CEC: Comparative Analysis by Envisionment Construction. - Hidde de Jong; Nicolaas J. I. Mars; Paul E. van der Vet (ECAI, 1996)

Comparative Analysis of STructurally Different Dynamical Systems. - Hidde de Jong; Frank van Raalte (IJCAI (1), 1997)

The Computer Revolution in Science: Steps Towards the Realization of Computer-Supported Discovery Environments. - Hidde de Jong; Arie Rip (Artif. Intell., 1997)

Computer-supported analysis of scientific measurements. - Hidde de Jong (1998)

Semi-Quantitative Comparative Analysis. - Ivayla Vatcheva; Hidde de Jong (IJCAI, 1999)

Comparative envisionment construction: A technique for the comparative analysis of dynamical systems. - Hidde de Jong; Frank van Raalte (Artif. Intell., 1999)

Qualitative Simulation of Large and Complex Genetic Regulation Systems. - Hidde de Jong; Michel Page (ECAI, 2000)

Selection of Perturbation Experiments for Model Discrimination. - Ivayla Vatcheva; Hidde de Jong; Nicolaas J. I. Mars (ECAI, 2000)

Qualitative Simulation of Genetic Regulatory Networks: Method and Application. - Hidde de Jong; Michel Page; Céline Hernandez; Johannes Geiselmann (IJCAI, 2001)

Discrimination of Semi-Quantitative Models by Experiment Selection: Method and Application in Population Biology. - Ivayla Vatcheva; Olivier Bernard 003; Hidde de Jong; Jean-Luc Gouzé; Nicolaas J. I. Mars (IJCAI, 2001)

Dealing with Discontinuities in the Qualitative Simulation of Genetic Regulatory Networks. - Hidde de Jong; Jean-Luc Gouzé; Céline Hernandez; Michel Page; Sari Tewfik; Johannes Geiselmann (ECAI, 2002)

Modeling and Simulation of Genetic Regulatory Systems: A Literature Review. - Hidde de Jong (J. Comput. Biol., 2002)

Multiscale Modeling of Alternative Splicing Regulation. - Damien Eveillard; Delphine Ropers; Hidde de Jong; Christiane Branlant; Alexander Bockmayr (CMSB, 2003)

Hybrid Modeling and Simulation of Genetic Regulatory Networks: A Qualitative Approach. - Hidde de Jong; Jean-Luc Gouzé; Céline Hernandez; Michel Page; Sari Tewfik; Johannes Geiselmann (HSCC, 2003)

Modeling and Simulation of Genetic Regulatory Networks. - Hidde de Jong (POSTA, 2003)

Genetic Network Analyzer: qualitative simulation of genetic regulatory networks. - Hidde de Jong; Johannes Geiselmann; Céline Hernandez; Michel Page (Bioinform., 2003)

Model Checking Genetic Regulatory Networks Using GNA and CADP. - Grégory Batt; Damien Bergamini; Hidde de Jong; Hubert Garavel; Radu Mateescu 001 (SPIN, 2004)

Qualitative simulation and related approaches for the analysis of dynamic systems. - Hidde de Jong (Knowl. Eng. Rev., 2004)

A multi-scale constraint programming model of alternative splicing regulation. - Damien Eveillard; Delphine Ropers; Hidde de Jong; Christiane Branlant; Alexander Bockmayr (Theor. Comput. Sci., 2004)

Stability of Equilibria for Piecewise-linear Models of Genetic Regulatory Networks. - Richard Casey; Hidde de Jong; Jean-Luc Gouzé (CDC/ECC, 2005)

Qualitative Analysis and Verification of Hybrid Models of Genetic Regulatory Networks: Nutritional Stress Response in. - Grégory Batt; Delphine Ropers; Hidde de Jong; Johannes Geiselmann; Michel Page; Dominique Schneider (HSCC, 2005)

Analysis and Verification of Qualitative Models of Genetic Regulatory Networks: A Model-Checking Approach. - Grégory Batt; Delphine Ropers; Hidde de Jong; Johannes Geiselmann; Radu Mateescu 001; Michel Page; Dominique Schneider (IJCAI, 2005)

Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli. - Grégory Batt; Delphine Ropers; Hidde de Jong; Johannes Geiselmann; Radu Mateescu 001; Michel Page; Dominique Schneider (ISMB (Supplement of Bioinformatics), 2005)

Reconstruction of Switching Thresholds in Piecewise-Affine Models of Genetic Regulatory Networks. - Samuel Drulhe; Giancarlo Ferrari-Trecate; Hidde de Jong; Alain Viari (HSCC, 2006)

Experiment selection for the discrimination of semi-quantitative models of dynamical systems. - Ivayla Vatcheva; Hidde de Jong; Olivier Bernard 003; Nicolaas J. I. Mars (Artif. Intell., 2006)

Strategies for dealing with incomplete information in the modeling of molecular interaction networks. - Hidde de Jong; Delphine Ropers (Briefings Bioinform., 2006)

Qualitative Analysis of Nonlinear Biochemical Networks with Piecewise-Affine Functions. - M. W. J. M. Musters; Hidde de Jong; P. P. J. van den Bosch; Natal A. W. van Riel (HSCC, 2007)

Analyse qualitative de la dynamique de réseaux de régulation génique par des modèles linéaires par morceaux. - Grégory Batt; Hidde de Jong; Johannes Geiselmann; Jean-Luc Gouzé; Michel Page; Delphine Ropers; Sari Tewfik; Dominique Schneider (Tech. Sci. Informatiques, 2007)

Computation Tree Regular Logic for Genetic Regulatory Networks. - Radu Mateescu 001; Pedro T. Monteiro 001; Estelle Dumas; Hidde de Jong (ATVA, 2008)

Qualitative Modeling and Simulation of Bacterial Regulatory Networks. - Hidde de Jong (CMSB, 2008)

Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks. - Pedro T. Monteiro 001; Delphine Ropers; Radu Mateescu 001; Ana T. Freitas; Hidde de Jong (ECAI, 2008)

Temporal logic patterns for querying dynamic models of cellular interaction networks. - Pedro T. Monteiro 001; Delphine Ropers; Radu Mateescu 001; Ana T. Freitas; Hidde de Jong (ECCB, 2008)

Symbolic reachability analysis of genetic regulatory networks using discrete abstractions. - Grégory Batt; Hidde de Jong; Michel Page; Johannes Geiselmann (Autom., 2008)

Structural Identification of Piecewise-Linear Models of Genetic Regulatory Networks. - Riccardo Porreca; Samuel Drulhe; Hidde de Jong; Giancarlo Ferrari-Trecate (J. Comput. Biol., 2008)

The Switching Threshold Reconstruction Problem for Piecewise-Affine Models of Genetic Regulatory Networks. - Samuel Drulhe; Giancarlo Ferrari-Trecate; Hidde de Jong (IEEE Trans. Autom. Control., 2008)

Search for Steady States of Piecewise-Linear Differential Equation Models of Genetic Regulatory Networks. - Hidde de Jong; Michel Page (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks. - Pedro T. Monteiro 001; Estelle Dumas; Bruno Besson; Radu Mateescu 001; Michel Page; Ana T. Freitas; Hidde de Jong (BMC Bioinform., 2009)

Modeling and formal verification of biological regulatory networks: An integrative approach. - Pedro T. Monteiro 001; Ana T. Freitas; Delphine Ropers; Radu Mateescu 001; Hidde de Jong (BIBM Workshops, 2010)

Efficient parameter search for qualitative models of regulatory networks using symbolic model checking. - Grégory Batt; Michel Page; Irene Cantone; Gregor Goessler; Pedro T. Monteiro 001; Hidde de Jong (Bioinform., 2010)

WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data. - Frédéric Boyer; Bruno Besson; Guillaume Baptist; Jérôme Izard; Corinne Pinel; Delphine Ropers; Johannes Geiselmann; Hidde de Jong (Bioinform., 2010)

Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria. - Hidde de Jong; Caroline Ranquet; Delphine Ropers; Corinne Pinel; Johannes Geiselmann (BMC Syst. Biol., 2010)

The Carbon Assimilation Network in Escherichia coli Is Densely Connected and Largely Sign-Determined by Directions of Metabolic Fluxes. - Valentina Baldazzi; Delphine Ropers; Yves Markowicz; Daniel Kahn; Johannes Geiselmann; Hidde de Jong (PLoS Comput. Biol., 2010)

Identification of metabolic network models from incomplete high-throughput datasets. - Sara Berthoumieux; Matteo Brilli; Hidde de Jong; Daniel Kahn; Eugenio Cinquemani (Bioinform., 2011)

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. - Rafael Silva-Rocha; Hidde de Jong; Javier Tamames; Víctor de Lorenzo (BMC Syst. Biol., 2011)

Model Reduction Using Piecewise-Linear Approximations Preserves Dynamic Properties of the Carbon Starvation Response in Escherichia coli. - Delphine Ropers; Valentina Baldazzi; Hidde de Jong (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

CTRL: Extension of CTL with regular expressions and fairness operators to verify genetic regulatory networks. - Radu Mateescu 001; Pedro T. Monteiro 001; Estelle Dumas; Hidde de Jong (Theor. Comput. Sci., 2011)

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. - Claudine Chaouiya; Duncan Bérenguier; Sarah M. Keating; Aurélien Naldi; Martijn P. van Iersel; Nicolas Rodriguez 001; Andreas Dräger; Finja Büchel; Thomas Cokelaer; Bryan M. Kowal; Benjamin Wicks; Emanuel J. V. Gonçalves; et al. (BMC Syst. Biol., 2013)

Fluorescent Reporter Genes and the Analysis of Bacterial Regulatory Networks. - Hidde de Jong; Johannes Geiselmann (HSB, 2014)

Robust reconstruction of gene expression profiles from reporter gene data using linear inversion. - Valentin Zulkower; Michel Page; Delphine Ropers; Johannes Geiselmann; Hidde de Jong (Bioinform., 2015)

Inference of Quantitative Models of Bacterial Promoters from Time-Series Reporter Gene Data. - Diana Stefan; Corinne Pinel; Stéphane Pinhal; Eugenio Cinquemani; Johannes Geiselmann; Hidde de Jong (PLoS Comput. Biol., 2015)

Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies. - Nils Giordano; Francis Mairet; Jean-Luc Gouzé; Johannes Geiselmann; Hidde de Jong (PLoS Comput. Biol., 2016)

Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data. - Eugenio Cinquemani; Valérie Laroute; Muriel Cocaign-Bousquet; Hidde de Jong; Delphine Ropers (Bioinform., 2017)

An ensemble of mathematical models showing diauxic growth behaviour. - Andreas Kremling; Johannes Geiselmann; Delphine Ropers; Hidde de Jong (BMC Syst. Biol., 2018)

Optimal control of bacterial growth for metabolite production: The role of timing and costs of control. - Eugenio Cinquemani; Francis Mairet; I. Yegorov; Hidde de Jong; Jean-Luc Gouzé (ECC, 2019)

WellInverter: a web application for the analysis of fluorescent reporter gene data. - Yannick Martin; Michel Page; Christophe Blanchet; Hidde de Jong (BMC Bioinform., 2019)

Enhanced production of heterologous proteins by a synthetic microbial community: Conditions and trade-offs. - Marco Mauri; Jean-Luc Gouzé; Hidde de Jong; Eugenio Cinquemani (PLoS Comput. Biol., 2020)

Dynamical Analysis and Optimization of a Generalized Resource Allocation Model of Microbial Growth. - Agustín Gabriel Yabo; Jean-Baptiste Caillau; Jean-Luc Gouzé; Hidde de Jong; Francis Mairet (SIAM J. Appl. Dyn. Syst., 2022)