| GOToolBox: functional analysis of gene datasets based on Gene Ontology D Martin, C Brun, E Remy, P Mouren, D Thieffry, B Jacq Genome biology 5, 1-8, 2004 | 477 | 2004 |
| Random walk with restart on multiplex and heterogeneous biological networks A Valdeolivas, L Tichit, C Navarro, S Perrin, G Odelin, N Levy, P Cau, ... Bioinformatics 35 (3), 497-505, 2019 | 276 | 2019 |
| Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework É Remy, P Ruet, D Thieffry Advances in Applied Mathematics 41 (3), 335-350, 2008 | 250 | 2008 |
| 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), 124, 2021 | 175 | 2021 |
| Dynamically consistent reduction of logical regulatory graphs A Naldi, E Remy, D Thieffry, C Chaouiya Theoretical Computer Science 412 (21), 2207-2218, 2011 | 169 | 2011 |
| Isoperimetry and heat kernel decay on percolation clusters P Mathieu, E Remy The Annals of Probability 32 (1A), 100-128, 2004 | 152 | 2004 |
| Petri net modelling of biological regulatory networks C Chaouiya, E Remy, D Thieffry Journal of Discrete Algorithms 6 (2), 165-177, 2008 | 138 | 2008 |
| Discovery of drug synergies in gastric cancer cells predicted by logical modeling Å Flobak, A Baudot, E Remy, L Thommesen, D Thieffry, M Kuiper, ... PLoS computational biology 11 (8), e1004426, 2015 | 131 | 2015 |
| 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 | 130 | 2005 |
| GeneANOVA—gene expression analysis of variance G Didier, P Brézellec, E Remy, A Hénaut Bioinformatics 18 (3), 490-491, 2002 | 125 | 2002 |
| 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 | 113 | 2015 |
| Qualitative analysis of regulatory graphs: a computational tool based on a discrete formal framework C Chaouiya, E Remy, B Mossé, D Thieffry Positive Systems: Proceedings of the First Multidisciplinary International …, 2003 | 110 | 2003 |
| A description of dynamical graphs associated to elementary regulatory circuits E Remy, B Mossé, C Chaouiya, D Thieffry Bioinformatics-Oxford 19 (2), 172-178, 2003 | 108 | 2003 |
| Qualitative modelling of genetic networks: From logical regulatory graphs to standard petri nets C Chaouiya, E Remy, P Ruet, D Thieffry Applications and Theory of Petri Nets 2004: 25th International Conference …, 2004 | 104 | 2004 |
| 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), 2013 | 83 | 2013 |
| A reduction of logical regulatory graphs preserving essential dynamical properties A Naldi, E Remy, D Thieffry, C Chaouiya Computational Methods in Systems Biology: 7th International Conference, CMSB …, 2009 | 77 | 2009 |
| From minimal signed circuits to the dynamics of Boolean regulatory networks E Remy, P Ruet Bioinformatics 24 (16), i220-i226, 2008 | 74 | 2008 |
| From logical regulatory graphs to standard petri nets: Dynamical roles and functionality of feedback circuits E Remy, P Ruet, L Mendoza, D Thieffry, C Chaouiya Transactions on Computational Systems Biology VII, 56-72, 2006 | 62 | 2006 |
| Petri net representation of multi-valued logical regulatory graphs C Chaouiya, A Naldi, E Remy, D Thieffry Natural Computing 10, 727-750, 2011 | 60 | 2011 |
| Mapping multivalued onto Boolean dynamics G Didier, E Remy, C Chaouiya Journal of theoretical biology 270 (1), 177-184, 2011 | 58 | 2011 |
