Hidde de Jong

Orcid: 0000-0002-2226-650X

According to our database1, Hidde de Jong authored at least 57 papers between 1996 and 2022.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

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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
WellInverter: a web application for the analysis of fluorescent reporter gene data.
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
An ensemble of mathematical models showing diauxic growth behaviour.
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
Fluorescent Reporter Genes and the Analysis of Bacterial Regulatory Networks.
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

Identification of metabolic network models from incomplete high-throughput datasets.
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

Structural Identification of Piecewise-Linear Models of Genetic Regulatory Networks.
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

Qualitative Modeling and Simulation of Bacterial Regulatory Networks.
Proceedings of the Computational Methods in Systems Biology, 6th International Conference, 2008

Computation Tree Regular Logic for Genetic Regulatory Networks.
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

Stability of Equilibria for Piecewise-linear Models of Genetic Regulatory Networks.
Proceedings of the 44th IEEE IEEE Conference on Decision and Control and 8th European Control Conference Control, 2005

2004
A multi-scale constraint programming model of alternative splicing regulation.
Theor. Comput. Sci., 2004

Qualitative simulation and related approaches for the analysis of dynamic systems.
Knowl. Eng. Rev., 2004

Model Checking Genetic Regulatory Networks Using GNA and CADP.
Proceedings of the Model Checking Software, 2004

2003
Genetic Network Analyzer: qualitative simulation of genetic regulatory networks.
Bioinform., 2003

Modeling and Simulation of Genetic Regulatory Networks.
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

Multiscale Modeling of Alternative Splicing Regulation.
Proceedings of the Computational Methods in Systems Biology, First International Workshop, 2003

2002
Modeling and Simulation of Genetic Regulatory Systems: A Literature Review.
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

Semi-Quantitative Comparative Analysis.
Proceedings of the Sixteenth International Joint Conference on Artificial Intelligence, 1999

1998
Computer-supported analysis of scientific measurements.
PhD thesis, 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


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