Thème de recherche : Modélisation discrète des réseaux de régulation

Mots-clés : réseaux booléens, graphes, systèmes dynamiques discrets, fonctions booléennes

Le cadre de mes travaux est la modélisation et l'analyse qualitative du comportement dynamique de réseaux de régulation génétique. Ces réseaux d'interaction sont des systèmes complexes, qui nous mettent face à des problèmes difficiles de propriétés émergentes et d'explosion combinatoire. Combinant des outils de systèmes dynamiques discrets, théorie des graphes et combinatoires, la principale motivation de ces travaux est d'analyser la dynamique de réseaux de régulation biologique pour en extraire les principales propriétés, apporter une compréhension mécanistique du phénomène biologique étudié, et proposer des prédictions à valider par le biologiste.

Publications

  • Paul Ruet and Elisabeth Remy. From multivalued to Boolean functions: preservation of soft nested canalization. Theoretical Computer Science, 982: 114277, 2024.

  • Stephen Chapman, Estelle Duprez and Elisabeth Remy. Logical modelling of myelofibrotic microenvironment predicts dysregulated progenitor stem cell crosstalk. BioSystems, 09, 2023.

  • Léonard Hérault, Mathilde Poplineau, Estelle Duprez and Elisabeth Remy. A novel boolean network inference strategy to model early hematopoiesis aging. Computational and Structural Biotechnology Journal, 21:21-33, 2023.

  • Léonard Hérault, Mathilde Poplineau, Elisabeth Remy, and Estelle Duprez. Single cell transcriptomics to understand hsc heterogeneity and its evolution upon aging. Cells, 11:3125, 10 2022.

  • Saran Pankaew, Delphine Potier, Clémence Grosjean, Mathis Nozais, Julie Quessada, Marie Loosveld, Élisabeth Remy, and Dominique Payet-Bornet. Calcium signaling is impaired in pten-deficient t cell acute lymphoblastic leukemia. Frontiers in Immunology, 13, 2022.

  • Léo Pio-Lopez, Alberto Valdeolivas, Laurent Tichit, Élisabeth Remy, and Anaïs Baudot. Multiverse: a multiplex and multiplex-heterogeneous network embedding approach. Scientific reports, 2021. vol. 11, no 1, p. 1-20.

  • Jean Fabre-Monplaisir, Brigitte Mossé, and Elisabeth REMY. Isometries of the hypercube: a tool for boolean regulatory networks analysis  . Physica D: Nonlinear Phenomena, 2021.

  • Léonard Hérault, Mathilde Poplineau, Adrien Mazuel, Nadine Platet, Élisabeth Remy, and Estelle Duprez. Single-cell rna-seq reveals a concomitant delay in differentiation and cell cycle of aged hematopoietic stem cells. BMC biology, 19(1):1--20, 2021.

  • Laura Cantini, Pooya Zakeri, Celine Hernandez, Aurelien Naldi, Denis Thieffry, Elisabeth Remy, and Anaïs Baudot. Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer. Nature communications, 12(1):1--12, 2021.

  • J. Béal, É. Remy and L. Calzone. Connecter les modèles logiques aux données omiques. Chapitre Ouvrage ISTE Sciences : Approches symboliques de la modélisation et de l'analyse des systèmes biologiques. C. Lhoussaine and É. Remy (Eds.). London, 2020.

  • M. Katsogiannou, JB. Boyer, A. Valdeolivas, É. Remy, L. Calzone, et al. Integrative proteomic and phosphoproteomic profiling of prostate cell lines. PLoS ONE, Public Library of Science, 2019, 14 (11).

  • B. Mossé and É. Remy. A Combinatorial Exploration of Boolean Dynamics Generated by Isolated and Chorded Circuits. Acta Biotheoretica, 2019.

  • Méline Wery, Olivier Dameron, Jacques Nicolas, Élisabeth Remy, and Anne Siegel. Formalizing and Enriching Phenotype Signatures using Boolean Networks. Journal of Theoretical Biology, 467 :66-79, 2019.

  • Nuno D. Mendes, Ricardo Henriques, Élisabeth Remy, Jorge Carneiro, Pedro T. Monteiro and Claudine Chaouiya. Estimating Attractor Reachability in Asynchronous Logical Models. Frontiers in Physiology, 2018.

  • Alberto Valdeolivas, Laurent Tichit, Claire Navarro, Sophie Perrin, Gaëlle Odelin, Nicolas Levy, Pierre Cau, Élisabeth Remy, and Anaïs Baudot. Random walk with restart on multiplex and heterogeneous biological networks. Bioinformatics, bty637, 2018.

  • 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. Petri Net representation of multi-valued logical regulatory graphs Natural Computing, 10, 727 – 750. Springer, 2011.

  • 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.

  • 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.

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

  • 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.

  • 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 circuitsTransactions on Computational Systems Biology VII, Springer LNCS 4230: 56-72, 2006.

  • 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.

  • 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, 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.

  • 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.

  • 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.

  • 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.

Activités d'animation de la recherche

  • Co-responsable du GDR BIMMM. (Bio-Informatique Moléculaire : Modélisation et méthodologie) depuis janvier 2024:
  • Création et Animation d'un Groupe de Travail IREM, Les biomathématiques, du labo au bahut. Janvier 2017
  • Vulgarisation scientifique Participation à la Nuit Européenne des chercheurs, Septembre 2017 Intervention auprès de lycéens
  • Organisation de workshops

Fonctions administratives

  • Responsable de l'équipe MABioS (depuis 2018)
  • Directrice adjointe de l' I2M (depuis février 2024)
  • Membre Commission Interdisciplinaire 51 - Modélisation mathématique, informatique et physique pour les sciences du vivant du Comité national de la recherche scientifique CID51 (depuis juillet 2024)
  • Membre du comité de pilotage de l'institut Convergence CenTuri
  • Responsable du parcours Mathématiques du Master interdisciplinaire Computational and Mathematical Biology