| Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle A Fauré, A Naldi, C Chaouiya, D Thieffry Bioinformatics 22 (14), e124-e131, 2006 | 691 | 2006 |
| Petri net modelling of biological networks C Chaouiya Briefings in bioinformatics 8 (4), 210-219, 2007 | 491 | 2007 |
| Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance Ö Sahin, H Fröhlich, C Löbke, U Korf, S Burmester, M Majety, J Mattern, ... BMC systems biology 3 (1), 1-20, 2009 | 242 | 2009 |
| GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks AG Gonzalez, A Naldi, L Sanchez, D Thieffry, C Chaouiya Biosystems 84 (2), 91-100, 2006 | 203 | 2006 |
| Logical modelling of regulatory networks with GINsim 2.3 A Naldi, D Berenguier, A Fauré, F Lopez, D Thieffry, C Chaouiya Biosystems 97 (2), 134-139, 2009 | 199 | 2009 |
| Logical modeling and dynamical analysis of cellular networks W Abou-Jaoudé, P Traynard, PT Monteiro, J Saez-Rodriguez, T Helikar, ... Frontiers in genetics 7, 94, 2016 | 183 | 2016 |
| Diversity and plasticity of Th cell types predicted from regulatory network modelling A Naldi, J Carneiro, C Chaouiya, D Thieffry PLoS computational biology 6 (9), e1000912, 2010 | 182 | 2010 |
| Logical modelling of gene regulatory networks with GINsim C Chaouiya, A Naldi, D Thieffry Bacterial Molecular Networks, 463-479, 2012 | 165 | 2012 |
| Path2Models: large-scale generation of computational models from biochemical pathway maps F Büchel, N Rodriguez, N Swainston, C Wrzodek, T Czauderna, R Keller, ... BMC systems biology 7 (1), 1-19, 2013 | 158 | 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 | 153 | 2013 |
| Decision diagrams for the representation and analysis of logical models of genetic networks A Naldi, D Thieffry, C Chaouiya International Conference on Computational Methods in Systems Biology, 233-247, 2007 | 142 | 2007 |
| Dynamically consistent reduction of logical regulatory graphs A Naldi, E Remy, D Thieffry, C Chaouiya Theoretical Computer Science 412 (21), 2207-2218, 2011 | 136 | 2011 |
| Petri net modelling of biological regulatory networks C Chaouiya, E Remy, D Thieffry Journal of Discrete Algorithms 6 (2), 165-177, 2008 | 125 | 2008 |
| Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.Coli E Simao, E Remy, D Thieffry, C Chaouiya Bioinformatics 21 (suppl_2), ii190-ii196, 2005 | 121 | 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 | 105 | 2020 |
| Qualitative analysis of regulatory graphs: a computational tool based on a discrete formal framework C Chaouiya, E Remy, B Mossé, D Thieffry Positive systems, 119-126, 2003 | 105 | 2003 |
| Qualitative modelling of genetic networks: From logical regulatory graphs to standard petri nets C Chaouiya, E Remy, P Ruet, D Thieffry International Conference on Application and Theory of Petri Nets, 137-156, 2004 | 100 | 2004 |
| A description of dynamical graphs associated to elementary regulatory circuits E Remy, B Mossé, C Chaouiya, D Thieffry Bioinformatics 19 (suppl_2), ii172-ii178, 2003 | 95 | 2003 |
| A Modeling Approach to Explain Mutually Exclusive and Co-Occurring Genetic Alterations in Bladder TumorigenesisMathematical Model of Bladder Tumorigenesis E Remy, S Rebouissou, C Chaouiya, A Zinovyev, F Radvanyi, L Calzone Cancer research 75 (19), 4042-4052, 2015 | 90 | 2015 |
| Model checking to assess T-helper cell plasticity W Abou-Jaoudé, PT Monteiro, A Naldi, M Grandclaudon, V Soumelis, ... Frontiers in bioengineering and biotechnology 2, 86, 2015 | 87 | 2015 |
