picture Pierre-Yves Bourguignon

Pierre-Yves Bourguignon
Max-Planck-Institut für Mathematik in den Naturwissenschaften
Inselstr. 22
04103 Leipzig

Office: A3 12
+49 341 9959 546
+49 341 9959 658

Pierre-Yves Bourguignon

Short Curriculum Vitae

I am currently manager of Isthmus SARL, a french biotech committed to the development of disruptive techniques in the field of synthetic biology. My main activity is to contribute to the Microme project. 

I graduated in applied mathematics in december 2008 from the University of Evry. My Ph.D. dissertation is titled Parsimony in Markovian models and applications to the analysis of biological sequences, and reports on work done at the Statistics and Genomes lab of the University of Evry under the supervision of Pr. Bernard Prum.

Current and previous positions

since 2011 - Scientific Investigator at Isthmus SARL, assigned to the Max-Planck-Institute for Mathematics in the Sciences.

2009-2011 - Post-doctoral fellow within the program in Systems Biology supported jointly by the French National Center for Scientific Research (CNRS) and the Max-Planck Society.

2005-2008 - Research fellow within the Computational Systems Biology group at the French Genome Center (Genoscope, CEA).

2002-2005 - Ph.D. fellow of the French government doctoral programme.

Research interests

  • Bayesian statistics

    • Motif discovery
    • Model selection
    • Markov chains and extensions
    • Computational methods (MCMC, ABC)

  • Bioinformatics

    • Metabolic modelling
    • Chemoinformatics
    • Identification of transcription factor binding sites
    • Phylogenetics
    • Aging process


  • Journal articles
    • Inhomogeneous Parsimonious Markov models. R. Eggeling, A. Gohr, P.-Y. Bourguignon, E. Wingender, I. Grosse. Lecture Notes in Computer Science, series LNAI 8188, pp. 321-336.
    • Core and Panmetabolism in Escherichia coli. G. Vieira, V. Sabarly, P.-Y. Bourguignon, M. Durot, F. Le Fèvre, D. Mornico, D. Vallenet, O. Bouvet, E. Denamur, V. Schachter and C. Médigue. Journal of Bacteriology, March 2011, Vol. 193, No. 6.
    • Challenges in experimental data integration within genome-scale metabolic models. P.-Y. Bourguignon, A. Samal, F. Képès, J. Jost and O. Martin. Algorithms in Molecular Biology, 2010.
    • Genome-scale models of bacterial metabolism: reconstruction and applications. M. Durot, P.-Y. Bourguignon and V. Schachter. FEMS Microbiology Reviews, 2009 Jan;33(1):164-90.
    • An EM algorithm for estimation in the Mixture Transition Distribution model. S. Lèbre and P.-Y. Bourguignon. Journal of Statistical Computation and Simulation, Volume 78, Issue 8 2008 , pages 713 - 729.
    • Property-driven statistics of biological networks. P.-Y. Bourguignon, V. Danos, S. Smidtas, F. Képès and V. Schachter. Transactions in Computational Systems Biology IV, 2006.
    • Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination “hot spots". J. Drouaud, C. Camilleri, P.-Y. Bourguignon, A. Canaguier, A. Bérard, D. Vezon, S. Giancola, D. Brunel, V. Colot, B. Prum, H. Quesneville, and C. Mézard. Genome Res. 2006. 16: 106-114.
    • Seq++: analyzing biological sequences with a range of Markov models. V. Miele, P.-Y. Bourguignon, D. Robelin, G. Nuel and H. Richard. Bioinformatics, 2005, Volume 21, Number 11, Pp. 2783-2784.


    • Conference papers

      • Modèles de Markov parcimonieux, P.-Y. Bourguignon, D. Robelin. JOBIM 2004, Montréal.
      • Bayesian non-parametric discovery of protein-binding sites, P. Benner, S. Poppe, P.-Y. Bourguignon. Selected for ECCS'12.
      • Gibbs sampling for parsimonious Markov models with latent variables, R. Eggeling, P.-Y. Bourguignon, André Gohr, Ivo Grosse.Accepted at the the Sixth European Workshop on Probabilistic Graphical Models (PGM 2012).



  • Synthetic biology

    • Philippe Marlière, Isthmus SARL
    • Rupert Mutzel, Freie Universität Berlin
    • Bruno Bienfait, Molecular Networks

  • Bayesian identification of transcription factor binding sites

    • Katja Nowick, University of Leipzig
    • Philipp Benner, Ph.D. student, MPI MiS (co-supervision with J. Jost)
    • Pr. Ivo Grosse's group, Martin-Luther University of Halle-Wittenberg.

  • Models of the aging process

    • Sofia Tsepletidou, Ph.D. student, University Paris Dauphine (co-supervision with C.P. Robert)
    • Christian P. Robert, University Paris Dauphine & CREST
    • Ariel Lindner, INSERM & CRI

  • Modelisation of microbial metabolism

    • Christine Dillmann's group, Ferme du Moulon, CNRS/INRA/Univ. Paris XI.
    • C. Médigue's group, Laboratoire de Génomique Comparative, Genoscope, CNRS/CEA/Univ. Evry.
    • E. Denamur and O. Bouvet, Ecology and Evolution of Microorganisms, INSERM/Univ. Paris VI-XIII.

09.02.2016, 09:22