferences

• 2001: 2nd Belgian Bioinformatics Conference 2001 (BBC'01, Gent - Belgique).
• 2001: Journées Ouvertes Biologie Informatique Mathématiques (JOBIM 2001, Toulouse - France).
• 2002: 3rd Belgian Bioinformatics Conference 2002 (BBC'02, Namur - Belgique).
• 2003. 4th Belgian Bioinformatics Conference (Leuven - Belgium).
• 9/2003. 3rd Workshop on Algorithms in Bioinformatics (Budapest - Hungary).
• 2003. XXI International Conference on Yeast Genetics and Molecular Biology (Göteborg - Sweden). Comparing genomes (workshop).
• 9/2007. International workshop on Machine Learning in Systems Biology. (Evry - France). Scientific committee.
• 4/2008. Benelux Bioinformatics Conference (Leuven - Belgium). Scientific committee.
• 8/2008. JOBIM 2008 (Lille - France). Programming committee.
• 8/2010. Capita Selecta in Complex Disease Analysis, Université de Liège (Liège - Belgium). Programming committee.
• 9/2010. ECCB 2010 - 9th European Conference on Computational Biology, Universiteit Gent (Gent - Belgium). Programming committee.
• 11/2010. Privacy and Scientific Research : from Obstruction to Construction, Privacy Commission Belgium (Bruxelles - Belgium). Scientific committee.
• 6/2011. JOBIM 2008 - Journées Ouvertes Biologie, Mathématiques et Biologie, Institut Pasteur (Paris - France). Programming committee.