| Modeling and simulation of genetic regulatory systems: a literature review H De Jong Journal of computational biology 9 (1), 67-103, 2002 | 3626 | 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 | 564 | 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 | 377 | 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 | 256 | 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 | 254 | 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 | 239 | 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 | 232 | 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, 1-15, 2013 | 198 | 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 | 183 | 2006 |
| 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 | 179 | 2013 |
| 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 | 171 | 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 | 131 | 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 | 121 | 2016 |
| 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 | 118 | 2008 |
| System modeling in cellular biology Z Szallasi, J Stelling, V Periwal From Concepts to 13, 2006 | 104 | 2006 |
| 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 | 103 | 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, 1-17, 2010 | 96 | 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 | 91 | 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 | 88 | 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 | 87 | 2010 |
