I moved to Paris Descartes

My new mail is etienne.birmele AT parisdescartes.fr

My new web page is here

Étienne Birmelé

MCF

tel : +33 1 83 94 58 49
fax :

Laboratoire Statistique et Génome
UMR CNRS 8071, USC INRA
23 boulevard de France
91037 Évry, France

I had last year an INRIA invited researcher position in the Baobab team in Lyon.

Here is my CV(in french, updated march 2013).

Research interests

  • Statistics on networks
  • Complexity, approximation, enumeration algorithms
  • Random graph models
  • Graph theory
  • Application of the former items to biology

Publications

Statistics on biological networks

  • Birmelé, E. (2012), Detecting local network motifs, Electronic Journal of Statistics, 6, 908–933. pdf
  • Birmelé, E., Elati, M., Rouveirol, C., and Ambroise, C. (2008). Identification of functional modules based on transcriptional regulation structure, BMC Proceedings, 2(4):S4.
  • Matias, C., Schbath, S., Birmelé, E., Daudin, J.-J., and Robin, S. (2006). Networks motifs: mean and variance for the count, Revstat, 4(1), 31–51.

Complexity and algorithms

  • Birmelé, E., Ferreira, R., Grossi, R., Marino, A., Pisanti, N., Rizzi, R. and Sacomoto, G. (2013), Optimal Listing of Cycles and st-Paths in Undirected Graphs, Proceedings of 24th ACM/SIAM Symposium On Discrete Algorithms (SODA) 2013, ACM Press, to appear.
  • Acuna, V., Birmelé, E., Cottret, L., Crescenzi, P., Jourdan, F., Lacroix, V., Marchetti-Spaccamela, A., Marino, A., Vieira Milreu, P., Sagot, M.-F. and Stougie, L. (2012), Telling Stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets, Theoretical Computer Science, 457(2), 1-9.
  • Birmelé, E., Crescenzi, P., Ferreira, R., Grossi, R., Lacroix, V., Marino, A., Pisanti, N., Sacomoto, G. and Sagot, F. (2012), Efficient bubble enumeration in directed graphs, accepted by String Processing and Information Retrieval (SPIRE) 2012, to appear in Lecture Notes in Computer Science.
  • Birmelé, E., Delbot, F., Laforest, C. and Thibaut, N. (2011), Analyse du nombre de perturbations lors du maintien d'un arbre de connexion de faible diamètre,Techniques et Sciences Informatiques, 30(7), 781-808. (in french)
  • Milreu, P., Acuna, V., Birmelé, E., Crescenzi, P., Marchetti-Spaccamela, A., Sagot, M.-F., Stougie, L., and Lacroix, V. (2010), Enumerating chemical organisations in consistent metabolic networks: Complexity and algorithms, WABI'2010, 6293, 226-237. pdf
  • Birmelé, E., Delbot, F. and Laforest, C. (2009), Mean analysis of an online algorithm for the vertex cover problem , Information Processing Letters, 109, 436-439.

Random graph models for networks

  • Latouche, P., Birmelé, E., and Ambroise, C. (2012), Variational Bayesian inference and complexity control for stochastic block models, Statistical Modelling, 12(1), 93–115. preprint
  • Latouche, P., Birmelé,E., and Ambroise, C. (2011), Overlapping stochastic block model with application to the french political blogosphere, Annals of Applied Statistics, 5(1), 309–336. preprint
  • Birmelé, E., A scale-free graph model based on bipartite graphs (2009). Discrete Applied Mathematics, 157(10), 2267-2284.

Graph theory

  • Birmelé,E., Bondy, J.A., and Reed, B.A. (2009). Tree-width of graphs without a 3 by 3 grid minor, Discrete Applied Mathematics, 157(12), 2577-2596.
  • Birmelé, E. (2008). Every longest circuit of a 3-connected, $K_{3,3}$-minor free graph has a chord, J. Graph Theory, 58(4), 293–298.
  • Birmelé, E., Bondy, J.A., and Reed, B.A. (2007). The Erdos-Posa property for long circuits, Combinatorica, 27(2), 135–145.
  • Birmelé, E., Bondy, J.A., and Reed, B.A. (2007). Brambles, prisms and grids, Graph Theory in Paris - Proceedings of a Conference in Memory of Claude Berge, Birkhauser.
  • Bessy, S., Birmelé, E., and Havet, F. (2006). Arc-chromatic number of digraphs in which every vertex has bounded outdegree or bounded indegree, J. Graph Theory, 53(4), 315–332.
  • Birmelé, E. (2003). Tree-width and circumference of graphs, J. Graph Theory, 43(1), 24–25.

Thesis

Habilitation à diriger des recherches


A complete list including non international communications can be found here.
If you want a copy of any of these publications, just send me an email.

Software

  • R-package mixer: estimation of the parameters for a mixture model of random graphs.
  • R-package nemo: detection of global network motifs (over-represented graphs in terms of overall counts).
  • R-package paloma: detection of local network motifs (locally over-represented graphs).

Working groups

Supervision

  • Pierre Latouche (PhD, 2007-2010, with C. Ambroise)
  • Jaouad Allaoui (M2, 2009)
  • Thomas Picchetti (M2 in 2012, PhD 2013 - ?)

Teachings

by Stat & Génome
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