• É. Remy, B. Mossé, and D. Thieffry. Boolean dynamics of regulatory compound circuits. In Dynamics of mathematical models in Biology, 43:53, 2016.

  • Élisabeth Remy, Sandra Rebouissou, Claudine Chaouiya, Andrei Zinovyev, Francois Radvanyi, and Laurence Calzone. A modelling approach to explain mutually exclusive and co-occurring genetic alterations in bladder tumorigenesis. Cancer research, 75(19):4042–52, August 2015.

  • Åsmund Flobak, Anaïs Baudot, Élisabeth Remy, Liv Thommesen, Denis Thieffry, Martin Kuiper, and Astrid Lægreid. Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling. PLoS computational biology, 11(8):e1004426, August 2015.

  • C. Chaouiya and É. Remy. Logical modelling of regulatory networks, methods and applications. Bulletin of mathematical biology, 75(6) :891–5, June 2013.

  • D. Bérenguier, C. Chaouiya, P.T. Monteiro, A. Naldi, É. Remy, D. Thieffry, and L. Tichit. Dynamical modeling and analysis of large cellular regulatory networks. Chaos, 23(2) :025114, June 2013.

  • G. Didier and É. Remy. Relations between gene regulatory networks and cell dynamics in boolean models. Discrete Applied Math., 160 :2147–57, 2012.

  • G. Didier, É. Remy, and C. Chaouiya. Mapping multivalued onto boolean dynamics. J. Theor. Biol., 270 :177–184, 2011.

  • C. Chaouiya, A. Naldi, É. Remy, and D. Thieffry. Natural Computing, chapter Petri Net representation of multi-valued logical regulatory graphs. Springer, 2010.

  • A. Naldi, É. Remy, D. Thieffry, and C. Chaouiya. Dynamically consistent reduction of logical regulatory graphs. Theoretical Computer Science, 412 :2207–2218, 2011.

  • A. Naldi, É. Remy, D. Thieffry, and C. Chaouiya. A reduction of logical regulatory graphs preserving essential dynamical properties. In Computational Methods in Systems Biology, volume 5688 of LNBI journal, pages 26 – 280, 2009.

  • F. Lopez, J. Textoris, A. Bergon, G. Didier, É. Remy, S. Granjeau, J. Imbert,  C. Nguyen and D. Puthier: TranscriptomeBrowser: A Powerfull and Flexible Toolbox to Explore Productively the Transcriptional Landscape of the Gene Expression Omnibus Database. PLoS ONE 3(12):e400. 2008. doi

  • É. Remy and P. Ruet: From elementary signed circuits to the dynamics of Boolean regulatory networks. Bioinformatics 24: i200-i226, 2008.

  • É. Remy, P. Ruet and D. Thieffry: Graphic requirement for multistability and attractive cycles in a Boolean dynamical framework. Advances in Applied Mathematics, 41(3):335-350, 2008. pdf

  • C. Chaouiya, É. Remy, D. Thieffry: Petri Net Modelling of Biological regulatory networks. Journal of Discrete Algorithms, 6:2, 165-77, 2008. doi

  • J. Textoris, F. Lopez, G. Didier, É. Remy, S. Granjeau, C. Nguyen and D. Puthier: DBF-MCL a new algorithm for rapidly and accurately axtracting cluster of co-regulated genes from microarray data. JOBIM Marseille, 2007.

  • É. Remy, P. Ruet, D. Thieffry: Positive or negative regulatory circuit inference from multilevel dynamics. Positive Systems: Theory and Applications, Springer LNCIS 341: 263-270, 2006.

  • É. Remy and P. Ruet: On differentiation and homeostatic behaviours of Boolean dynamical systems.Transactions on Computational Systems Biology VII, Springer LNCS 4230: 153-162, 2006. http://www.springerlink.com/content/f671307011402685/

  • É. Remy, P. Ruet , L. Mendoza, D. Thieffry and C. Chaouiya: From logical regulatory graphs to standard Petri nets: Dynamical roles and functionality of feedback circuits.Transactions on Computational Systems Biology VII, Springer LNCS 4230: 56-72, 2006. http://www.springerlink.com/content/w30180884311g787/

  • E. Simao, É. Remy, D. Thieffry and C. Chaouiya: Qualitative modelling of regulated metabolic pathway: Application to the Tryptophan biosynthesis in E. Coli. Bioinformatics. 21: ii190-196 (2005).

  • C. Chaouiya, É. Remy, D. Thieffry: Qualitative Petri Net Modelling of Genetic Networks. In C.Priami and G.Plotkin (Eds), Trans. on Comput. Syst. Biol. VI, LNBI 4220:95-112. 2006.doi

  • C. Chaouiya, É. Remy, P. Ruet , D. Thieffry: Qualitative Modelling of Genetic Networks: From Logical Regulatory Graphs to Standard Petri Nets. In ICATPN'04, LNCS 3099, pp.137-156. 2004. doi

  • D. Martin, C. Brun, É. Remy, P. Mouren, D. Thieffry and B. Jacq: GOToolBox: functional analysis of gene datasets based on Gene Ontology. Genome Biology, vol.5,n. R101, 2004. 

  • P. Mathieu and É. Remy: Isoperimetry and heat kernel decay on percolation clusters. Annals of Probability, 32,n. 1A, pp100--128, 2004. Arxiv

  • C. Chaouiya , É. Remy, B. Mossé, and D. Thieffry: Qualitative analysis of regulatory graphs: a computational tool based on a discrete formal framework. In "First multidisciplinary international symposium on POsitive Systems: Theory and Applications" (POSTA 2003), L. Benvenuti, A. De Santis, L. Farina (Eds), Springer-Verlag, LNCIS 294, pp. 119-126, 2003.doi

  • É. Remy, B. Mossé, C. Chaouiya and D. Thieffry: A description of dynamical graphs associated to elementary regulatory circuits. Bioinformatics vol.19 (Suppl. 2), pp.172--178, 2003.

  • G. Didier, P. Brézellec, É. Remy and A. Hénaut: GeneANOVA - gene expression analysis of variance. Bioinformatics Applications Note vol. 18, pp.1-2, 2002.

  • P. Mathieu and É. Remy: Décroissance du noyau de la chaleur et isop\'erim\'etrie sur un amas de percolation CRAS Paris, T. 332, série I, pp. 927-931, 2001.

  •  A. Piatnitski and É. Remy: Homogenization of elliptic difference operator. SIAM J. Math. Anal. vol. 33, n.1, pp.53-83, 2001.