Hidde de Jong
Orcid: 0000-0002-2226-650X
According to our database1,
Hidde de Jong
authored at least 57 papers
between 1996 and 2022.
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Bibliography
2022
Dynamical Analysis and Optimization of a Generalized Resource Allocation Model of Microbial Growth.
SIAM J. Appl. Dyn. Syst., 2022
2020
Enhanced production of heterologous proteins by a synthetic microbial community: Conditions and trade-offs.
PLoS Comput. Biol., 2020
2019
BMC Bioinform., 2019
Optimal control of bacterial growth for metabolite production: The role of timing and costs of control.
Proceedings of the 17th European Control Conference, 2019
2018
BMC Syst. Biol., 2018
2017
Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data.
Bioinform., 2017
2016
Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies.
PLoS Comput. Biol., 2016
2015
Inference of Quantitative Models of Bacterial Promoters from Time-Series Reporter Gene Data.
PLoS Comput. Biol., 2015
Robust reconstruction of gene expression profiles from reporter gene data using linear inversion.
Bioinform., 2015
2014
Proceedings of the Hybrid Systems Biology, 2014
2013
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
BMC Syst. Biol., 2013
2011
CTRL: Extension of CTL with regular expressions and fairness operators to verify genetic regulatory networks.
Theor. Comput. Sci., 2011
Model Reduction Using Piecewise-Linear Approximations Preserves Dynamic Properties of the Carbon Starvation Response in Escherichia coli.
IEEE ACM Trans. Comput. Biol. 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.
BMC Syst. Biol., 2011
Bioinform., 2011
2010
The Carbon Assimilation Network in <i>Escherichia coli</i> Is Densely Connected and Largely Sign-Determined by Directions of Metabolic Fluxes.
PLoS Comput. Biol., 2010
Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria.
BMC Syst. Biol., 2010
WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data.
Bioinform., 2010
Efficient parameter search for qualitative models of regulatory networks using symbolic model checking.
Bioinform., 2010
Modeling and formal verification of biological regulatory networks: An integrative approach.
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2010
2009
A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks.
BMC Bioinform., 2009
2008
Search for Steady States of Piecewise-Linear Differential Equation Models of Genetic Regulatory Networks.
IEEE ACM Trans. Comput. Biol. Bioinform., 2008
The Switching Threshold Reconstruction Problem for Piecewise-Affine Models of Genetic Regulatory Networks.
IEEE Trans. Autom. Control., 2008
J. Comput. Biol., 2008
Symbolic reachability analysis of genetic regulatory networks using discrete abstractions.
Autom., 2008
Temporal logic patterns for querying dynamic models of cellular interaction networks.
Proceedings of the ECCB'08 Proceedings, 2008
Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks.
Proceedings of the ECAI 2008, 2008
Proceedings of the Computational Methods in Systems Biology, 6th International Conference, 2008
Proceedings of the Automated Technology for Verification and Analysis, 2008
2007
Analyse qualitative de la dynamique de réseaux de régulation génique par des modèles linéaires par morceaux.
Tech. Sci. Informatiques, 2007
Qualitative Analysis of Nonlinear Biochemical Networks with Piecewise-Affine Functions.
Proceedings of the Hybrid Systems: Computation and Control, 10th International Workshop, 2007
2006
Strategies for dealing with incomplete information in the modeling of molecular interaction networks.
Briefings Bioinform., 2006
Experiment selection for the discrimination of semi-quantitative models of dynamical systems.
Artif. Intell., 2006
Reconstruction of Switching Thresholds in Piecewise-Affine Models of Genetic Regulatory Networks.
Proceedings of the Hybrid Systems: Computation and Control, 9th International Workshop, 2006
2005
Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in <i>Escherichia coli</i>.
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005
Analysis and Verification of Qualitative Models of Genetic Regulatory Networks: A Model-Checking Approach.
Proceedings of the IJCAI-05, Proceedings of the Nineteenth International Joint Conference on Artificial Intelligence, Edinburgh, Scotland, UK, July 30, 2005
Qualitative Analysis and Verification of Hybrid Models of Genetic Regulatory Networks: Nutritional Stress Response in.
Proceedings of the Hybrid Systems: Computation and Control, 8th International Workshop, 2005
Proceedings of the 44th IEEE IEEE Conference on Decision and Control and 8th European Control Conference Control, 2005
2004
Theor. Comput. Sci., 2004
Knowl. Eng. Rev., 2004
Proceedings of the Model Checking Software, 2004
2003
Bioinform., 2003
Proceedings of the Positive Systems, 2003
Hybrid Modeling and Simulation of Genetic Regulatory Networks: A Qualitative Approach.
Proceedings of the Hybrid Systems: Computation and Control, 2003
Proceedings of the Computational Methods in Systems Biology, First International Workshop, 2003
2002
J. Comput. Biol., 2002
Dealing with Discontinuities in the Qualitative Simulation of Genetic Regulatory Networks.
Proceedings of the 15th European Conference on Artificial Intelligence, 2002
2001
Discrimination of Semi-Quantitative Models by Experiment Selection: Method and Application in Population Biology.
Proceedings of the Seventeenth International Joint Conference on Artificial Intelligence, 2001
Qualitative Simulation of Genetic Regulatory Networks: Method and Application.
Proceedings of the Seventeenth International Joint Conference on Artificial Intelligence, 2001
2000
Selection of Perturbation Experiments for Model Discrimination.
Proceedings of the ECAI 2000, 2000
Qualitative Simulation of Large and Complex Genetic Regulation Systems.
Proceedings of the ECAI 2000, 2000
1999
Comparative envisionment construction: A technique for the comparative analysis of dynamical systems.
Artif. Intell., 1999
Proceedings of the Sixteenth International Joint Conference on Artificial Intelligence, 1999
1998
1997
The Computer Revolution in Science: Steps Towards the Realization of Computer-Supported Discovery Environments.
Artif. Intell., 1997
Comparative Analysis of STructurally Different Dynamical Systems.
Proceedings of the Fifteenth International Joint Conference on Artificial Intelligence, 1997
1996
CEC: Comparative Analysis by Envisionment Construction.
Proceedings of the 12th European Conference on Artificial Intelligence, 1996