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
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), 10.1128/jb. 00147-19, 2019
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
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
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
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
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
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
Benjamin J. Bornstein, NASA Jet Propulsion Laboratory, 4800 Oak Grove Drive, Pasadena, CA 91109, USA. Emery Conrad, Department of Biological Sciences, MC 0406, Virginia …
H de Jong, F Saint Ismier CEDEX
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
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
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
Hybrid modeling and simulation of genetic regulatory networks: A qualitative approach
H De Jong, JL Gouzé, C Hernandez, M Page, T Sari, J Geiselmann
International Workshop on Hybrid Systems: Computation and Control, 267-282, 2003
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
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