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2020 – today
- 2022
[j31]Agustín Gabriel Yabo
, Jean-Baptiste Caillau, Jean-Luc Gouzé, Hidde de Jong, Francis Mairet:
Dynamical Analysis and Optimization of a Generalized Resource Allocation Model of Microbial Growth. SIAM J. Appl. Dyn. Syst. 21(1): 137-165 (2022)- 2020
- [j30]Marco Mauri, Jean-Luc Gouzé, Hidde de Jong, Eugenio Cinquemani:
Enhanced production of heterologous proteins by a synthetic microbial community: Conditions and trade-offs. PLoS Comput. Biol. 16(4) (2020)
2010 – 2019
- 2019
- [j29]Yannick Martin, Michel Page, Christophe Blanchet, Hidde de Jong:
WellInverter: a web application for the analysis of fluorescent reporter gene data. BMC Bioinform. 20(1): 309:1-309:18 (2019) - [c25]Eugenio Cinquemani, Francis Mairet, I. Yegorov, Hidde de Jong, Jean-Luc Gouzé:
Optimal control of bacterial growth for metabolite production: The role of timing and costs of control. ECC 2019: 2657-2662 - 2018
- [j28]Andreas Kremling, Johannes Geiselmann, Delphine Ropers, Hidde de Jong:
An ensemble of mathematical models showing diauxic growth behaviour. BMC Syst. Biol. 12(1): 82:1-82:16 (2018) - 2017
- [j27]Eugenio Cinquemani, Valérie Laroute, Muriel Cocaign-Bousquet, Hidde de Jong, Delphine Ropers:
Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data. Bioinform. 33(14): i301-i310 (2017) - 2016
- [j26]Nils Giordano, Francis Mairet, Jean-Luc Gouzé, Johannes Geiselmann, Hidde de Jong:
Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies. PLoS Comput. Biol. 12(3) (2016) - 2015
- [j25]Valentin Zulkower, Michel Page, Delphine Ropers, Johannes Geiselmann, Hidde de Jong:
Robust reconstruction of gene expression profiles from reporter gene data using linear inversion. Bioinform. 31(12): 71-79 (2015) - [j24]Diana Stefan, Corinne Pinel, Stéphane Pinhal, Eugenio Cinquemani, Johannes Geiselmann, Hidde de Jong:
Inference of Quantitative Models of Bacterial Promoters from Time-Series Reporter Gene Data. PLoS Comput. Biol. 11(1) (2015) - 2014
- [c24]Hidde de Jong, Johannes Geiselmann:
Fluorescent Reporter Genes and the Analysis of Bacterial Regulatory Networks. HSB 2014: 27-50 - 2013
- [j23]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:
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst. Biol. 7: 135 (2013) - 2011
- [j22]Sara Berthoumieux, Matteo Brilli, Hidde de Jong, Daniel Kahn, Eugenio Cinquemani:
Identification of metabolic network models from incomplete high-throughput datasets. Bioinform. 27(13): 186-195 (2011) - [j21]Rafael Silva-Rocha, Hidde de Jong, Javier Tamames, Víctor 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 Syst. Biol. 5: 191 (2011) - [j20]Delphine Ropers, Valentina Baldazzi, Hidde de Jong:
Model Reduction Using Piecewise-Linear Approximations Preserves Dynamic Properties of the Carbon Starvation Response in Escherichia coli. IEEE ACM Trans. Comput. Biol. Bioinform. 8(1): 166-181 (2011) - [j19]Radu Mateescu, Pedro T. Monteiro, Estelle Dumas, Hidde de Jong:
CTRL: Extension of CTL with regular expressions and fairness operators to verify genetic regulatory networks. Theor. Comput. Sci. 412(26): 2854-2883 (2011) - 2010
- [j18]Frédéric Boyer, Bruno Besson, Guillaume Baptist, Jérôme Izard, Corinne Pinel, Delphine Ropers, Johannes Geiselmann, Hidde de Jong:
WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data. Bioinform. 26(9): 1262-1263 (2010) - [j17]Grégory Batt, Michel Page, Irene Cantone, Gregor Goessler, Pedro T. Monteiro, Hidde de Jong:
Efficient parameter search for qualitative models of regulatory networks using symbolic model checking. Bioinform. 26(18) (2010) - [j16]Hidde de Jong, Caroline Ranquet, Delphine Ropers, Corinne Pinel, Johannes Geiselmann:
Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria. BMC Syst. Biol. 4: 55 (2010) - [j15]Valentina Baldazzi, Delphine Ropers, Yves Markowicz, Daniel Kahn, Johannes Geiselmann, Hidde de Jong:
The Carbon Assimilation Network in Escherichia coli Is Densely Connected and Largely Sign-Determined by Directions of Metabolic Fluxes. PLoS Comput. Biol. 6(6) (2010) - [c23]Pedro T. Monteiro, Ana T. Freitas, Delphine Ropers, Radu Mateescu, Hidde de Jong:
Modeling and formal verification of biological regulatory networks: An integrative approach. BIBM Workshops 2010: 812-813
2000 – 2009
- 2009
- [j14]Pedro T. Monteiro, Estelle Dumas, Bruno Besson, Radu Mateescu, Michel Page, Ana T. Freitas, Hidde de Jong:
A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks. BMC Bioinform. 10: 450 (2009) - 2008
- [j13]Grégory Batt, Hidde de Jong, Michel Page, Johannes Geiselmann:
Symbolic reachability analysis of genetic regulatory networks using discrete abstractions. Autom. 44(4): 982-989 (2008) - [j12]Riccardo Porreca, Samuel Drulhe, Hidde de Jong, Giancarlo Ferrari-Trecate:
Structural Identification of Piecewise-Linear Models of Genetic Regulatory Networks. J. Comput. Biol. 15(10): 1365-1380 (2008) - [j11]Samuel Drulhe, Giancarlo Ferrari-Trecate, Hidde de Jong:
The Switching Threshold Reconstruction Problem for Piecewise-Affine Models of Genetic Regulatory Networks. IEEE Trans. Autom. Control. 53: 153-165 (2008) - [j10]Hidde de Jong, Michel Page:
Search for Steady States of Piecewise-Linear Differential Equation Models of Genetic Regulatory Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 5(2): 208-222 (2008) - [c22]Radu Mateescu, Pedro T. Monteiro, Estelle Dumas, Hidde de Jong:
Computation Tree Regular Logic for Genetic Regulatory Networks. ATVA 2008: 48-63 - [c21]Hidde de Jong:
Qualitative Modeling and Simulation of Bacterial Regulatory Networks. CMSB 2008: 1 - [c20]Pedro T. Monteiro, Delphine Ropers, Radu Mateescu, Ana T. Freitas, Hidde de Jong:
Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks. ECAI 2008: 229-233 - [c19]Pedro T. Monteiro, Delphine Ropers, Radu Mateescu, Ana T. Freitas, Hidde de Jong:
Temporal logic patterns for querying dynamic models of cellular interaction networks. ECCB 2008: 227-233 - 2007
- [j9]Grégory Batt, Hidde de Jong, Johannes Geiselmann, Jean-Luc Gouzé, Michel Page, Delphine Ropers, Sari Tewfik, Dominique Schneider:
Analyse qualitative de la dynamique de réseaux de régulation génique par des modèles linéaires par morceaux. Tech. Sci. Informatiques 26(1-2): 11-45 (2007) - [c18]M. W. J. M. Musters, Hidde de Jong, P. P. J. van den Bosch, Natal A. W. van Riel:
Qualitative Analysis of Nonlinear Biochemical Networks with Piecewise-Affine Functions. HSCC 2007: 727-730 - 2006
- [j8]Ivayla Vatcheva, Hidde de Jong, Olivier Bernard, Nicolaas J. I. Mars:
Experiment selection for the discrimination of semi-quantitative models of dynamical systems. Artif. Intell. 170(4-5): 472-506 (2006) - [j7]Hidde de Jong, Delphine Ropers:
Strategies for dealing with incomplete information in the modeling of molecular interaction networks. Briefings Bioinform. 7(4): 354-363 (2006) - [c17]Samuel Drulhe, Giancarlo Ferrari-Trecate, Hidde de Jong, Alain Viari:
Reconstruction of Switching Thresholds in Piecewise-Affine Models of Genetic Regulatory Networks. HSCC 2006: 184-199 - 2005
- [c16]Richard Casey, Hidde de Jong, Jean-Luc Gouzé:
Stability of Equilibria for Piecewise-linear Models of Genetic Regulatory Networks. CDC/ECC 2005: 3693-3698 - [c15]Grégory Batt, Delphine Ropers, Hidde de Jong, Johannes Geiselmann, Michel Page, Dominique Schneider:
Qualitative Analysis and Verification of Hybrid Models of Genetic Regulatory Networks: Nutritional Stress Response in. HSCC 2005: 134-150 - [c14]Grégory Batt, Delphine Ropers, Hidde de Jong, Johannes Geiselmann, Radu Mateescu, Michel Page, Dominique Schneider:
Analysis and Verification of Qualitative Models of Genetic Regulatory Networks: A Model-Checking Approach. IJCAI 2005: 370-375 - [c13]Grégory Batt, Delphine Ropers, Hidde de Jong, Johannes Geiselmann, Radu Mateescu, Michel Page, Dominique Schneider:
Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli. ISMB (Supplement of Bioinformatics) 2005: 19-28 - 2004
- [j6]Hidde de Jong:
Qualitative simulation and related approaches for the analysis of dynamic systems. Knowl. Eng. Rev. 19(2): 93-132 (2004) - [j5]Damien Eveillard, Delphine Ropers, Hidde de Jong, Christiane Branlant, Alexander Bockmayr:
A multi-scale constraint programming model of alternative splicing regulation. Theor. Comput. Sci. 325(1): 3-24 (2004) - [c12]Grégory Batt, Damien Bergamini, Hidde de Jong, Hubert Garavel, Radu Mateescu:
Model Checking Genetic Regulatory Networks Using GNA and CADP. SPIN 2004: 158-163 - 2003
- [j4]Hidde de Jong, Johannes Geiselmann, Céline Hernandez, Michel Page:
Genetic Network Analyzer: qualitative simulation of genetic regulatory networks. Bioinform. 19(3): 336-344 (2003) - [c11]Damien Eveillard, Delphine Ropers, Hidde de Jong, Christiane Branlant, Alexander Bockmayr:
Multiscale Modeling of Alternative Splicing Regulation. CMSB 2003: 75-87 - [c10]Hidde de Jong, Jean-Luc Gouzé, Céline Hernandez, Michel Page, Sari Tewfik, Johannes Geiselmann:
Hybrid Modeling and Simulation of Genetic Regulatory Networks: A Qualitative Approach. HSCC 2003: 267-282 - [c9]Hidde de Jong:
Modeling and Simulation of Genetic Regulatory Networks. POSTA 2003: 111-118 - 2002
- [j3]Hidde de Jong:
Modeling and Simulation of Genetic Regulatory Systems: A Literature Review. J. Comput. Biol. 9(1): 67-103 (2002) - [c8]Hidde de Jong, Jean-Luc Gouzé, Céline Hernandez, Michel Page, Sari Tewfik, Johannes Geiselmann:
Dealing with Discontinuities in the Qualitative Simulation of Genetic Regulatory Networks. ECAI 2002: 412-416 - 2001
- [c7]Hidde de Jong, Michel Page, Céline Hernandez, Johannes Geiselmann:
Qualitative Simulation of Genetic Regulatory Networks: Method and Application. IJCAI 2001: 67-73 - [c6]Ivayla Vatcheva, Olivier Bernard, Hidde de Jong, Jean-Luc Gouzé, Nicolaas J. I. Mars:
Discrimination of Semi-Quantitative Models by Experiment Selection: Method and Application in Population Biology. IJCAI 2001: 74-82 - 2000
- [c5]Hidde de Jong, Michel Page:
Qualitative Simulation of Large and Complex Genetic Regulation Systems. ECAI 2000: 141-145 - [c4]Ivayla Vatcheva, Hidde de Jong, Nicolaas J. I. Mars:
Selection of Perturbation Experiments for Model Discrimination. ECAI 2000: 191-198
1990 – 1999
- 1999
- [j2]Hidde de Jong, Frank van Raalte:
Comparative envisionment construction: A technique for the comparative analysis of dynamical systems. Artif. Intell. 115(2): 145-214 (1999) - [c3]Ivayla Vatcheva, Hidde de Jong:
Semi-Quantitative Comparative Analysis. IJCAI 1999: 1034-1040 - 1998
- [b1]Hidde de Jong:
Computer-supported analysis of scientific measurements. University of Twente, Enschede, Netherlands, 1998 - 1997
- [j1]Hidde de Jong, Arie Rip:
The Computer Revolution in Science: Steps Towards the Realization of Computer-Supported Discovery Environments. Artif. Intell. 91(2): 225-256 (1997) - [c2]Hidde de Jong, Frank van Raalte:
Comparative Analysis of STructurally Different Dynamical Systems. IJCAI (1) 1997: 486-493 - 1996
- [c1]Hidde de Jong, Nicolaas J. I. Mars, Paul E. van der Vet:
CEC: Comparative Analysis by Envisionment Construction. ECAI 1996: 476-480
Coauthor Index
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