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Hidde de Jong

 

Senior research scientist INRIA

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INRIA Grenoble - Rhône-Alpes
655 avenue de l’Europe, Montbonnot
38334 Saint-Ismier cedex
France

Tel. +33 4 76 61 53 35
Fax +33 4 56 52 71 20
Hidde.de-Jong@inria.fr
Web page

Secretary (Françoise de Coninck)
Tel. +33 4 76 61 53 63

 
 


-  Curriculum vitae
-  Research interests
-  Projects and collaborations
-  Courses
-  Organizational and other activities
-  Selected publications

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, 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.


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Research interests

-  Mathematical modeling of biological systems
-  Development of mathematical and computational approaches for the qualitative analysis of dynamical systems
-  Analysis of gene regulation and metabolism in bacteria, notably in the model organism Escherichia coli
-  Identification of bacterial regulatory networks from experimental data
-  Development of the computer tool Genetic Network Analyzer (GNA)


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Projects and collaborations

-  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.
-  GDyn : Dynamic analysis of genetic regulatory networks (2002-2004), Action de Recherche Coopérative INRIA. Article in INRIA newsletter
-  BacAttract : Theoretical and experimental analysis of the attractors of genetic regulatory networks : Global regulation of transcription in Escherichia coli and Synechocystis PCC 6803 (2003-2006), ACI IMPBio
-  Hygeia : Hybrid systems for biochemical network modeling and analysis (2005-2007), NEST-2003-1 ADVENTURE. Article in INRIA year report
-  Experimental verification of the predictions of a model of the E. coli nutritional stres response (2005-2007), CPER.
-  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.
-  RESET : Arrest and restart of the gene expression machinery in bacteria : from mathematical models to biotechnological applications (2012-2016), Investissements d’Avenir, Bioinformatique


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Courses

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 and other 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 Board of the Microbiology and Food Chain department of INRA and on the Review Committee of the International Human Frontier Science Program (HFSP).


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Selected publications

2014

-  V. Acary, H. de Jong, B. Brogliato (2014), Numerical simulation of piecewise-linear models of gene regulatory networks using complementarity systems, Physica D : Nonlinear Phenomena, 269:103-119
-  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. To appear.

2013

-  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.
-  S. Berthoumieux, H. de Jong, G. Baptist, C. Pinel, C. Ranquet, D. Ropers, J. Geiselmann (2013), Shared control of gene expression in bacteria by transcription factors and global physiology of the cell, Molecular Systems Biology, 9:634. Editors’ choice in Science
-  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.

2012

-  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.

2011

-  S. Berthoumieux, M. Brilli, H. de Jong, D. Kahn, E. Cinquemani (2011), Identification of metabolic network models from incomplete high-throughput datasets, Bioinformatics, 17(13) :i186-i195, 2011. Special issue ISMB/ECCB 2011. Outstanding student paper award at ISMB/ECCB 2011
-  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.
-  R. Silva-Rocha, H. de Jong, J. Tamames, V. de Lorenzo, The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene, BMC Systems Biology, 5:191, 2011

2010

-  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.
-  G. Batt, M. Page, I. Cantone, G. Goessler, P. Monteiro, H. de Jong (2010), Efficient parameter search for qualitative models of regulatory networks using symbolic model checking, Bioinformatics, 26(18) :i603-i610. Special issue ECCB 2010
-  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.

2009

-  H. de Jong (2009), Vers la cellule virtuelle, DocSciences, 8:20-25.
-  P.T. Monteiro, E. Dumas, B. Besson, R. Mateescu, M. Page, A.T. Freitas, H. de Jong (2009), A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks, BMC Bioinformatics, 10:450, 2009
-  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.

2008

-  G. Batt, H. de Jong, M. Page, J. Geiselmann (2008), Symbolic reachability analysis of genetic regulatory networks using qualitative abstractions, Automatica, 44(4):982-989. For longer version, see Technical Report INRIA, RR-6136.
-  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.

2007

-  G. Batt, H. de Jong, J. Geiselmann, J.-L. Gouzé, M. Page, D. Ropers, T. Sari, D. Schneider (2007), Analyse qualitative de la dynamique de réseaux de régulation génique par des modèles linéaires par morceaux, Technique et Science Informatique, 26(1-2):11-45.
-  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.
-  D. Ropers, H. de Jong, J. Geiselmann (2007), Modélisation de la réponse au stress nutritionnel de la bactérie Escherichia coli, Biofutur, 275:36-39.

2006

-  G. Batt, R. Casey, H. de Jong, J. Geiselmann, J.-L. Gouzé, M. Page, D. Ropers, T. Sari, D. Schneider (2006), Qualitative analysis of the dynamics of genetic regulatory networks using piecewise-linear models, E. Pecou, S. Martinez, A. Maass (eds.), Mathematical and Computational Methods in Biology, Editions Hermann, Paris, 206-239.
-  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.
-  C. Chaouiya, H. de Jong, D. Thieffry (2006), Dynamical modeling of biological regulatory networks, BioSystems, 84(2):77-80. Introduction to special issue.
-  H. de Jong, D. Ropers (2006), Strategies for dealing with incomplete information in the modeling of molecular interaction networks, Briefings in Bioinformatics, 7(4):354-363.
-  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.
-  D. Ropers, H. de Jong, M. Page, D. Schneider, J. Geiselmann (2006), Qualitative simulation of the carbon starvation response in Escherichia coli, BioSystems, 84(2):124-152. Top 10 most cited articles
-  I. Vatcheva, O. Bernard, H. de Jong, N.J.I. Mars (2006), Experiment selection for the discrimination of semi-quantitative models of dynamical systems, Artificial Intelligence, 170(4-5):472-506.

2005

-  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 (2005), Qualitative simulation and related approaches for the analysis of dynamical systems, Knowledge Engineering Review, 19(2):93-132.
-  H. de Jong, J. Geiselmann (2005), Modeling and simulation of genetic regulatory networks by ordinary differential equations, J. Chen, E.R. Dougherty, I. Shmulevich, Z.J. Wang (eds), Genomic Signal Processing and Statistics, Hindawi Publishing Corporation, New York, 201‑239.
-  H. de Jong, D. Ropers, C. Chaouiya, D. Thieffry (2005), Modélisation, analyse et simulation de réseaux de régulation génique, Biofutur, 252:36-40.
-  C. Ranquet, A. Toussaint, H. de Jong, G. Maenhaut-Michel, J. Geiselmann (2005), Control of bacteriophage Mu lysogenic repression, Journal of Molecular Biology, 353(1):186-195.
-  F. Rechenmann, H. de Jong (2005), Le vivant en équations, La Recherche, 383:32-37.

2004

-  G. Batt, D. Bergamini, H. de Jong, H. Gavarel, R. Mateescu (2004), Model checking genetic regulatory networks using GNA and CADP, Eleventh International SPIN Workshop on Model Checking of Software, SPIN 2004, Lecture Notes in Computer Science 2989, Springer-Verlag, Berlin, 158-163.
-  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. Geiselmann, G. Batt, C. Hernandez, M. Page (2004), Qualitative simulation of the initiation of sporulation in Bacillus subtilis, Bulletin of Mathematical Biology, 66(2):261-300.
-  H. de Jong, J.-L. Gouzé, C. Hernandez, M. Page, T. Sari, J. Geiselmann (2004), Qualitative simulation of genetic regulatory networks using piecewise-linear models, Bulletin of Mathematical Biology, 66(2):301-340. Recommended by Faculty of 1000
-  D. Eveillard, D. Ropers, H. de Jong, C. Branlant, A. Bockmayr (2004), A multi-scale constraint programming model of alternative splicing regulation, Theoretical Computer Science, 135(1):3-24.

2003

-  H. de Jong (2003), Simulation qualitative, L. Travé-Massuyès and P. Dague (eds), Modèles et raisonnements qualitatifs, Hermès, Paris, 269-329.
-  H. de Jong (2003), Modeling and simulation of genetic regulatory networks, L. Benvenuti, A. De Santis, L. Farina (eds), Positive Systems, POSTA 2003, Lectures Notes in Control and Information Sciences 294, Springer-Verlag, Berlin, 111-118.
-  H. de Jong, J. Geiselmann, C. Hernandez, M. Page (2003), Genetic Network Analyzer : Qualitative simulation of genetic regulatory networks, Bioinformatics, 19(3):336-344. Recommended by Faculty of 1000
-  H. de Jong, J. Geiselmann, D. Thieffry (2003), Qualitative modeling and simulation of developmental regulatory networks, S. Kumar, P.J. Bentley (eds), On Growth, Form, and Computers, Academic Press, London, 109-134.
-  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.
-  D. Eveillard, D. Ropers, H. de Jong, C. Branlant, A. Bockmayr (2003), Multiscale modeling of alternative splicing regulation, C.Priami (ed.), Computational Methods in Systems Biology, CMSB-03, Lecture Notes in Computer Science 2602, Springer-Verlag, Berlin, 75-87.
-  D. Schneider, A. Latifi, H. de Jong, J. Geiselmann (2003), Dynamics and simulation of the genetic regulatory networks in bacteria, S.G. Pandalai (ed.), Recent Research Developments in Genetics 3:55-83.

2002

-  H. de Jong(2002), Modeling and simulation of genetic regulatory Systems : A literature review, Journal of Computational Biology, 9(1):67-103. Top 5 most cited papers
-  H. de Jong, J.-L. Gouzé, C. Hernandez, M. Page, T. Sari, J. Geiselmann (2002), Dealing with discontinuities in the qualitative simulation of genetic regulatory networks, Proceedings of Fifteenth European Conference on Artifical Intelligence, ECAI-02, F. van Harmelen (ed.), IOS Press, Amsterdam, 412-416.
-  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.
-  D. Thieffry, H. de Jong (2002), Modélisation, analyse et simulation des réseaux génétiques, Médécine/Sciences,18(4):492-502.

2001

-  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.

2000

-  H.de Jong, M. Page (2000), Qualitative simulation of large and complex genetic regulatory systems, W.Horn (ed.), Proceedings of the Fourteenth European Conference on Artificial Intelligence, ECAI 2000, IOS Press, Amsterdam, 141-145.
-  I. Vatcheva, H. de Jong, N.J.I. Mars (2000), Selection of perturbation experiments for model discrimination, W.Horn (ed.), Proceedings of the Fourteenth European Conference on Artificial Intelligence, ECAI 2000, IOS Press, Amsterdam, 191-195.

1999

-  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.
-  I. Vatcheva, H. de Jong (1999), Semi-quantitativecomparative analysis, T.D. Dean (ed.), Proceedings of the Sixteenth International Joint Conference on Artificial Intelligence, IJCAI-99, Morgan Kaufmann, San Francisco, CA, 1034-1040.

1998

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

1997

-  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, F. van Raalte (1997), Comparative analysis of structurally different dynamical systems, M.E. Pollack(ed.), Proceedings of the Fifteenth International Joint Conference on Artificial Intelligence, IJCAI-97, Morgan Kaufmann, San Francisco, CA, 486-491.

1996

-  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.

1995

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

1994

-  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.

1993

-  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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