| GOATOOLS: A Python library for Gene Ontology analyses DV Klopfenstein, L Zhang, BS Pedersen, F Ramírez, AW Vesztrocy, ... Scientific Reports 8 (1), 10872, 2018 | 900 | 2018 |
| 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 | 784 | 2006 |
| 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), 2020 | 239 | 2020 |
| 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 | 236 | 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 | 215 | 2009 |
| 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 | 198 | 2013 |
| Logical Modelling of Gene Regulatory Networks with GINsim. C Chaouiya, A Naldi, D Thieffry Methods in molecular biology (Clifton, NJ) 804, 463, 2012 | 198 | 2012 |
| 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 | 198 | 2010 |
| Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer L Cantini, P Zakeri, C Hernandez, A Naldi, D Thieffry, E Remy, A Baudot Nature Communications 12 (1), 1-12, 2021 | 180 | 2021 |
| Dynamically consistent reduction of logical regulatory graphs A Naldi, E Remy, D Thieffry, C Chaouiya Theoretical Computer Science 412 (21), 2207-2218, 2011 | 170 | 2011 |
| Decision diagrams for the representation and analysis of logical models of genetic networks A Naldi, D Thieffry, C Chaouiya Proceedings of the 2007 international conference on Computational methods in …, 2007 | 161 | 2007 |
| MaBoSS 2.0: an environment for stochastic Boolean modeling G Stoll, B Caron, E Viara, A Dugourd, A Zinovyev, A Naldi, G Kroemer, ... Bioinformatics, 2017 | 136 | 2017 |
| 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 | 112 | 2015 |
| Logical modelling and analysis of cellular regulatory networks with GINsim 3.0 A Naldi, C Hernandez, W Abou-Jaoudé, PT Monteiro, C Chaouiya, ... Frontiers in Physiology 9, 646, 2018 | 99 | 2018 |
| 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 | 99 | 2018 |
| Cooperative development of logical modelling standards and tools with CoLoMoTo A Naldi, PT Monteiro, C Müssel, HA Kestler, D Thieffry, I Xenarios, ... Bioinformatics 31 (7), 1154-1159, 2015 | 92 | 2015 |
| COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms M Ostaszewski, A Niarakis, A Mazein, I Kuperstein, R Phair, ... Molecular systems biology 17 (10), e10387, 2021 | 90 | 2021 |
| Dynamical modeling and analysis of large cellular regulatory networks D Bérenguier, C Chaouiya, PT Monteiro, A Naldi, E Remy, D Thieffry, ... Chaos: An Interdisciplinary Journal of Nonlinear Science 23 (2), 025114, 2013 | 84 | 2013 |
| A reduction of logical regulatory graphs preserving essential dynamical properties A Naldi, E Remy, D Thieffry, C Chaouiya Computational Methods in Systems Biology, 266-280, 2009 | 77 | 2009 |
| Modular logical modelling of the budding yeast cell cycle A Fauré, A Naldi, F Lopez, C Chaouiya, A Ciliberto, D Thieffry Mol. BioSyst. 5 (12), 1787-1796, 2009 | 76 | 2009 |
Denis ThieffryProfessor of Systems Biology, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), ParisVerified email at ens.fr
