Loïc Paulevé, PhD, HDR

CNRS senior researcher (directeur de recherche) at LaBRI (Laboratoire Bordelais de Recherche en Informatique, UMR CNRS 5800), Bordeaux, France.
Member of MTV team of the Formal Methods and Models department.
Member and co-facilitator of Digital Health axis of LaBRI.
Member and co-facilitator of GT Bioss CNRS working group.

Contact

Research interests

Publications

Selected/recent:

List of publications

Software

The CoLoMoTo Interactive Notebook

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

Homepage: http://colomoto.org/notebook - Tutorial notebooks - Case study
+ Tutorial video @ CMSB 2020

BoNesis

Synthesis of Most Permissive Boolean Networks from network architecture and dynamical properties

Homepage: https://bnediction.github.io/bonesis - Tutorial

mpbn

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

Pint

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.

Homepage: https://loicpauleve.name/pint

Other research-related tools include:

See my GitHub profile.

Resume

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 Théo Roncalli (2023-now, co-supervised with Élisabeth Rémy); 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 Athénaïs Vaignay (2024-now); Déborah Boyenval (2023-now). Previously, co-supervisor for PhD studies of Stéphanie Chevalier (2018-2022; co-supervised with Christine Froidevaux, LISN, and Andrei Zinovyev, Institut Curie; now post-doctoral researcher in industry); Juraj Kolčák (2017-2021, co-supervised with Stefan Haar, Inria Saclay; now post-doctoral researcher at Univ of Southern Denmark); Hugues Mandon (2016-2019, co-supervised with Stefan Haar, Inria Saclay; now in industry); and for post-doctoral research of Sara Riva (2022-2023; now assistant professor (MCF) at Université de Lille and CRIStAL laboratory).

PC member of CMSB'24; ISMB'24; Previously, PC member of CMSB'23; ISMB/ECCB'23; 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); Albin Salazar (reviewer; École normale supérieure de Paris, 2023); Felix Weidner (reviewer; Ulm University, 2023); Maxime Mahout (reviewer; Université Paris-Saclay, 2023); Mitsuhiro Odaka (NII, Japon/École centrale de Nantes, 2024); Luis Cabrera Crot (Univ Concepción, Chili, 2024).

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) by CNRS.