Hidde de Jong

Hidde de Jong
INRIA Grenoble – Rhône-Alpes
655 avenue de l’Europe, Montbonnot
38334 Saint-Ismier cedex, France
Tel. +33 4 76 61 53 35

Secretary: Catherine Bessiere
Tel. +33 4 76 61 53 61

Curriculum vitae

I was born on July 7th 1968 in Delft (the Netherlands). I completed secondary school (VWO) at the Twents Carmellyceum in Oldenzaal, after which I went to study at the University of Twente in Enschede. Between 1986 and 1994 I obtained M.Sc. degrees in Computer Science (cum laude), Management Science (cum laude), and Philosophy of Science, Technology, and Society (cum laude).

In 1993 I started my Ph.D. thesis in the Knowledge-Based Systems group, headed by professor Nicolaas Mars, at the faculty of Computer Science of the University of Twente. My thesis research focused on the development and use of qualitative reasoning techniques for the model-based analysis of measurements in science and engineering. In addition, I maintained a strong interest in the potential role of computers in making scientific discoveries. In 1998 I obtained my Ph.D. degree (cum laude).

In the same year, I joined the Institut National de Recherche en Informatique et en Automatique (INRIA) in France as a research scientist (chargé de recherche). I started to work in the SHERPA research group at the Grenoble – Rhône-Alpes research unit of INRIA in Grenoble. From 2000 to 2007, I was a member of the HELIX research group in bioinformatics, created by François Rechenmann.

In the fall of 2004, I obtained my `Habilitation à diriger des recherches’ from the Université Joseph Fourier in Grenoble. I was appointed senior research scientist (directeur de recherche) at INRIA in the next year. In 2008 I founded with Hans Geiselmann the IBIS group, focusing on the analysis of bacterial regulatory networks by means of experimental and modelling aproaches.

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Research interests

  • Mathematical modeling of biological systems
  • Systems biology of microorganisms
  • Analysis of metabolic networks and biotechnological applications
  • Measurement of gene expression dynamics using fluorescent reporter genes and development of computer tools WellReader and WellInverter
  • Identification of gene regulatory networks from experimental data
  • Qualitative analysis of gene regulatory networks, using the computer tool Genetic Network Analyzer (GNA)

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Research projects

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I have given courses in bioinformatics and systems biology, in particular on the modeling and simulation of bacterial regulatory networks, at the Institut National des Sciences Appliquées (INSA) in Lyon, at the Ecole Normale Supérieure in Paris, and in the Ph.D. Program in Computational Biology of the Instituto Gulbenkian de Ciencia in Lisbon (Portugal). The latest version of these courses, as well as a set of computer exercises for a practical training course on Genetic Network Analyzer (GNA) are available from the INSA course web site.

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Organizational activities

I have been a member of the editorial board of the ACM/IEEE Transactions on Computational Biology and Bioinformatics (2005-), the Journal of Mathematical Biology (2008-), and Biosystems (2010-). I am also serving on the Scientific Advisory Boards of the Microbiology and Food Chain department of INRA and of the INRIA Grenoble – Rhône-Alpes research centre.

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Selected publications


  • E. Cinquemani, V. Laroute, M. Cocaign-Bousquet, H. de Jong, D. Ropers. Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data. Bioinformatics, 33 (14), i301-i310, 2017. Special issue ISMB/ECCB 2017
  • H. de Jong, S. Casagranda, N. Giordano, E. Cinquemani, D. Ropers, J. Geiselmann, J.-L. Gouzé. Mathematical modeling of microbes: Metabolism, gene expression, and growth. Journal of the Royal Society Interface. Accepted for publication
  • H. de Jong, , J. Geiselmann, D. Ropers. Resource reallocation in bacteria by reengineering the gene expression machinery. Trends in Microbiology, 25(6):480-493, 2017



















  • H. de Jong, F. van Raalte. Comparative envisionment construction: A technique for the comparative analysis of dynamical systems. Artificial Intelligence, 115(2):145-214, 1999
  • H. de Jong, N.J.I. Mars, P.E. van der Vet. Computer-supported resolution of measurement conflicts: A case-study in materials science. Foundations of Science, 4(4):427-461, 1999
  • I. Vatcheva, H. de Jong. Semi-quantitative comparative analysis. In: T.D. Dean (ed.), Proceedings of the Sixteenth International Joint Conference on Artificial Intelligence (IJCAI-99), Morgan Kaufmann, San Francisco, CA, 1999, 1034-1040


- H. de Jong. Computer-supported analysis of scientific measurements. CTIT Ph.D. Series 98-23, Ph.D. thesis in Computer Science, University of Twente, Enschede, the Netherlands, 1998


  • H. de Jong, A. Rip. The computer revolution in science: Steps towards the realization of computer-supported discovery environments. Artificial Intelligence, 91(2):225-256, 1997
  • H. de Jong, F. van Raalte. Comparative analysis of structurally different dynamical systems. In: M.E. Pollack(ed.), Proceedings of the Fifteenth International Joint Conference on Artificial Intelligence (IJCAI-97), Morgan Kaufmann, San Francisco, CA, 486-491, 1997


  • H. de Jong, N.J.I. Mars, P.E. van der Vet. CEC: Comparative analysis by envisionment construction. In: W. Wahlster (ed.), Proceedings of the Twelfth European Conference on Artificial Intelligence (ECAI-96), John Wiley & Sons, Chichester, 1996, 476-480


  • H. de Jong, A. Rip. Ontdekkingspraktijk in plaats van logica: Wetenschappelijk ontdekken in computerondersteunde ontdekkingsomgevingen. Kennis en Methode, XIX(2):131-159, 1995


  • N.J.I. Mars, H. de Jong, P.-H. Speel, W.G. ter Stal, P.E. van der Vet. Semi-automatic knowledge acquisition in Plinius: An engineering approach. In: B. Gaines, M. Musen (eds), Proceedings of the Eighth Banff Knowledge Acquisition for Knowledge-based Systems Workshop (KAW-94), Banff, 1994, 4-1-4-15


  • H. de Jong, N.J.I. Mars, P.E. van der Vet. Consistency of scientific knowledge bases. In: A.D. Preece, K. Bellman, J. Combs, C. Culbert, D. O’Leary, L. Miller, N. Sizemore, R. Stachowitz (eds), Working Notes of the AAAI-93 Workshop on Validation and Verification of Knowledge-Based Systems, AAAI Press, Menlo Park, CA, 1993, 64-65

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