Morgan Magnin

Associate professor – Bioinformatics – Centrale Nantes & IRCCyN


I have been strongly involved in the management of national scientific projects. I have co-supervised 4 PhD theses and 4 Master’s theses. I am regularly involved in bioinformatics evaluation skills (scientific expert for the INSERM Cancer program, journal referee). Well aware of the necessity to build not only strong scientific theories, but also to implement them in a software tool, I am co-supervisor of the development of the free software MarkUs. Since starting as an associate professor in 2008, I have written 5 papers in refereed international journals, 1 paper in refereed national journal, 2 book chapters, 14 papers in international peer-reviewed conferences.

Recent works

  • International conferences: Computational Approaches to Analyze Complex Dynamic Systems : Model-Checking and its Applications. NII International advanced lectures series on ICT: series of 4 lectures of 2 hours in Spring 2013 at National Institute of Informatics, Tōkyō, Japan (Apr 2013)
  • Publication: [Sch2013b] N. Schwind, M. Magnin and K. Inoue. Resilience of Event-Driven Dynamic Systems. In the 27th Annual Conference on Japanese Society of Artificial Intelligence (JSAI 2013). 8 pages. Toyama, Japan. June 2013.
  • Publication: C. Chancellor, A. Ammar, F. Chinesta, M. Magnin, and O. Roux. Linking Discrete and Stochastic Models: the Chemical Master Equation as a bridge between Process Hitting and PGD. In Computational Methods in Systems Biology (CMSB’2013), Klosterneuburg, Austria. September 2013.


  • 2011: Special mention prize at the third French “Trophées des Technologies Educatives” for the project “MarkUs, an application to manage and grade students’ papers on-line”
  • 2008: Recipient of the “HP Technology for Teaching Grant”, with G. Moreau and S. Tichadou, for the project “Most complex systems are designed with simplest tools” about the use of Tablets PC to improve pedagogy at Centrale Nantes (prize: 100.000 US$)
  • 2004: Recipient of a “CNRS BDI Grant/ PhD Fellowship”

Past Research

  • I obtained my PhD in 2007, under the supervision of Olivier Henri Roux and Pierre Molinaro. My thesis focused on model-checking through time extensions of Petri nets (the so-called stopwatch Petri nets): many critical applications (for example, those involving task scheduling issues, e.g. the representation of interactions inside the circadian clock system in biology) require taking into account the time between transitions and/or some actions. To achieve this, logical time – usually captured by models like finite automata – is no longer sufficient. That is why our previous works focused on timed models in which time is handled explicitly. In previous works, we have examined the respective merits of discrete-time and dense-time semantics.
  • Since 2008 and my recruitment as an associate professor at the Computer Science and Mathematics department of École Centrale de Nantes/IRCCyN, (France), I am much interested in the application of formal methods to biological systems. More precisely, we have considered new approaches to tackle large-scale concurrent systems. Inspired by the works around pi-calculus, we have introduced a new formalism, named the Process Hitting (PH), to model concurrent systems having components with a few qualitative levels. Thanks to the particular structure of interactions within PH, efficient static analysis methods have been developed to tackle the formal analysis of biological systems with hundreds of components. We have recently illustrated the merits of constraint programming (especially Answer Set Programming) applied to this framework in a context of automatic inference of biological models.


Scientific activities

  • Since September 2010: appointed “Project Manager” for Information and Communication Technology applied to Education at École Centrale de Nantes.
  • Since September 2008: Associate Professor in Computer Science at École Centrale de Nantes, affected to IRCCyN / MeForBio team for research
  • 2004-2008: Teaching assistant (“moniteur” then “ATER”) at École Centrale de Nantes


  • PhD thesis in Automatics and Applied Computer Science, Université de Nantes, École Centrale de Nantes, defended December, 13th 2007.
  • Master thesis in Automatics and Applied Computer Science, École Centrale de Nantes, 2004.
  • Engineer diploma, École Centrale de Nantes, 2004.

Cultural activities

  • 2006-2012: Permanent member of the Organizing Committee of the International Science-Fiction Festival of Nantes, Les Utopiales
  • 2007-2011: Co-creator of Univers partagés, a french organization dedicated to the promotion of graphical pop-culture
  • 2001-2005: Journalist for the webzine (then nationally distributed magazine) Mangajima


Tel: 02 40 37 16 28
// 02 40 37 69 78

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Last update: 2014-02-04
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