Source: https://ibis.inrialpes.fr/article165.html
Timestamp: 2019-04-23 06:02:48+00:00

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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, headed by François Rechenmann, at the 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.
Modeling and simulation of genetic regulatory networks : Signal transduction by cyclic nucleotides in the cyanobacterium Synechocystis PCC 6803 (2000-2002), Programme Bioinformatique inter-EPST.
Validation of models of genetic regulatory networks : Global regulation of transcription in Escherichia coli and Synechocystis PCC 6803 (2002-2004), Programme Bioinformatique inter-EPST.
COBIOS : Engineering and control of biological systems : A new way to tackle complex diseases and biotechnological innovation (2007-2009), NEST-2005-2 PATHFINDER.
EC-MOAN : Scalable modeling and analysis techniques to study emergent cell behavior : Understanding the E. coli stress response (2007-2009), NEST-2005-2 PATHFINDER.
MetaGenoReg : Towards an understanding of the interrelations between metabolic and gene regulation : E. coli carbon metabolism as a test case (2006-2010), ANR Biologie systémique (BIOSYS).
ColAge : Natural and engineering solutions to the control of bacterial growth and aging (2009-2013), Large-Scale Initiative Action INRIA-INSERM.
GemCO : Model reduction, experimental validation, and control for the gene expression machinery in E. coli (2010-2013), ANR Blanc.
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.
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 viagra in australia the Scientific Advisory Board of the Microbiology and Food Chain department of INRA and on the Selection and Review Committees of the International Human Frontier Science Program (HFSP).
J. Izard, C. Gomez Balderas, D. Ropers, S. Lacour, X. Song, Y. Yang, A.B. Lindner, J. Geiselmann, H. de Jong (2015). A synthetic growth switch based on controlled expression of RNA polymerase, Molecular Systems Biology. In press.
A. Kremling, J. Geiselmann, D. Ropers, H. de Jong (2015), Understanding carbon catabolite repression in Escherichia coli using quantitative models, Trends in Microbiology, 23(2):99-109.
D. Stefan, C. Pinel, S. Pinhal, E. Cinquemani, J. Geiselmann, H. de Jong (2015), Inference of quantitative models of bacterial promoters from time-series reporter gene data, PLoS Computational Biology, 11(1) :e1004028.
V. Zulkower, M. Page, D. Ropers, J. Geiselmann, H. de Jong (2015), Robust reconstruction of gene expression profiles from reporter gene data using linear inversion, Bioinformatics, 31(12) :i71-i79, 2015. ISMB/ECCB 2015 special issue.
M. Trauchessec, M. Jaquinod, A. Bonvalot, V. Brun, C. Bruley, D. Ropers, H. de Jong, J. Garin, G. Bestel-Corre, M. Ferro (2014), Mass spectrometry-based workflow for accurate quantification of E. coli enzymes : how proteomics can play a key role in metabolic engineering, Molecular and Cellular Proteomics, 13(4):954-968.
G. Baptist, C. Pinel, C. Ranquet, J. Izard, D. Ropers, H. de Jong, J. Geiselmann (2013), A genome-wide screen for identifying all regulators of a target gene, Nucleic Acids Research, 41(17) :e164.
S. Berthoumieux, M. Brilli, D. Kahn, H. de Jong, E. Cinquemani (2013), On the identifiability of metabolic network models, Journal of Mathematical Biology, 67(6-7):1795-1832.
C. Chaouiya, D. Berenguier, S.M. Keating, A. Naldi, M.P. van Iersel, N. Rodriguez, A. Dräger, F. Büchel, T. Cokelaer, B. Kowal, B. Wicks, E. Gonçalves, J. Dorier, M. Page, P.T. Monteiro, A. von Kamp, I. Xenarios, H. de Jong, M. Hucka, S. Klamt, D. Thieffry, N. Le Novère, J. Saez-Rodriguez, T. Helikar (2013), SBML Qualitative Models : a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools, BMC Systems Biology, 7(1):135.
V. Baldazzi, N. Bertin, H. de Jong, M. Génard (2012), Towards multi-scale plant models : integrating cellular networks, Trends in Plant Science, 17(12):728-736.
V. Baldazzi, D. Ropers, J. Geiselmann, D. Kahn, H. de Jong (2012), Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in E. coli, Journal of Theoretical Biology, 295:100-115.
G. Batt, B. Besson, P.-E. Ciron, H. de Jong, E. Dumas, J. Geiselmann, R. Monte, P.T. Monteiro, M. Page, F. Rechenmann, D. Ropers (2012), Genetic Network Analyzer : A tool for the qualitative modeling and simulation of bacterial regulatory networks, J. van Helden, A. Toussaint, D. Thieffry (eds), Bacterial Molecular Networks : Methods and Protocols, Methods in Molecular Biology, Humana Press, Springer, New York, 439-462.
R. Mateescu, P. Monteiro, E. Dumas, H. de Jong (2011), CTRL : Extension of CTL with regular expressions and fairness operators to verify genetic regulatory networks, Theoretical Computer Science, 412(26):2854-2883. Special issue CMSB 2008.
D. Ropers, V. Baldazzi, H. de Jong (2011), Model reduction using piecewise-linear approximations preserves dynamic properties of the carbon starvation response in Escherichia coli, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(1):166-181.
V. Baldazzi, D. Ropers, Y. Markowicz, D. Kahn, J. Geiselmann, H. de Jong (2010), The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes, PLoS Computational Biology, 6(6) : e1000812.
F. Boyer, B. Besson, G. Baptist, J. Izard, C. Pinel, D. Ropers, J. Geiselmann, H. de Jong (2010), A MATLAB program for the analysis of fluorescence and luminescence reporter gene data, Bioinformatics, 26(9):1262-1263.
H. de Jong, C. Ranquet, D. Ropers, C. Pinel, J. Geiselmann (2010), Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria, BMC Systems Biology, 4:55.
H. de Jong (2009), Vers la cellule virtuelle, DocSciences, 8:20-25.
D. Ropers, H. de Jong, J. Geiselmann (2009), Mathematical modeling of genetic regulatory networks : Stress responses in Escherichia coli, P. Fu, M. Latterich, S. Panke, Systems and Synthetic Biology, Wiley & Sons, Hoboken NJ, 235-271.
H. de Jong (2008), Qualitative modeling and simulation of bacterial regulatory networks, In : A. Uhrmacher, M. Heiner (eds.), Computational Methods in Systems Biology (CMSB-08), Lecture Notes in Bioinformatics 5307, Springer-Verlag, Berlin, 1.
H. de Jong, M. Page (2008), Search for steady states of piecewise-linear differential equation models of genetic regulatory networks, ACM/IEEE Transactions on Computational Biology and Bioinformatics, 5(2):508-522.
S. Drulhe, G. Ferrari-Trecate, H. de Jong (2008), The switching threshold reconstruction problem for piecewise affine models of genetic regulatory networks, IEEE Transactions on Automatic Control & IEEE Transactions on Circuits and Systems I, 53(1):153-165. Joint special issue on systems biology.
R. Mateescu, P.T. Monteiro, E. Dumas, H. de Jong (2008), Computation tree regular logic for genetic regulatory networks, In : S. Cha, J.-Y. Choi, M. Kim, I. Lee, M. Viswanathan (eds.), Proceedings of the 6th International Symposium on Automated Technology for Verification and Analysis (ATVA’08), Lecture Notes in Computer Science 5311, Springer, Berlin, 48-63, 2008. For longer version, see Technical Report INRIA, RR-6521.
P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas, H. de Jong (2008), Temporal logic patterns for querying dynamic models of cellular interaction networks, Bioinformatics, 24(16) :i227-i233. Special issue ECCB-2008.
P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas, H. de Jong (2008), Temporal logic patterns for querying qualitative models of genetic regulatory networks, In : M. Ghallab, C.D. Spyropoulos, N. Fakotakis, N. Avouris (eds.), Proceedings of 18th European Conference on Artificial Intelligence (ECAI2008), IOS Press, Amsterdam, 229-233, 2008.
R. Porreca, S. Drulhe, H. de Jong, G. Ferrari-Trecate (2008), Structural identification of piecewise-linear models of genetic regulatory networks, Journal of Computational Biology, 15(10):1365-1380, 2008.
F. Grognard, H. de Jong, J.-L. Gouzé (2007), Piecewise-linear models of genetic regulatory networks : Theory and example, I. Queinnec, S. Tarbouriech, G. Garcia, S. Niculescu (eds), Biology and Control Theory : Current Challenges, Lecture Notes in Control and Information Sciences (LNCIS) 357, Springer-Verlag, Berlin, 137-159.
M.W.J.M. Musters, H. de Jong, P.P.J. van den Bosch, N.A.W. van Riel (2007), Qualitative analysis of nonlinear biochemical networks with piecewise-affine functions, A. Bemporad, A. Bicchi, G. Buttazzo (eds), Hybrid Systems : Computation and Control, HSCC 2007, Lecture Notes in Computer Science 4416, Springer-Verlag, Berlin, 727-730.
R. Casey, H. de Jong, J.-L. Gouzé (2006), Piecewise-linear models of genetic regulatory networks : Equilibria and their stability, Journal of Mathematical Biology, 52(1):27-56.
S. Drulhe, G. Ferrari-Trecate, H. de Jong, A. Viari (2006), Reconstruction of switching thresholds in piecewise-affine models of genetic regulatory networks, J. Hespanha, A. Tiwari (eds), Hybrid Systems : Computation and Control, HSCC 2006, Lecture Notes in Computer Science 3927, Springer-Verlag, Berlin, 184-199.
H. de Jong, D. Ropers (2006), Qualitative approaches towards the analysis of genetic regulatory networks, Z. Szallasi, V. Periwal, J. Stelling (eds), System Modeling in Cellular Biology : From Concepts to Nuts and Bolts, MIT Press, Cambridge, MA, 125-148.
G. Batt, D. Ropers, H. de Jong, J. Geiselmann, R. Mateescu, M. Page, D. Schneider (2005), Analysis and verification of qualitative models of genetic regulatory networks : A model-checking approach. L.P. Kaelbling (ed.), Proceedings of the Nineteenth International Joint Conference on Artificial Intelligence (IJCAI-05), Morgan Kauffman, San Francisco, CA., 370-375.
G. Batt, D. Ropers, H. de Jong, J. Geiselmann, R. Mateescu, M. Page, D. Schneider (2005), Validation of qualitative models of genetic regulatory networks by model checking : Analysis of the nutritional stress response in Escherichia coli, Bioinformatics, 21(Suppl 1) :i19-i28, special issue ISMB-2005.
G. Batt, H. de Jong, J. Geiselmann, M. Page, D. Ropers, D. Schneider (2005), Qualitative analysis and verification of hybrid models of genetic regulatory networks : Nutritional stress response in Escherichia coli, M. Morari, L. Thiele (eds), Hybrid Systems : Computation and Control, HSCC 2005, Lecture Notes in Computer Science 3414, Springer-Verlag, Berlin, 134-150.
H. de Jong (2004), Modélisation et simulation qualitative de réseaux de régulation génique, report presented for obtaining the `Habilitation à diriger des recherches’, Joseph Fourier University, Grenoble.
H. de Jong, J. Geiselmann (2004), Modélisation et simulation de réseaux de régulation génique par des équations différentielles ordinaires, J.-F. Boulicaut, O. Gandrillon (eds), Informatique pour l’analyse du transcriptome, Hermès, Paris, 143-185.
H. de Jong, J.-L. Gouzé, C. Hernandez, M. Page, T. Sari, J. Geiselmann (2003), Hybrid modeling and simulation of genetic regulatory networks : A qualitative approach, A. Pnueli, O. Maler (eds), Hybrid Systems : Computation and Control, HSCC 2003, Lecture Notes in Computer Science 2623, Springer-Verlag, Berlin, 267-282.
C. Hernandez, H. de Jong, J. Geiselmann, M. Page (2002), VisualGNA : A graphical interface for the qualitative simulation of genetic regulatory networks, J. Nicolas, C. Thermes (eds), Recueil des Actes des Journées Ouvertes Biologie Informatique Mathématiques, JOBIM 2002, Saint-Malo, 335-336.
H. de Jong, M. Page, C. Hernandez, J. Geiselmann (2001), Qualitative simulation of genetic regulatory networks : Method and application, B. Nebel (ed.), Proceedings of the Seventeenth International Joint Conference on Artificial Intelligence, IJCAI-01, Morgan Kaufmann, San Francisco, CA, 67-73.
I. Vatcheva, O. Bernard,H.de Jong, J.-L. Gouzé, N.J.I. Mars (2001), Discrimination of semi-quantitative models by experiment selection : Method and application in population biology, B. Nebel (ed.), Proceedings of the Seventeenth International Joint Conference on Artificial Intelligence, IJCAI-01, Morgan Kaufmann, San Francisco, CA, 74-79.
H. de Jong, F. van Raalte (1999), Comparative envisionment construction : A technique for the comparative analysis of dynamical systems, Artificial Intelligence, 115(2), 145-214.
H. de Jong, N.J.I. Mars, P.E. van der Vet (1999), Computer-supported resolution of measurement conflicts : A case-study in materials science, Foundations of Science, 4(4):427-461.
H. de Jong, A. Rip (1997), The computer revolution in science : Steps towards the realization of computer-supported discovery environments, Artificial Intelligence, 91(2):225-256.
H. de Jong, N.J.I. Mars, P.E. van der Vet (1996), CEC : Comparative analysis by envisionment construction, W. Wahlster (ed.), Proceedings of the Twelfth European Conference on Artificial Intelligence, ECAI-96, John Wiley & Sons, Chichester, 476-480.
H. de Jong, A. Rip (1995), Ontdekkingspraktijk in plaats van logica : Wetenschappelijk ontdekken in computerondersteunde ontdekkingsomgevingen, Kennis en Methode, XIX(2):131-159.
N.J.I. Mars, H. de Jong, P.-H. Speel, W.G. ter Stal, P.E. van der Vet (1994), Semi-automatic knowledge acquisition in Plinius : An engineering approach, 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 (1993), Consistency of scientific knowledge bases, 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, 64-65.

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