H. Jong

发表

Modeling and Simulation of Genetic Regulatory Systems: A Literature Review

Hidde de Jong, H. D. Jong, H. Jong, 2002, J. Comput. Biol..

Inference of Quantitative Models of Bacterial Promoters from Time-Series Reporter Gene Data

Eugenio Cinquemani, Hidde de Jong, Diana Stefan, 2015, PLoS Comput. Biol..

Fluorescent Reporter Genes and the Analysis of Bacterial Regulatory Networks

Hidde de Jong, Johannes Geiselmann, H. D. Jong, 2014, HSB.

The Computer Revolution in Science: Steps Towards the Realization of Computer-Supported Discovery Environments

Arie Rip, Hidde de Jong, H. D. Jong, 1997, Artif. Intell..

Qualitative Analysis and Verification of Hybrid Models of Genetic Regulatory Networks: Nutritional Stress Response in

Dominique Schneider, Hidde de Jong, Grégory Batt, 2005, HSCC.

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

Steffen Klamt, Aurélien Naldi, Denis Thieffry, 2013, BMC Systems Biology.

Shared control of gene expression in bacteria by transcription factors and global physiology of the cell

J. Geiselmann, D. Ropers, H. de Jong, 2013, Molecular systems biology.

Experiment selection for the discrimination of semi-quantitative models of dynamical systems

Olivier Bernard, Hidde de Jong, Ivayla Vatcheva, 2006, Artif. Intell..

Qualitative simulation of genetic regulatory networks using piecewise-linear models

H. D. Jong, J. Gouzé, Céline Hernandez, 2004, Bulletin of mathematical biology.

Piecewise-Linear Models of Genetic Regulatory Networks: Theory and Example

Frédéric Grognard, Jean-Luc Gouzé, Hidde de Jong, 2007 .

Piecewise-linear Models of Genetic Regulatory Networks: Equilibria and their Stability

H. D. Jong, J. Gouzé, Richard Casey, 2006, Journal of mathematical biology.

Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli

Radu Mateescu, Dominique Schneider, Hidde de Jong, 2005, ISMB.

Modeling the Dynamics of Genetic Regulatory Networks: Continuous and Discrete Approaches

H. D. Jong, R. Lima, H. De Jong, 2005 .

Understanding carbon catabolite repression in Escherichia coli using quantitative models.

J. Geiselmann, A. Kremling, D. Ropers, 2015, Trends in microbiology.

Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria

Hidde de Jong, Corinne Pinel, Johannes Geiselmann, 2010, BMC Systems Biology.

Numerical simulation of piecewise-linear models of gene regulatory networks using complementarity systems

B. Brogliato, V. Acary, H. Jong, 2012 .

Efficient parameter search for qualitative models of regulatory networks using symbolic model checking

Gregor Gößler, Hidde de Jong, Pedro T. Monteiro, 2010, Bioinform..

Symbolic reachability analysis of genetic regulatory networks using discrete abstractions

Hidde de Jong, Grégory Batt, Johannes Geiselmann, 2008, Autom..

Search for Steady States of Piecewise-Linear Differential Equation Models of Genetic Regulatory Networks

M. Page, H. D. Jong, M. Page, 2008, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Strategies for dealing with incomplete information in the modeling of molecular interaction networks

Hidde de Jong, Delphine Ropers, H. D. Jong, 2006, Briefings Bioinform..

Qualitative simulation of the initiation of sporulation in Bacillus subtilis

H. D. Jong, Céline Hernandez, M. Page, 2004, Bulletin of mathematical biology.

Analysis of Genetic Regulatory Networks: A Model-Checking Approach

Hidde de Jong, H. Jong, 2003 .

Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data

Eugenio Cinquemani, Hidde de Jong, Delphine Ropers, 2017, Bioinform..

Course 10Modeling, analysis, and simulation of genetic regulatory networks: From differential equations to logical models

Hidde de Jong, Denis Thieffry, H. D. Jong, 2005 .

Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies

Jean-Luc Gouzé, Hidde de Jong, Johannes Geiselmann, 2016, PLoS Comput. Biol..

Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies

J. Gouzé, J. Geiselmann, N. Giordano, 2016, PLoS Comput. Biol..

Efficient parameter search for qualitative models of regulatory networks using symbolic model checking

M. Page, H. Jong, Grégory Batt, 2010, Bioinform..

The Carbon Assimilation Network in Escherichia coli Is Densely Connected and Largely Sign-Determined by Directions of Metabolic Fluxes

Hidde de Jong, Daniel Kahn, Valentina Baldazzi, 2010, PLoS Comput. Biol..

Dynamical Analysis and Optimization of a Generalized Resource Allocation Model of Microbial Growth

H. D. Jong, J. Gouzé, Jean-Baptiste Caillau, 2022, SIAM J. Appl. Dyn. Syst..

Dynamic optimisation of resource allocation in microorganisms

H. D. Jong, J. Gouzé, J. Geiselmann, 2014 .

On the identifiability of metabolic network models

H. D. Jong, D. Kahn, E. Cinquemani, 2013, Journal of mathematical biology.

Structural and practical identifiability of approximate metabolic network models

Eugenio Cinquemani, Hidde de Jong, Daniel Kahn, 2012 .

Structural Identification of Piecewise-Linear Models of Genetic Regulatory Networks

Hidde de Jong, Riccardo Porreca, Giancarlo Ferrari-Trecate, 2008, J. Comput. Biol..

Qualitative Simulation of Large and Complex Genetic Regulation Systems

Hidde de Jong, Michel Page, H. D. Jong, 2000, ECAI.

Practical exercises CompSysBio course: modelling integrated networks of metabolism and gene expression

H. Jong, 2022 .

Qualitative simulation and related approaches for the analysis of dynamic systems

Hidde de Jong, H. D. Jong, H. Jong, 2004, The Knowledge Engineering Review.

Optimal protein production by a synthetic microbial consortium: coexistence, distribution of labor, and syntrophy

J. Gouzé, E. Cinquemani, Carlos Martínez, 2022, bioRxiv.

Selection of Perturbation Experiments for Model Discrimination

Hidde de Jong, Ivayla Vatcheva, Nicolaas J. I. Mars, 2000, ECAI.

Consistency of scientific knowledge bases (Extended abstract)

Hidde de Jong, Paul E. van der Vet, P. V. D. Vet, 1993 .

CEC: Comparative Analysis by Envisionment Construction

Hidde de Jong, Nicolaas J. I. Mars, Paul E. van der Vet, 1996, European Conference on Artificial Intelligence.

Comparative envisionment construction: A technique for the comparative analysis of dynamical systems

Hidde de Jong, Frank van Raalte, H. D. Jong, 1999, Artif. Intell..

Model-based identification of Systematic errors in measurements

P. E. van der Vet, Hidde de Jong, Nicolaas Mars, 1998 .

A multi-scale constraint programming model of alternative splicing regulation

Alexander Bockmayr, Hidde de Jong, Christiane Branlant, 2004, Theor. Comput. Sci..

Computer-supported analysis of scientific measurements

Hidde de Jong, H. D. Jong, H. Jong, 1998 .

Temporal logic patterns for querying dynamic models of cellular interaction networks

Radu Mateescu, Hidde de Jong, Pedro T. Monteiro, 2008, ECCB.

Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks

Radu Mateescu, Hidde de Jong, Pedro T. Monteiro, 2008, ECAI.

Numerical simulation of piecewise-linear models of gene regulatory networks using complementarity systems

B. Brogliato, H. Jong, Vincent Acary, 2012 .

A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks

Radu Mateescu, Hidde de Jong, Pedro T. Monteiro, 2009, BMC Bioinformatics.

The Switching Threshold Reconstruction Problem for Piecewise-Affine Models of Genetic Regulatory Networks

Giancarlo Ferrari-Trecate, Hidde de Jong, Samuel Drulhe, 2008, IEEE Transactions on Automatic Control.

Model Reduction Using Piecewise-Linear Approximations Preserves Dynamic Properties of the Carbon Starvation Response in Escherichia coli

Hidde de Jong, Valentina Baldazzi, Delphine Ropers, 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Identification of metabolic network models from incomplete high-throughput datasets

D. Kahn, E. Cinquemani, Sara Berthoumieux, 2011, Bioinform..

6 – Qualitative modelling and simulation of developmental regulatory networks

Hidde de Jong, Johannes Geiselmann, Denis Thieffry, 2003 .

Reconstruction of Switching Thresholds in Piecewise-Affine Models of Genetic Regulatory Networks

Giancarlo Ferrari-Trecate, Hidde de Jong, Samuel Drulhe, 2006, HSCC.

Genetic Network Analyzer: qualitative simulation of genetic regulatory networks

Hidde de Jong, Johannes Geiselmann, Michel Page, 2003, Bioinform..