| 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 | 818 | 2006 |
| Petri net modelling of biological networks C Chaouiya Briefings in bioinformatics 8 (4), 210-219, 2007 | 545 | 2007 |
| 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 | 305 | 2020 |
| 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 | 289 | 2016 |
| 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, 2009 | 257 | 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 | 242 | 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 | 236 | 2009 |
| 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 | 217 | 2010 |
| The systems biology markup language (SBML): language specification for level 3 version 2 core release 2 M Hucka, FT Bergmann, C Chaouiya, A Dräger, S Hoops, SM Keating, ... Journal of integrative bioinformatics 16 (2), 20190021, 2019 | 215 | 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), 135, 2013 | 211 | 2013 |
| Logical modelling of gene regulatory networks with GINsim C Chaouiya, A Naldi, D Thieffry Bacterial Molecular Networks: Methods and Protocols, 463-479, 2011 | 210 | 2011 |
| 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), 116, 2013 | 200 | 2013 |
| Dynamically consistent reduction of logical regulatory graphs A Naldi, E Remy, D Thieffry, C Chaouiya Theoretical Computer Science 412 (21), 2207-2218, 2011 | 181 | 2011 |
| 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 | 163 | 2007 |
| Petri net modelling of biological regulatory networks C Chaouiya, E Remy, D Thieffry Journal of Discrete Algorithms 6 (2), 165-177, 2008 | 145 | 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 | 135 | 2005 |
| A modeling approach to explain mutually exclusive and co-occurring genetic alterations in bladder tumorigenesis E Remy, S Rebouissou, C Chaouiya, A Zinovyev, F Radvanyi, L Calzone Cancer research 75 (19), 4042-4052, 2015 | 127 | 2015 |
| The CoLoMoTo interactive notebook: accessible and reproducible computational analyses for qualitative biological networks A Naldi, C Hernandez, N Levy, G Stoll, PT Monteiro, C Chaouiya, ... Frontiers in physiology 9, 680, 2018 | 126 | 2018 |
| 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 | 119 | 2015 |
| Bringing dicynodonts back to life: paleobiology and anatomy of a new emydopoid genus from the Upper Permian of Mozambique R Castanhinha, R Araújo, LC Júnior, KD Angielczyk, GG Martins, ... PLoS One 8 (12), e80974, 2013 | 118 | 2013 |
