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Overview

Hidde de Jong is affiliated with the French Institute for Research in Computer Science and Automation (INRIA) in France. Their research primarily focuses on the interdisciplinary fields of Biochemistry, Genetics, and Molecular Biology, with particular emphasis on Molecular Biology and Genetics. De Jong's subfield expertise includes Physical and Theoretical Chemistry, Ecology, and Control and Systems Engineering.

Their main research topics cover a range of subjects within microbial and genetic systems:

  • Microbial Metabolic Engineering and Bioproduction
  • Gene Regulatory Network Analysis
  • Bacterial Genetics and Biotechnology
  • Evolution and Genetic Dynamics
  • Thermodynamics and calorimetric analyses
  • Protein Structure and Dynamics
  • Environmental DNA in Biodiversity Studies

De Jong has published extensively, with a total of 41 publications in relevant scientific domains. Their recent papers include:

  • <scp>SBML</scp> Level 3: an extensible format for the exchange and reuse of biological models (2020), published in Molecular Systems Biology
  • Enhanced production of heterologous proteins by a synthetic microbial community: Conditions and trade-offs (2020), published in PLoS Computational Biology
  • Optimal proteome allocation and the temperature dependence of microbial growth laws (2021), published in npj Systems Biology and Applications
  • Single-cell data reveal heterogeneity of investment in ribosomes across a bacterial population (2025), published in Nature Communications
  • Dynamical Analysis and Optimization of a Generalized Resource Allocation Model of Microbial Growth (2022), published in SIAM Journal on Applied Dynamical Systems

The venues where de Jong frequently publishes include:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • HAL (Le Centre pour la Communication Scientifique Directe)
  • Molecular Systems Biology
  • PLoS Computational Biology
  • npj Systems Biology and Applications

Collaborations are a notable part of de Jong's work. Frequent co-authors include Jean-Luc Gouzé, Eugenio Cinquemani, Johannes Geiselmann, Delphine Ropers, and Corinne Pinel.

In addition to journal articles, de Jong has contributed to book publications, including a work titled Economic Principles in Cell Biology, published by the Centre National de la Recherche Scientifique in 2025.

Best Publications

  • Modeling and simulation of genetic regulatory systems: a literature review.

    Hidde de Jong

  • Qualitative Simulation of Genetic Regulatory Networks Using Piecewise-Linear Models

    Hidde de Jong;Jean-Luc Gouzé;Céline Hernandez;Michel Page;Michel Page

  • Genetic Network Analyzer: qualitative simulation of genetic regulatory networks.

    Hidde de Jong;Johannes Geiselmann;Céline Hernandez;Michel Page

  • SBML Level 3: an extensible format for the exchange and reuse of biological models

    Sarah M. Keating;Sarah M. Keating;Dagmar Waltemath;Matthias König;Fengkai Zhang

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

    Grégory Batt;Delphine Ropers;Hidde De Jong;Johannes Geiselmann

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

    Claudine Chaouiya;Duncan Bérenguier;Sarah M. Keating;Aurélien Naldi

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

    Nils Giordano;Nils Giordano;Francis Mairet;Jean-Luc Gouzé;Johannes Geiselmann;Johannes Geiselmann

  • Temporal logic patterns for querying dynamic models of cellular interaction networks

    Pedro T. Monteiro;Delphine Ropers;Radu Mateescu;Ana T. Freitas

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

    Hidde de Jong;Caroline Ranquet;Caroline Ranquet;Delphine Ropers;Corinne Pinel;Corinne Pinel

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

    Ivayla Vatcheva;Hidde de Jong;Olivier Bernard;Nicolaas J. I. Mars

  • Hybrid Modeling and Simulation of Genetic Regulatory Networks: A Qualitative Approach

    Hidde de Jong;Jean-Luc Gouzé;Céline Hernandez;Michel Page

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

    Gregory Batt;Michel Page;Irene Cantone;Gregor Goessler

  • The computer revolution in science: steps towards the realization of computer-supported discovery environments

    Hidde de Jong;Arie Rip

  • Qualitative simulation of genetic regulatory networks: method and application

    Hidde De Jong;Michel Page;Cane Hernandez;Johannes Geiselmann

  • Symbolic reachability analysis of genetic regulatory networks using discrete abstractions

    Grégory Batt;Hidde de Jong;Michel Page;Johannes Geiselmann

  • Qualitative analysis and verification of hybrid models of genetic regulatory networks: nutritional stress response in Escherichia coli

    Grégory Batt;Delphine Ropers;Hidde de Jong;Johannes Geiselmann

  • Structural identification of piecewise-linear models of genetic regulatory networks.

    Riccardo Porreca;Samuel Drulhe;Hidde de Jong;Giancarlo Ferrari-Trecate

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

    Valentina Baldazzi;Delphine Ropers;Yves Markowicz;Daniel Kahn

  • Towards multiscale plant models: integrating cellular networks.

    Valentina Baldazzi;Nadia Bertin;Hidde de Jong;Michel Génard

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

    Pedro T Monteiro;Pedro T Monteiro;Estelle Dumas;Bruno Besson;Radu Mateescu

Frequent Co-Authors

Denis Thieffry
Denis Thieffry École Normale Supérieure
Daniel Kahn
Daniel Kahn Claude Bernard University Lyon 1
Claudine Chaouiya
Claudine Chaouiya Aix-Marseille University
Nicolas Le Novère
Nicolas Le Novère Babraham Institute
Myriam Ferro
Myriam Ferro Grenoble Alpes University
Steffen Klamt
Steffen Klamt Max Planck Institute for Dynamics of Complex Technical Systems
Christiane Branlant
Christiane Branlant University of Lorraine
Julio Saez-Rodriguez
Julio Saez-Rodriguez Heidelberg University
Ioannis Xenarios
Ioannis Xenarios University of Lausanne
Michael Hucka
Michael Hucka California Institute of Technology

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