Hidde de Jong

58 papers A* 4A 5B 1C 1Journal 32Unranked 14
YearRankTypeTitle / Venue / Authors
2025 J jnl
Predicting coarse-grained representations of biogeochemical cycles from metabarcoding data.
Bioinform.
Arnaud Belcour, Loris Megy, Sylvain Stephant, Caroline Michel, Sétareh Rad, Petra Bombach, Nicole Dopffel, Hidde de Jong, Delphine Ropers
2022 J jnl
Dynamical Analysis and Optimization of a Generalized Resource Allocation Model of Microbial Growth.
SIAM J. Appl. Dyn. Syst.
Agustín Gabriel Yabo, Jean-Baptiste Caillau, Jean-Luc Gouzé, Hidde de Jong, Francis Mairet
2020 J jnl
Enhanced production of heterologous proteins by a synthetic microbial community: Conditions and trade-offs.
PLoS Comput. Biol.
Marco Mauri, Jean-Luc Gouzé, Hidde de Jong, Eugenio Cinquemani
2019 — conf
Optimal control of bacterial growth for metabolite production: The role of timing and costs of control.
ECC
Eugenio Cinquemani, Francis Mairet, I. Yegorov, Hidde de Jong, Jean-Luc Gouzé
2019 J jnl
WellInverter: a web application for the analysis of fluorescent reporter gene data.
BMC Bioinform.
Yannick Martin, Michel Page, Christophe Blanchet, Hidde de Jong
2018 J jnl
An ensemble of mathematical models showing diauxic growth behaviour.
BMC Syst. Biol.
Andreas Kremling, Johannes Geiselmann, Delphine Ropers, Hidde de Jong
2017 J jnl
Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data.
Bioinform.
Eugenio Cinquemani, Valérie Laroute, Muriel Cocaign-Bousquet, Hidde de Jong, Delphine Ropers
2016 J jnl
Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies.
PLoS Comput. Biol.
Nils Giordano, Francis Mairet, Jean-Luc Gouzé, Johannes Geiselmann, Hidde de Jong
2015 J jnl
Inference of Quantitative Models of Bacterial Promoters from Time-Series Reporter Gene Data.
PLoS Comput. Biol.
Diana Stefan, Corinne Pinel, Stéphane Pinhal, Eugenio Cinquemani, Johannes Geiselmann, Hidde de Jong
2015 J jnl
Robust reconstruction of gene expression profiles from reporter gene data using linear inversion.
Bioinform.
Valentin Zulkower, Michel Page, Delphine Ropers, Johannes Geiselmann, Hidde de Jong
2014 — conf
Fluorescent Reporter Genes and the Analysis of Bacterial Regulatory Networks.
HSB
Hidde de Jong, Johannes Geiselmann
2013 J jnl
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
BMC Syst. Biol.
Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan M. Kowal, Benjamin Wicks, Emanuel J. V. Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomás Helikar
2011 J jnl
CTRL: Extension of CTL with regular expressions and fairness operators to verify genetic regulatory networks.
Theor. Comput. Sci.
Radu Mateescu, Pedro T. Monteiro, Estelle Dumas, Hidde de Jong
2011 J jnl
Identification of metabolic network models from incomplete high-throughput datasets.
Bioinform.
Sara Berthoumieux, Matteo Brilli, Hidde de Jong, Daniel Kahn, Eugenio Cinquemani
2011 J jnl
Model Reduction Using Piecewise-Linear Approximations Preserves Dynamic Properties of the Carbon Starvation Response in Escherichia coli.
IEEE ACM Trans. Comput. Biol. Bioinform.
Delphine Ropers, Valentina Baldazzi, Hidde de Jong
2011 J jnl
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 Syst. Biol.
Rafael Silva-Rocha, Hidde de Jong, Javier Tamames, Víctor de Lorenzo
2010 J jnl
Efficient parameter search for qualitative models of regulatory networks using symbolic model checking.
Bioinform.
Grégory Batt, Michel Page, Irene Cantone, Gregor Goessler, Pedro T. Monteiro, Hidde de Jong
2010 J jnl
Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria.
BMC Syst. Biol.
Hidde de Jong, Caroline Ranquet, Delphine Ropers, Corinne Pinel, Johannes Geiselmann
2010 — conf
Modeling and formal verification of biological regulatory networks: An integrative approach.
BIBM Workshops
Pedro T. Monteiro, Ana T. Freitas, Delphine Ropers, Radu Mateescu, Hidde de Jong
2010 J jnl
The Carbon Assimilation Network in
PLoS Comput. Biol.
Valentina Baldazzi, Delphine Ropers, Yves Markowicz, Daniel Kahn, Johannes Geiselmann, Hidde de Jong
2010 J jnl
WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data.
Bioinform.
Frédéric Boyer, Bruno Besson, Guillaume Baptist, Jérôme Izard, Corinne Pinel, Delphine Ropers, Johannes Geiselmann, Hidde de Jong
2009 J jnl
A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks.
BMC Bioinform.
Pedro T. Monteiro, Estelle Dumas, Bruno Besson, Radu Mateescu, Michel Page, Ana T. Freitas, Hidde de Jong
2008 B conf
Computation Tree Regular Logic for Genetic Regulatory Networks.
ATVA
Radu Mateescu, Pedro T. Monteiro, Estelle Dumas, Hidde de Jong
2008 — conf
Qualitative Modeling and Simulation of Bacterial Regulatory Networks.
CMSB
Hidde de Jong
2008 J jnl
Search for Steady States of Piecewise-Linear Differential Equation Models of Genetic Regulatory Networks.
IEEE ACM Trans. Comput. Biol. Bioinform.
Hidde de Jong, Michel Page
2008 J jnl
Structural Identification of Piecewise-Linear Models of Genetic Regulatory Networks.
J. Comput. Biol.
Riccardo Porreca, Samuel Drulhe, Hidde de Jong, Giancarlo Ferrari-Trecate
2008 J jnl
Symbolic reachability analysis of genetic regulatory networks using discrete abstractions.
Autom.
Grégory Batt, Hidde de Jong, Michel Page, Johannes Geiselmann
2008 A conf
Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks.
ECAI
Pedro T. Monteiro, Delphine Ropers, Radu Mateescu, Ana T. Freitas, Hidde de Jong
2008 C conf
Temporal logic patterns for querying dynamic models of cellular interaction networks.
ECCB
Pedro T. Monteiro, Delphine Ropers, Radu Mateescu, Ana T. Freitas, Hidde de Jong
2008 J jnl
The Switching Threshold Reconstruction Problem for Piecewise-Affine Models of Genetic Regulatory Networks.
IEEE Trans. Autom. Control.
Samuel Drulhe, Giancarlo Ferrari-Trecate, Hidde de Jong
2007 J jnl
Analyse qualitative de la dynamique de réseaux de régulation génique par des modèles linéaires par morceaux.
Tech. Sci. Informatiques
Grégory Batt, Hidde de Jong, Johannes Geiselmann, Jean-Luc Gouzé, Michel Page, Delphine Ropers, Sari Tewfik, Dominique Schneider
2007 — conf
Qualitative Analysis of Nonlinear Biochemical Networks with Piecewise-Affine Functions.
HSCC
M. W. J. M. Musters, Hidde de Jong, P. P. J. van den Bosch, Natal A. W. van Riel
2006 J jnl
Experiment selection for the discrimination of semi-quantitative models of dynamical systems.
Artif. Intell.
Ivayla Vatcheva, Hidde de Jong, Olivier Bernard, Nicolaas J. I. Mars
2006 — conf
Reconstruction of Switching Thresholds in Piecewise-Affine Models of Genetic Regulatory Networks.
HSCC
Samuel Drulhe, Giancarlo Ferrari-Trecate, Hidde de Jong, Alain Viari
2006 J jnl
Strategies for dealing with incomplete information in the modeling of molecular interaction networks.
Briefings Bioinform.
Hidde de Jong, Delphine Ropers
2005 A* conf
Analysis and Verification of Qualitative Models of Genetic Regulatory Networks: A Model-Checking Approach.
IJCAI
Grégory Batt, Delphine Ropers, Hidde de Jong, Johannes Geiselmann, Radu Mateescu, Michel Page, Dominique Schneider
2005 — conf
Qualitative Analysis and Verification of Hybrid Models of Genetic Regulatory Networks: Nutritional Stress Response in.
HSCC
Grégory Batt, Delphine Ropers, Hidde de Jong, Johannes Geiselmann, Michel Page, Dominique Schneider
2005 — conf
Stability of Equilibria for Piecewise-linear Models of Genetic Regulatory Networks.
CDC/ECC
Richard Casey, Hidde de Jong, Jean-Luc Gouzé
2005 — conf
Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in
ISMB (Supplement of Bioinformatics)
Grégory Batt, Delphine Ropers, Hidde de Jong, Johannes Geiselmann, Radu Mateescu, Michel Page, Dominique Schneider
2004 J jnl
A multi-scale constraint programming model of alternative splicing regulation.
Theor. Comput. Sci.
Damien Eveillard, Delphine Ropers, Hidde de Jong, Christiane Branlant, Alexander Bockmayr
2004 — conf
Model Checking Genetic Regulatory Networks Using GNA and CADP.
SPIN
Grégory Batt, Damien Bergamini, Hidde de Jong, Hubert Garavel, Radu Mateescu
2004 J jnl
Qualitative simulation and related approaches for the analysis of dynamic systems.
Knowl. Eng. Rev.
Hidde de Jong
2003 J jnl
Genetic Network Analyzer: qualitative simulation of genetic regulatory networks.
Bioinform.
Hidde de Jong, Johannes Geiselmann, Céline Hernandez, Michel Page
2003 — conf
Hybrid Modeling and Simulation of Genetic Regulatory Networks: A Qualitative Approach.
HSCC
Hidde de Jong, Jean-Luc Gouzé, Céline Hernandez, Michel Page, Sari Tewfik, Johannes Geiselmann
2003 — conf
Modeling and Simulation of Genetic Regulatory Networks.
POSTA
Hidde de Jong
2003 — conf
Multiscale Modeling of Alternative Splicing Regulation.
CMSB
Damien Eveillard, Delphine Ropers, Hidde de Jong, Christiane Branlant, Alexander Bockmayr
2002 A conf
Dealing with Discontinuities in the Qualitative Simulation of Genetic Regulatory Networks.
ECAI
Hidde de Jong, Jean-Luc Gouzé, Céline Hernandez, Michel Page, Sari Tewfik, Johannes Geiselmann
2002 J jnl
Modeling and Simulation of Genetic Regulatory Systems: A Literature Review.
J. Comput. Biol.
Hidde de Jong
2001 A* conf
Discrimination of Semi-Quantitative Models by Experiment Selection: Method and Application in Population Biology.
IJCAI
Ivayla Vatcheva, Olivier Bernard, Hidde de Jong, Jean-Luc Gouzé, Nicolaas J. I. Mars
2001 A* conf
Qualitative Simulation of Genetic Regulatory Networks: Method and Application.
IJCAI
Hidde de Jong, Michel Page, Céline Hernandez, Johannes Geiselmann
2000 A conf
Qualitative Simulation of Large and Complex Genetic Regulation Systems.
ECAI
Hidde de Jong, Michel Page
2000 A conf
Selection of Perturbation Experiments for Model Discrimination.
ECAI
Ivayla Vatcheva, Hidde de Jong, Nicolaas J. I. Mars
1999 J jnl
Comparative envisionment construction: A technique for the comparative analysis of dynamical systems.
Artif. Intell.
Hidde de Jong, Frank van Raalte
1999 A* conf
Semi-Quantitative Comparative Analysis.
IJCAI
Ivayla Vatcheva, Hidde de Jong
1998 — —
Computer-supported analysis of scientific measurements.
Hidde de Jong
1997 — conf
Comparative Analysis of STructurally Different Dynamical Systems.
IJCAI (1)
Hidde de Jong, Frank van Raalte
1997 J jnl
The Computer Revolution in Science: Steps Towards the Realization of Computer-Supported Discovery Environments.
Artif. Intell.
Hidde de Jong, Arie Rip
1996 A conf
CEC: Comparative Analysis by Envisionment Construction.
ECAI
Hidde de Jong, Nicolaas J. I. Mars, Paul E. van der Vet