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Great advances in molecular biology, genomics and functional genomics open the way for a better understanding of regulatory mechanisms. These mechanisms interplay and operate at diverse levels (transcription and translation of the genetic material, protein modifications, etc.). They define large and complex networks, which in turn constitute a relevant functional framework to integratively study the control of cellular processes. To assess the behaviours induced by such networks, dedicated mathematical and computational tools are deeply needed.

In this context, our goal is to develop generic tools for the modelling and analysis of large molecular networks. For this purpose, we mainly rely on a qualitative modelling framework combining the generalised logical formalism and Petri nets. In a close collaboration with biologists, methodological developments are systematically challenged with real case applications, specifying and analysing models for the control of cell proliferation and differentiation.


  • CoMEDy, A COmputational Modelling platform for Epithelial DYnamics to explore the role of epithelial to mesenchymal transition and stemness acquisition in cancer recurrence (PTDC/BEX-BCB/0772/2014), Coordinator.
  • CANCEL STEM, Tackling cancer stem cells: a challenge and an opportunity to advance in anti-cancer therapy(POCI-01-0145-FEDER-016390), Partner.
  • ERGODiC, Formal methods for the analysis of modular gEnetic ReGulatOry network DynamiCs (PTDC/EEI-CTP/2914/2014), Partner.
  • CANTROL, Deciphering the mechanisms of transcriptional regulation that control antifungal drug resistance in the pathogenic yeast Candida glabrata: aiming the development of improved diagnosis and therapeutic approaches (PTDC/BBB-BIO/4004/2014, Partner).

  • MALIN, Modular modelling and Analysis of Large biological Interacting Networks, funded by the Fundação para a Ciência e a Tecnologia (FCT, Project PTDC/EIA-CCO/099229/2008).
  • CALAMAR, Compositional modelling and Analysis of LArge MoleculAr Regulatory networks - application to the control of human cell proliferation. Funded by the French National Research Agency (Agence Nationale de la Recherche), ANR-08-SYSC-003.