| 2008 | ATVA | Computation Tree Regular Logic for Genetic Regulatory Networks. | Radu Mateescu, Pedro T. Monteiro, Estelle Dumas, Hidde de Jong |
| 2008 | ECAI | Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks. | Pedro T. Monteiro, Delphine Ropers, Radu Mateescu, Ana T. Freitas, Hidde de Jong |
| 2008 | ECCB | Temporal logic patterns for querying dynamic models of cellular interaction networks. | Pedro T. Monteiro, Delphine Ropers, Radu Mateescu, Ana T. Freitas, Hidde de Jong |
| 2005 | IJCAI | Analysis and Verification of Qualitative Models of Genetic Regulatory Networks: A Model-Checking Approach. | Grgory Batt, Delphine Ropers, Hidde de Jong, Johannes Geiselmann, Radu Mateescu, Michel Page, Dominique Schneider |
| 2005 | ISMB | Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in | Grgory Batt, Delphine Ropers, Hidde de Jong, Johannes Geiselmann, Radu Mateescu, Michel Page, Dominique Schneider |
| 2002 | ECAI | Dealing with Discontinuities in the Qualitative Simulation of Genetic Regulatory Networks. | Hidde de Jong, Jean-Luc Gouz, Cline Hernandez, Michel Page, Sari Tewfik, Johannes Geiselmann |
| 2001 | IJCAI | Qualitative Simulation of Genetic Regulatory Networks: Method and Application. | Hidde de Jong, Michel Page, Cline Hernandez, Johannes Geiselmann |
| 2001 | IJCAI | Discrimination of Semi-Quantitative Models by Experiment Selection: Method and Application in Population Biology. | Ivayla Vatcheva, Olivier Bernard, Hidde de Jong, Jean-Luc Gouz, Nicolaas J. I. Mars |
| 2000 | ECAI | Qualitative Simulation of Large and Complex Genetic Regulation Systems. | Hidde de Jong, Michel Page |
| 2000 | ECAI | Selection of Perturbation Experiments for Model Discrimination. | Ivayla Vatcheva, Hidde de Jong, Nicolaas J. I. Mars |
| 1999 | IJCAI | Semi-Quantitative Comparative Analysis. | Ivayla Vatcheva, Hidde de Jong |
| 1997 | IJCAI | Comparative Analysis of STructurally Different Dynamical Systems. | Hidde de Jong, Frank van Raalte |
| 1996 | ECAI | CEC: Comparative Analysis by Envisionment Construction. | Hidde de Jong, Nicolaas J. I. Mars, Paul E. van der Vet |