(Laboratoire Bordelais de Recherche en Informatique, UMR CNRS 5800), Bordeaux, France.
Member of Formal Methods 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.
Coordinator of the project AlgoReCell (ANR-FNR, 2017-2020). Previously, involved in the projects 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.
Co-supervisor for the PhD studies of Stéphanie Chevalier (2018-2021; funded by ITMO Cancer) on inference of models of cellular differentiation; Juraj Kolčák (2017-2020; funded by ANR-FNR AlgoReCell project) on parametric regulatory networks and Hugues Mandon (2016-2019; funded by Digicosme Labex) on Boolean network reprogramming.
PC member of CMSB'21 (co-chair); ISMB/ECCB'21. Previously, PC member of 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 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).
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 September 2020, I got my Habilitation à Diriger des Recherches (HDR) from Université Paris-Saclay.