(Laboratoire Bordelais de Recherche en Informatique, UMR CNRS 5800), Bordeaux, France.
Member of Méthodes Formelles group.
Associate member of Bioinfo group at LRI UMR CNRS 8623, Université Paris-Sud, Orsay, France.
- E-mail: loic.pauleve labri.fr – PGP key: E7E7D63A – ORCID:0000-0002-7219-2027.
- LaBRI UMR CNRS 5800
351, cours de la Libération 33405 Talence cedex, France.
- Office: 305.
- Formal analysis of dynamics of large-scale biological networks.
- Abstract interpretation of traces in concurrent systems.
- Computational methods for cellular reprogramming.
My main research focuses on the abstract interpretation of traces in automata networks. I introduced the Local Causality Graphs which represent necessary and/or sufficient intermediary steps for changing a local state of a given automaton. Local Causality Graphs bring a very compact representation of all the possible traces of an Automata Network. They have been applied for deriving highly scalable necessary or sufficient conditions for reachability properties in Automata Networks. Local Causality Graphs have also been applied for deducing correct cut sets for transient reachability, i.e. sets of mutations that make impossible the concerned reachability to occur; and for goal-oriented model reduction preserving minimal traces for reachability. Such analysis have been applied to networks ranging from 100 to 10,000 nodes, which was unprecedented.
I created and maintain the software Pint which provides a language for specifying Automata Networks and Process Hitting models, and several static analysis tools (reachability, fixed point, stochastic simulation). Recently, I supervised the development of the software CausaLex for visualizing and scripting Local Causality Graphs that can be generated using Pint.
I am coordinator of the project AlgoReCell (ANR-FNR, 2017-2020) and FormaReBio (DIM RFSI, région Île-de-France). Previously, I was involved in the projects 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).
I am co-supervising 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.
I am PC member of CMSB'18; MLCSB'18; SASB'18; I was PC co-chair of SASB'15; SASB'14; PC member of CMSB'17; SASB'17; JOBIM'17; SASB'16; CMSB'15; MEMICS'15; SASB'13; SASB'12; and organizing committee member of SeqBio 2015. I was member of the PhD commitee of Adrien Rougny (Univ. Paris-Saclay, 2016); Séverine Affeldt (Institut Curie, 2015).
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 researcher at CNRS, between 2013 and 2018 in LRI laboratory (Orsay, France), and since 2018, in LaBRI laboratory (Bordeaux, France).