Jacques van Helden - curriculum vitae
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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:
chargé de cours at the l'Université Libre de
Bruxelles.
Director of the Service de Bioinformatique des Génomes et
des Réseaux (BiGRe).
Research interest: bioinformatics of the regulation.
Teaching: bioinformatics and biostatistics.
Competence:
Languages
French (mother tongue), English, Spanish, Dutch.
Training
- 1987: Ingénieur agronome (i.e.: Master of Technology in
Agronomic Sciences), orientation: zoologie
appliquée. Université Libre de Bruxelles -
Belgium. Qualification : grande distinction (high mark).
- 1995: Docteur en Sciences Agronomiques (PhD Thesis in Agronomic
Sciences). Université Libre de Bruxelles -
Belgium. Qualification : la plus grande distinction (highest
mark).
Research experience
- 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].
- 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.
- 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].
- 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.
- 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.
- 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.
- 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.
- 2003: Researcher at the new Interdisciplinary Research
Institute (IRI, Lille - France). Research topic: analysis of
regulatory networks.
- From September 2003: Chargé de cours (Professor) at the
Université Libre de Bruxelles (Bruxelles - Belgium).
- September-December 2006: sabbatical trimester at the
Centro de Ciencias
Genomicas (Cuernavaca - Mexico). Collaboration with Julio
Collado-Vides on the analysis of bacterial regulation.
- Since June 2007: Head of the Laboratoire de Bioinformatique des
Génomes et des Réseaux (BiGRe), Université
Libre de Bruxelles, Belgium
Publications
List of publications
http://www.bigre.ulb.ac.be/Users/jvanheld/HTML_CV/publications_JvH.html
Oral presentations at conferences
- 9/1996. Annual meeting of the Society for Mathematical Biology
(Seattle - USA). Pattern formation and feedback loops. Oral
presentation.
- 3/1998. International Workshop on the Linguistics of Biology and
the Biology of Language (Cuernavaca - Mexico). Word frequency
analysis, if appropriately calibrated, allows to extract regulatory
sites from yeast upstream sequences. Oral presentation.
- 4/1998. EUROFAN (The Netherlands). A web site for the analysis
of upstream regions from the yeast Saccharomyces cerevisiae. Oral
presentation.
- 6/1998. Seminar on modelling and simulation of gene regulation and
metabolic pathways (Daghstuhl - Germany). A web site for
computational analysis of yeast regulatory sequences. Oral
presentation.
- 5/1999. XIXth International Conference on Yeast Genetics and
Molecular Biology. (Rimini - Italy). Computational Analysis of
Yeast Regulatory Sequences. Oral presentation.
- 4/2000. Belgian Bioinformatics Conference (Bruxelles -
Belgium). Graph-based tools for analysing biochemical
pathways. Oral presentation.
- 5/2000. JOBIM - Journées Ouvertes : Biologie, Informatique et
Mathématiques (Montpellier - France). Application de l'analyse des
mots et de l'analyse des graphes à l'interprétation des données
d'expression génomique. Oral presentation.
- 6/2001. ISMB, Biopathway Consortium satellite meeting (Copenhagen
- Denmark). Representing and analyzing biological function with
aMAZE, a database of molecular interactions and processes. Invited
speaker.
- 7/2001. HPNC conference, Universiteit van Amsterdam (Amsterdam -
The Netherlands). Representing and analyzing biological function
with aMAZE, a database of molecular interactions and
processes. Invited speaker.
- 7/2001. Workshop on Bioinformatics and Genome Analysis, Ernst
Schering Research Foundation (Berlin - Germany). Bioinformatics
Approaches to Pathway Analysis. Invited speaker.
- 4/2002. EMBO conference - Prokaryotes in the Third Millenium, EMBL
(Heidelberg - Germany). Analysing and predicting metabolic pathways
on the basis of genomic and functional genomic data. Invited
speaker.
- 6/2002. JOBIM - Satellite meeting on transcriptional regulation
(Saint Malo - France). Gene classification on the basis of upstream
motifs. Invited speaker (opening talk).
- 9/2002. Avances laboratoriales en Biologia molecular y Oncologia,
Sociedad de Bioquimica Clinica (Cochabamba - Bolivia). Invited
speaker.
- 1/2003. Conférence des directeurs d'unité INSERM, Institut
National de la Santé et de la Recherche Médicale (Paris -
France). Approches mathématiques et informatiques pour
l'interprétation les données du transcriptome et du
protéome. Invited speaker.
- 11/2003. Biotecnologia Habana
2003 (La Havana - Cuba). Statistical analysis of non-coding
sequences. Invited speaker.
- 7/2004. Dagstuhl Seminars -
Integrative Bioinformatics - Aspects of the Virtual Cell, Schloss
Dagstuhl (Wadern - Germany). Predicting Gene Regulation by the
Analysis of Non-Coding Sequences. Invited speaker.
- 4/2005. 2nd Barbados Workshop on Genomics and Gene Regulation
(Barbados). Evaluation of pattern discovery results. Invited
speaker.
- 5/2005. ESF Workshop on
Transcription Networks: a global view (Madrid -
Spain). Inferring meaningful pathways and functional distances in
weighted metabolic networks. Invited speaker.
- 7/2005. JOBIM
2005 (Lyon - France). Prediction of regulatory elements in
non-coding sequences : Evaluation of pattern discovery results in
microbes and higher organisms. Invited speaker.
- 9/2005. Otto Warburg
International Summer School and Workshop on Networks and
Regulation, Zuse Institute Berlin (ZIB) (Berlin -
Germany). Assessment of pattern detection approaches for the
prediction of cis-regulatory elements. Invited speaker.
- 11/2005. Cis-regulation workshop, European Bioinformatics
Institute (Hinxton - UK). Evaluating predictions of cis-regulatory
elements. Invited speaker.
- 12/2005. Colloque
LIX polytechnique, Ecole polytechnique (Paris -
France). Inferring meaningful pathways in weighted metabolic
networks. Invited speaker.
- 1/2006. Conférence PRO-A (Programme National sur les Maladies des
OS et des Articulations), INSERM (Paris - France). Apport des
nouvelles approches bio-informatiques et biostatistiques dans la
recherche clinique - vers de possibles applications aux pathologies
articulaires. Invited speaker.
- 4/2006. INSERM Workshop - Identification of non-coding functional
regions in genomes, INSERM (La Londe les Maure - France). Pattern
discovery in genomic sequences. Invited speaker.
- 9/2007. XIVe
Rencontre de la Société francophone de classification, Ecole
nationale supérieure des télécommunications (Paris -
France). Classification de séquences génomiques sur base
d'occurrences de motifs de régulation. Invited speaker.
- 9/2008. New ideas for an old
family: Heat Shock Factors at crossroads between stress, epigenetics
and development, Conférence Jacques Monod: (Roscoff -
France). Bioinformatics approaches for the detection of HSF binding
sites in genomic sequences.. Invited speaker.
- 1/2009. Bioinformatique de Plasmodium falciparum, Museum
d'Histoire Naturelle (Paris - France). Découverte de signaux
cis-régulateurs dans les séquences génomiques de
Plasmodium. Invited speaker.
- 5/2009. Journées de Biologie, Université de
Boumerdes (Boumerdes - Algérie). Ce que nous enseigne
l'analyse des génomes au sujet de
l'évolution. Keynote speaker.
- 6/2009. Colloque
"Cent cinquante ans après l'Origine des espèces : du
darwinisme de Darwin à l'évolutionnisme
contemporain", Collège de France (Paris -
France). Évolution de la régulation génomique:
hiérarchies, rétroaction, modules et
réseaux. Invited speaker. [Video]
- 10/2009. 9ème journée thématique du
Théâtre des Doms: "Darwin et la question des origines: un
défi pour la pensée", Théâtre des Doms
(Avignon - France). Enjeux épistémologiques et
sociétaux du débat
évolution-créationnisme. Invited speaker.
- 10/2009. BioMagnet annual meeting, Universiteit Gent (Gent -
Belgium). The powerful law of the power law and other myths in
network biology. Invited speaker.
- 3/2010. Atelier INSERM: "Biological networks: from molecular
biology to bioinformatics" (Saint Raphaël - France). Neetwork
Analysis Tools. Invited speaker.
Invited seminars
- 3/2000. Séminaire Algorithmique et Biologie, Institut Pasteur
(Paris - France). String-based approaches to pattern discovery in
non-coding DNA sequences.
- 3/2001. Réunion IMPG, ESIL Marseille Luminy (Marseille -
France). Représentation et analyse de la fonction biologique au
moyen d'une base de données d'interactions et de processus
moléculaires.
- 6/2001. Séminaire génopole, Génopole (Evry - France). Détection
d'éléments de régulation dans les séquences non-codantes.
- 6/2001. Séminaire génopole, Génopole (Evry -
France). Représentation et analyse des fonctions biologiques au
moyen d'aMAZE, une base de données d'interactions et de processus
moléculaires.
- 9/2001. Séminaire Algorithmique et Biologie (Lyon -
France). Prediction of transcriptional regulation by the analysis
of non-coding sequences.
- 9/2001. Séminaire génopole, ESIL Marseille Luminy (Marseille -
France). Détection d'éléments de régulation par analyse des
séquences non-codantes.
- 1/2002. Génopole (Lille - France). Analyse des séquences
régulatrices et des données d'expression.
- 5/2002. Institut Pasteur (Paris - France). Prédiction des
éléments cis-régulateurs de levure par analyse des séquences
non-codantes.
- 10/2002. Institut de Recherche Interdisciplinaire en Biologie
humaine et moléculaire (Bruxelles - Belgique). Inferring metabolic
pathways from microarray data.
- 11/2002. Séminaire "Langage du
Génome", IGM Orsay (Orsay - France). Analyse de séquences
régulatrices - Détection de motifs et classification de gènes sur base
de comptages de mots..
- 5/2003. Institut Henri Poincaré (Paris - France). Classifying
genes on the basis of cis-acting regulatory elements.
- 1/2004. University of Gottingen (Gottingen -
Germany). Classifying regulatory sequences on the basis of
predicted signals.
- 3/2004. Workshop on Regulatory
Sequence Motif Discovery, MCB (Uppsala - Sweden). Random models
for pattern discovery.
- 3/2004. Universitat de Valencia (Valencia - Spain). Prediction
of regulatory elements by the analysis of non-coding
sequences.
- 3/2006. Colloquium MAPA, Université Catholique de Louvain
(Louvain-La-Neuve - Belgium). Applications de la théorie des
graphes pour l'analyse des réseaux
métaboliques. Invited speaker.
- 2/2007. BioMagnet Kick-off meeting, Université de Liège (Liège -
Belgique). Research activites of the Service des Conformation des
Macromolécules Biologiques et de Bioinformatique. Invited speaker.
- 3/2007. Séminaire GIGA, Université de Liège (Liège -
Belgique). Inferring co-regulation networks from microbial
genomes. Invited speaker.
- 7/2007. Technische Universitat Dresden (Dresden -
Germany). Inferring co-regulation networks from microbial
genomes. Invited speaker.
Other scientific meetings
- 1989: NATO course "Systems Approaches to Developmental
Neurobiology" (Varenna - Italy).
- 1991: 3rd EMBO Practical Course on Advanced Digital Light
Microscopy (Heidelberg - Germany).
- 1994: I took an active part in the organization of the Vth
European Symposium on Drosophila Neurobiology (La Grande Motte -
France).
- 1997: International Symposium on Nitrogen metabolism in
Ascomycetes (Cuernavaca - Mexico).
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
Teaching
Courses currently taught
- Statistiques appliquées à la bioinformatique
(STAT-F-419 (ex-STAT-F-506))
Statistics applied to bioinformatics
2ECTS cours + 1 ECTS travaux pratiques
- Analyse des réseaux d'interactions moléculaires
(BMOL-F-501)
Analysis of molecular interaction networks
1ECTS cours + 1ECTS travaux personnels
- Génomique, protéomique et évolution
(BIOL-F-449)
Genomics, proteomics and evolution
Bruno André, Jacques van Helden & Patrick Mardulyn
Je donne 2ECTS de cours
- Biologie et société
(BIOL-F-105)
Biology and Society
2ECTS cours
- Enjeux sociaux et écologiques de la biologie
(BIOL-D-101)
Social and ecological issues of biology
2ECTS cours + 1ECTS travaux personnels
- Bioinformatique appliquée au secteur agro-alimentaire
(BING-F-527)
Bioinformatics applied to the agri-food domain.
Dimitri Gillis & Jacques van Helden
Je donne 1ECTS de cours
Courses taught in the past
- 2000-2002. DiplĂ´me Inter-Universitaire d'Études Approfondies en
Bioinformatique. Contribution au DEA:
- membre du comité fondateur et organisateur
- Coordinateur (30h) et enseignant (12h) pour le cours de
Statistiques appliquées à la bioinformatique
- Enseignant (6h) pour le cours de Génomique fonctionnelle
- Enseignant (2h) pour le cours de Modélisation
- Enseignant (1h) pour le cours de Bases de données
- 2002-2003.DEA/DES inter-universitaire en Bioinformatique. ULB
(Bruxelles - Belgique).
- Statistics applied to bioinformatics. Coordinateur (30h) et
enseignant (15h).
- Analysis of microarray data (5h TP).
- Analysis of regulatory sequences (2h + 3h TP).
- Application of graph theory to the analysis of metabolic
pathways (2h).
- Bioinformatics : practical projects (40h TP).
- 2003 - 2005. Candidatures en sociologie et anthropologie. ULB
(Bruxelles - Belgique).
- Enjeux sociaux et écologiques
de la biologie (30h + 15h séminaire).
Occasional courses as invited teacher
- 1999: Bioinformatica 99 (La Havana, Cuba): Atelier d'introduction
à la Bioinformatique : analyse des séquences d'acides
nucléiques et protéiques.
- Genomics and its impact in pharmaceutical industry and
biotechnology.
- Internet resources for sequence analysis (Cours +
travaux pratiques).
- 2000 (Janvier). Cours de formation interdisciplinaire pour
doctorants. Université de Namur (Belgique).
- Génomique fonctionnelle : l'analyse des séquences
non-codantes (2h).
- 2000 (Avril). BioCentrum AIO Course on Bioinformatics in Molecular
Biology. Biocentrum, Universiteit van Amsterdam, Amsterdam - Pays-Bas.
- Pattern recognition and searching in non-coding
sequences (3h cours + 3h travaux pratiques).
- 2000 (Novembre). BioCentrum AIO Course on Bioinformatics in
Molecular Biology. Biocentrum, Universiteit van Amsterdam, Amsterdam -
Pays-Bas.
- Regulatory sequence analysis (3h cours + 3h travaux pratiques).
- 2000 (Décembre). Wageningen (Pays-Bas) - Winterschool in
bioinformatics. Conférencier invité. Exposés :
- Detection of regulatory elements in non-coding sequences (45')
- Representations of biological function and processes in databases (45')
- 2001 (Février). LIRMM (Montpellier - France). Séminaire
dans le cadre du DiplĂ´me d'Enseignement Approfondi (DEA) en
Informatique.
- aMAZE: représentation et analyse de la fonction biologique au
moyen d'une base de données d'interactions et de processus
moléculaires (2h).
- 2001 (Mai). Université de Montpellier II. Séminaire dans le cadre
du DiplĂ´me d'Enseignement Approfondi (DEA) en Neurogénétique.
-
Approches bioinformatiques pour la détection d'éléments de
régulation dans les séquences non-codantes (2h)
- 2001 (Mai). BioCentrum AIO Course on Bioinformatics in
Molecular Biology. Biocentrum, Universiteit van Amsterdam, Amsterdam -
Pays-Bas.
- Regulatory sequence analysis (3h cours + 3h travaux pratiques).
- 2001 (Septembre). DEA BBSG Bioinformatique fonctionnelle (20-23
Novembre) (Marseille - France).
- aMAZE: représentation et analyse de la fonction biologique au
moyen d'une base de données d'interactions et de processus
moléculaires (2h)
- 2001 (Novembre). BioCentrum AIO Course on Bioinformatics in
Molecular Biology. Biocentrum, Universiteit van Amsterdam, Amsterdam -
Pays-Bas.
- Regulatory sequence analysis (3h cours + 3h travaux pratiques).
- 2001 (Décembre). Wageningen (Pays-Bas) - Winterschool in
bioinformatics. Conférencier invité (extended talk).
- Representations and analysis of biochemical networks
- 2002 (Février). Université de Gand (Belgique).
- Graph-based analysis of metabolic pathways (2h).
- 2002 (Juin). BioCentrum AIO Course on Bioinformatics in Molecular
Biology. Biocentrum, Universiteit van Amsterdam, Amsterdam - Pays-Bas.
- Regulatory sequence analysis (3h cours + 3h travaux pratiques).
- 2002.Mission de la Coopération Universitaire au
Développement. Universidad de Cochabamba (Cochabamba -
Bolivie).
- Bioinformatica (15h + 30h TP).
- 2002.Atelier de formation INSERM "From functional genomic data to
the dynamical analysis of molecular networks". INSERM (La
Londe-Les-Maures - France).
- Analysis of regulatory
sequences (1h + 3h TP).
- 2002.Interdisciplinary school
Imaging, modelling, manipulating transcriptional regulatory
networks. Université de Lille (Ambleteuse -
France).
- Inferring metabolic pathways from gene expression
data (1h).
- 2002.Master of
Bioinformatics. Katholieke Universiteit Leuven (Leuven -
Belgique).
- Application of graph theory to the analysis of
metabolic pathways (2h).
- 2003.BioCentrum AIO Course on Bioinformatics in Molecular
Biology. Universiteit van Amsterdam (Amsterdam -
Pays-Bas).
- Analysis of regulatory sequences (2h + 3h
semin).
- 2003.Trimestre
"maths/info/genome" . Institut Henri Poincaré (Paris -
France).
- L'analyse des séquences régulatrices.
- 2003.Bioinformatica 2003 - Taller de introduccion a la
bioinformatica. Instituto de Biotecnologia (La Havana -
Cuba).
- Analysis of regulatory sequences (3h + 3h
TP).
- 2003.Formation INSERM. Génop&ohat;le (Lille -
France).
- Analyse statistiques des données de puces à ADN
(6h + 6h TP).
Programming
- Environments: Unix, Windows and Macintosh.
- Languages: java, object-oriented Perl,
SQL (and previously Prolog, C, Pascal).
Software development
- 1997-now: Regulatory Sequence Analysis
Tools (http://rsat.ulb.ac.be/rsat/).
A software suite for the analysis of regulatory sequences: sequence
retrieval, detection of putative regulatory sites, pattern matching,
automatic drawing of feature maps.
The web interface provides a user-friendly access for biologists, and
is currently installed in several countries (Belgium, Mexico,
Sweden). The current access rate is ~10,000 queries per month.
This project started during my postdoc in Cuernavaca (Mexico). In
1998, the programs were made available on the web, under the name
Yeast-tools. Since 2000, additional genomes have been
installed, and the web interface currently provides access to 108
genomes.
The programs were developed in Perl, and the Web interface in
perl-cgi.
- 1998-2000: aMAZE, a database of Protein Function and Biochemical
Pathways.
(http://www.amaze.ulb.ac.be/). I
developed several components of the database. I wrote the parsers for
data import (in Object-oriented -Perl), and I developed java classes
(diagram management, automatic layout and display of metabolic
pathways, query tools, ...).
- 1998-1999: Pathway analysis . In collaboration with
David Gilbert (City University, London - UK). Prototype programs for
the graph-based analysis of metabolic pathways. The development was
based on the use of constrained logical programming
(prolog). Inbetween, the programs have been re-coded in java and
integrated in the aMAZE database.
- 1991-1996: Image analysis. I developed extensions for the
programs NIH-Image (in Pascal on Macintosh platform), and IPLab (in C
on Macintosh platform). These extensions add functionalities to image
analysis programs, such as control of microscope devices (focus
controller, shutter, filter wheel), image improvement (rank filtering,
deconvolution), image analysis (axonal tracking).
- 1996: MorphoLogical. Analysis of regulatory networks
involved in the development of multicellular organisms, implementation
of the Logical Method (developed by René Thomas and
coworkers). Written in Pascal for Macintosh.
- 1994: AjustePoils. This program was developed for the
comparison of bristle positions between mutant strains of
Drosophila melanogaster (Huang et al., 1995). Written in Think
Pascal on a Macintosh Platform, with use of Macintosh Toolbox (menus,
dialog boxes, event handling).
Extra-academic activities
- 1984 : Vice-president of the "Cercle du libre-examen", student
association organizing conferences and social activities.
- 1985 : Member of the committee in the Cercle d'Information sur le
Service Civil et la Coopération au Développement (student association
organizing debates and activities about North-South relationships).
- 1989-1992 : Founder and vice-president of the non-governmental
organization (NGO) APRAD : Association pour la Recherche-Action en
matière de Développement (http://www.aprad.org).
- 1991: Organizer of the First Belgian Festival of NGO movie
- 1992: Organizer of the Second International Festival of NGO
movie
- 1999-2001 : representative of non-governmental Organizations in
the Belgian Federal Council for Sustainable Development (commissions
"Research orientation" and "Genetically Modified Organisms").
- 2001 (March): involved in the organization of the workshop
Sustainable agriculture in the third world: defining a role for
transgenic crops and research. Member of the editing committee for
the acts of the workshop.
- 2002 (October): organisation of a round-table on the partneship between
University and Non-Governmental Organisations (Université Libre de
Bruxelles, Belgium).