"All life is problem solving." Karl Popper

Current research contracts

  • ANR ∂ifference (2020-2023) coord. Olivier Bournez, LIX, Palaiseau.


  • IBM France Lab. (2020-2023): Learning rules from time-dependent data.
  • Johnson&Johnson beauté santé France (2020-2023): Development and implementation of a mathematical model of inflammation in human skin.
  • Servier Research Lab (2019-2022): Learning Mechanistic Models from Data for Screening Experiment Design and Drug Discovery
  • Inria Exploratory Action GRAM: biochemical programming (2019-2022)
  • ANR-DFG SYMBIONT: Symbolic Methods for Biological Networks (T. Sturm, LORIA Nancy, A. Weber, Univ. Bonn, coordinators, 2018-2022) - (Paris meeting 4-5 April 2019)
  • ANR-MOST BIOPSY: Biochemical Programming Systems (F. Molina CNRS Sys2diag, Montpellier, and J.H. Jiang, Dept. Electrical Engineering, NTU, Taiwan, coordinators, 2016-2021)


  • access grant to Occigen supercomputer 500000h

Current research working groups



  • CNRS GT BIOSS Biologie Systémique Symbolique
  • CNRS GDR BIM Bioinformatique Moléculaire
  • CNRS GDR IA Intelligence Artificielle
  • Consortium CoLoMoTo Logical Models and Tools
  • Consortium DiseaseMaps, and notably its Covid-19 working group

Research Topics

Most of our theoretical work on biochemical reaction systems consists in analyzing the interplay between the structure

  • Petri net invariants and properties,
  • circuits in the influence graph,
  • subgraph epimorphisms between reaction systems, ...

and the dynamics

© Inria / Photo C. Morel
  • boolean transition systems,
  • continuous-time Markov chains (CTMC),
  • ordinary differential equations (ODE),
  • time scale separations,...

of reaction networks. These studies provide necessary or sufficient conditions for the existence of some dynamical properties which can be predicted in large biochemical reaction networks by static analyses without making simulation.

Furthermore, the logical paradigm for systems biology that we have developed for building models from formal specifications in temporal logic can be summarized by the following identifications :

  • biological model = transition system,
  • biological property = temporal logic formula,
  • model validation = model-checking,
  • model inference = constraint solving.

This is used with optimization algorithms to develop efficient parameter search strategies in high dimension.

Our collaborations with biologists and experimentalists are focused on concrete biological questions and on the building of predictive models of biological systems to answer them. More specifically, we mainly work on mammalian cells, on

  • cell cycle regulation and circadian clock
  •  cell signaling
  • biosensor design
  • biochemical programming of artificial vesicles

Because of the importance of optimization techniques in our research, we keep some activity purely dedicated to optimization problems. The objective is to develop optimization algorithms for biological problems at the right level of generality, allowing comparisons with other methods, confrontations to other problems, and better insight on the optimization processes.


Past contracts

  • Exploratory Action with Pasteur Institute in Paris InBio headed by Grégory Batt (2017-2019)
  • ANR-Austria CyberCircuits with Jakob Ruess (2018-2022)
  • 2020 FET-OPEN Cosy-Bio “Control Engineering of Biological Systems for Reliable Synthetic Biology Applications”, coordinated by Diego di Bernardo (Tigem), with Filippo Menolascina (Edinburgh U), Mario di Bernardo (Naples U), Pascal Hersen (Paris7 U), Mustafa Khammash (ETHZ), Gregory Batt, Guy-Bart Stan (Imperial College), and Lucia Marucci (Bristol U) (2017-2020)
  • ANR Memip (G. Batt coordinator, 2017-2020)
  • ANR Cogex (P. Hersen, CNRS MSC lab Paris, coordinator, 2017-2019)
  • ANR Blanc HyClock (F. Delaunay, CNRS Nice, coordinator, 2014-2018)
  • Procope (O. Radulescu, Univ. Montpellier, France, Andreas Weber, Univ. Bonn, Germany, 2015-2018)
  • ANR Blanc STOCH-MC (B. Genest Inria Rennes coordinator, 2014-2018)
  • ANR Avenir ICEBERG (G. Batt coordinator, 2011-2016))
  • ANR Blanc Net-WMS-2 (F. Fages coordinator, 2011-2015)
  • OSEO-BPI BioIntelligence (2009-2014)
  • General-Electric Transportation (2009-2014)
  • ANR Blanc BioTempo (2010-2014)
  • ANR Cosinus Syne2arti (G. Batt coordinator, 2010-2013)
  • EU EraNet SysBio C5Sys (2010-2013)
  • Initiative Action COLAGE (2008-2013)
  • Initiative Action REGATE (2008-2013)
  • ANR Calamar (S. Soliman coordinator, 2009-2011)
  • European 6th PCRD Strep Net-WMS (F. Fages coordinator, 2006-2010)
  • European 6th PCRD Strep Tempo (2006-2009)
  • AgroBI INRA Project INSIGHT (2006-2008)
  • INRIA Cooperative Research Initiative ARC MOCA (S. Soliman coordinator, 2006-2007)
  • European 6th PCRD NoE Rewerse (2004-2008)
  • European 6th PCRD Strep April-2 (2004-2007)
  • ACI VICANNE (2004-2007)
  • RNTL MANIFICO (2003-2006)
  • RNTL OADymPPaC (P. Deransart coordinator, 2000-2004)
  • INRIA Cooperative Research Initiative ARC CPBIO (F. Fages coordinator, 2002-2004)