Hidde de Jong
Hidde de Jong
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Modeling and simulation of genetic regulatory systems: a literature review
H De Jong
Journal of computational biology 9 (1), 67-103, 2002
Qualitative simulation of genetic regulatory networks using piecewise-linear models
H De Jong, JL Gouzé, C Hernandez, M Page, T Sari, J Geiselmann
Bulletin of mathematical biology 66 (2), 301-340, 2004
Genetic Network Analyzer: qualitative simulation of genetic regulatory networks
H De Jong, J Geiselmann, C Hernandez, M Page
Bioinformatics 19 (3), 336-344, 2003
Piecewise-linear models of genetic regulatory networks: equilibria and their stability
R Casey, H Jong, JL Gouzé
Journal of mathematical biology 52 (1), 27-56, 2006
Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli
G Batt, D Ropers, H De Jong, J Geiselmann, R Mateescu, M Page, ...
Bioinformatics 21 (suppl_1), i19-i28, 2005
Shared control of gene expression in bacteria by transcription factors and global physiology of the cell
S Berthoumieux, H De Jong, G Baptist, C Pinel, C Ranquet, D Ropers, ...
Molecular systems biology 9 (1), 634, 2013
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
C Chaouiya, D Bérenguier, SM Keating, A Naldi, MP Van Iersel, ...
BMC systems biology 7 (1), 1-15, 2013
Qualitative simulation of the carbon starvation response in Escherichia coli
D Ropers, H De Jong, M Page, D Schneider, J Geiselmann
Biosystems 84 (2), 124-152, 2006
Qualitative simulation of the initiation of sporulation in Bacillus subtilis
H De Jong, J Geiselmann, G Batt, C Hernandez, M Page
Bulletin of mathematical biology 66, 261-299, 2004
SBML Level 3: an extensible format for the exchange and reuse of biological models
SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ...
Molecular systems biology 16 (8), e9110, 2020
Acetate metabolism and the inhibition of bacterial growth by acetate
S Pinhal, D Ropers, J Geiselmann, H De Jong
Journal of bacteriology 201 (13), e00147-19, 2019
Temporal logic patterns for querying dynamic models of cellular interaction networks
PT Monteiro, D Ropers, R Mateescu, AT Freitas, H De Jong
Bioinformatics 24 (16), i227-i233, 2008
Understanding carbon catabolite repression in Escherichia coli using quantitative models
A Kremling, J Geiselmann, D Ropers, H de Jong
Trends in microbiology 23 (2), 99-109, 2015
Dynamical allocation of cellular resources as an optimal control problem: novel insights into microbial growth strategies
N Giordano, F Mairet, JL Gouzé, J Geiselmann, H De Jong
PLoS computational biology 12 (3), e1004802, 2016
Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria
H De Jong, C Ranquet, D Ropers, C Pinel, J Geiselmann
BMC systems biology 4 (1), 1-17, 2010
A synthetic growth switch based on controlled expression of RNA polymerase
J Izard, CDC Gomez Balderas, D Ropers, S Lacour, X Song, Y Yang, ...
Molecular systems biology 11 (11), 840, 2015
Experiment selection for the discrimination of semi-quantitative models of dynamical systems
I Vatcheva, H De Jong, O Bernard, NJI Mars
Artificial Intelligence 170 (4-5), 472-506, 2006
Efficient parameter search for qualitative models of regulatory networks using symbolic model checking
G Batt, M Page, I Cantone, G Goessler, P Monteiro, H De Jong
Bioinformatics 26 (18), i603-i610, 2010
Hybrid modeling and simulation of genetic regulatory networks: A qualitative approach
H De Jong, JL Gouzé, C Hernandez, M Page, T Sari, J Geiselmann
Hybrid Systems: Computation and Control: 6th International Workshop, HSCC …, 2003
The computer revolution in science: Steps towards the realization of computer-supported discovery environments
H De Jong, A Rip
Artificial intelligence 91 (2), 225-256, 1997
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