CNRS senior researcher (directeur de recherche)
(Laboratoire Bordelais de Recherche en Informatique, UMR CNRS 5800), Bordeaux, France.
Member of MTV team of the Formal Methods and Models department and Digital Health axis.
Member and co-facilitator of BIOSS CNRS working group.
Accessible and Reproducible Computational Analyses for Qualitative Biological Networks The CoLoMoTo Interactive Notebook relies on Docker and Jupyter technologies to provide a unified environment to edit, execute, share, and reproduce analyses of qualitative models of biological networks
- Tutorial notebooks
- Case study
+ Tutorial video @ CMSB 2020
Python implementation of Most Permissive Boolean Networks (MPBNs). MPBNs formally guarantee not to miss any behavior achievable by a quantitative refinement of the Boolean model. Moreover, MPBNs significantly reduce the complexity of reachability and attractor analysis. See Reconciling Qualitative, Abstract, and Scalable Modeling of Biological Networks.
Source code: https://github.com/pauleve/mpbn - Example notebooks
Synthesis of Most Permissive Boolean Networks from network architecture and dynamical properties
Source code: https://github.com/bioasp/bonesis - Tutorial
Static analyses for dynamical properties on very large-scale Automata Networks. Provided analyses include notably the listing of fixed points, successive reachability properties, cut sets and mutations for reachability, and model reduction preserving transient dynamics. The translation to related formalisms, in particular Boolean and multi-valued networks, is also provided.
Other research-related tools include:
See my GitHub profile.
Principal investigator of the project BNediction (ANR, 2021-2025). Previously, AlgoReCell (coordinator; ANR-FNR, 2017-2021); FormaReBio (PI; DIM RFSI, région Île-de-France). FoRCe (PI; CNRS PEPS INS2I, 2017); RNALands (ANR-FWF, 2015-2017); HyClock (ANR, 2015-2017); BioTempo (ANR Blanc, 2011-2014); CirClock (PEPII CNRS, 2011-2012). From 2016 to 2018, initiated and coordinated the Paris-Saclay/DigiCosme working group GT TheoBioR on computational methods for modelling and analyzing biological networks.
Supervisor for the PhD studies of Gustavo Magaña López (2022-now); Chabname Ghassemi Nedjad (2022-now, co-supervised with Clémence Frioux, Inria Bordeaux); Kerian Thuillier (2021-now, co-supervised with Anne Siegel, IRISA Rennes); post-doctoral research of Sara Riva (2022-2023; now assistant professor (MCF) at Université de Lille and CRIStAL laboratory); PhD studies of Stéphanie Chevalier (2018-2022; co-supervised with Christine Froidevaux, LISN, and Andrei Zinovyev, Institut Curie; now post-doctoral researcher in industry) on inference of models of cellular differentiation); Juraj Kolčák (2017-2021, co-supervised with Stefan Haar, Inria Saclay; now post-doctoral researcher at Univ of Southern Denmark) on parametric regulatory networks and Hugues Mandon (2016-2019, co-supervised with Stefan Haar, Inria Saclay; now in industry) on Boolean network reprogramming.
PC member of CMSB'23; ISMB/ECCB'23; Previously, PC member of CMSB'22; ISMB'22; CMSB'21 (co-chair); ISMB/ECCB'21; CMSB'20; CMSB'19; SASB'19; MLCSB'18; CMSB'18; SASB'18; CMSB'17; SASB'17; JOBIM'17; SASB'16; SASB'15 (co-chair); CMSB'15; MEMICS'15; SASB'14 (co-chair); SASB'13; SASB'12; and organizing committee member of SeqBio 2015. Member of the HDR committee of Kévin Perrot (Aix-Marseille Université, 2022); member of the PhD commitee of Séverine Affeldt (Institut Curie, 2015); Adrien Rougny (Univ. Paris-Saclay, 2016); Célia Biane (Univ. Paris-Saclay, 2018); Xinwei Chai (École centrale de Nantes, 2019); Cui Su (reviewer; University of Luxembourg, 2020); Pacôme Perrotin (Aix-Marseille Université, 2021); Émilie Allart (reviewer; Université de Lille, 2021); Léonard Hérault (reviewer; Aix-Marseille Université, 2021); Honghao Li (reviewer; Institut Curie, 2021); Jérémie Pardo (reviewer; Université Paris-Saclay, 2022); Colin Thomas (Université Paris-Saclay, 2022); Athénaïs Vaginay (reviewer; Université de Lorraine, 2023).
I got my M.Sc. in computer science from École Normale Supérieure de Cachan, Brittany extension, France, in 2008 and my Ph.D. from École Centrale de Nantes, France, in 2011, supervised by Olivier Roux and Morgan Magnin. Between 2011 and 2012, I have been a postdoc at Laboratoire d'Informatique de l'École Polytechnique (LIX), France, in the AMIB group. Between 2012 and 2013, I have been a postdoc at ETH Zürich, Switzerland, in the BISON group of Heinz Koeppl. Since 2013, I am a full-time researcher at CNRS (permanent position, chargé de recherche), between 2013 and 2018 in LRI laboratory (Orsay, France), and since 2018, in LaBRI laboratory (Bordeaux, France). In 2020, I got my Habilitation à Diriger des Recherches (HDR) from Université Paris-Saclay. In 2023, I have been promoted to Directeur de Recherche (DR2).