S. Strogatz, Exploring complex networks, Nature, vol.410, pp.268-276, 2001.

M. Newman, D. Watts, and S. Strogatz, Random graph models of social networks, vol.99, pp.2566-2572, 2002.

A. Barabási and R. Albert, Emergence of scaling in random networks, Science, vol.286, pp.509-512, 1999.

R. Albert and A. Barabási, Statistical mechanics of complex networks. R Modern Physics, vol.74, pp.47-97, 2002.

M. Girvan and M. Newman, Community structure in social and biological networks, vol.99, pp.7821-7826, 2002.

F. Radicchi, C. Castellano, D. Cecconi, V. Loreto, and D. Parisi, Defining and identifying communities in networks, vol.101, pp.2658-2663, 2004.

J. Daudin, F. Picard, and S. Robin, A mixture model for random graphs, Stat and Computing, vol.18, pp.173-183, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00428180

R. Guimera and L. N. Amaral, Functional cartography of complex metabolic networks, Nature, vol.433, pp.895-900, 2005.

K. Nowicki and T. Snijders, Estimation and prediction for stochastic blockstructures, JASA, vol.96, issue.455, pp.1077-1087, 2001.

M. Newman and E. Leicht, Mixture models and exploratory analysis in networks, vol.104, pp.9564-9569, 2007.

M. Jordan, Z. Ghahramani, T. Jaakkola, and L. Saul, An Introduction to Variational Methods for Graphical Models, Mach Learn, vol.37, issue.2, pp.183-233, 1999.

M. Lavielle, Using penalized contrasts for the change-point problem, Signal Processing, vol.85, issue.8, pp.1501-1510, 2005.
URL : https://hal.archives-ouvertes.fr/inria-00070662

G. Balazsi, A. L. Barabasi, and Z. Oltvai, Topological units of environmental signal processign in the transcriptional network of Escherichia Coli, vol.102, pp.7841-7846, 2005.

S. Shen-orr, M. R. Mangan, S. Alon, and U. , Network motifs in the transcriptional regulation network of Escherichia coli, Nature genetics, vol.31, pp.64-68, 2002.

O. Sporns, C. Honey, and R. Kotter, Identification and classification of hubs in brain networks, PLoS ONE, vol.2, p.1049, 2007.

J. Dunne, R. Williams, and N. Martinez, Food-web structure and network theory: the role of connectance and size, vol.99, pp.12917-12922, 2002.

A. Clauset, C. Moore, and M. Newman, Hierarchical structrure and the prediction of missing links in networks, Nature, vol.453, pp.98-101, 2008.

H. Dawah, B. Hawkins, and M. Claridge, Structure of the parasitoid communities of grass-feeding chalcid wasps, Journal of animal ecology, vol.64, pp.708-720, 1995.

N. Martinez, B. Hawkins, H. Dawah, and B. Feifarek, Effects of sampling effort on characterization of food-web structure, Ecology, vol.80, issue.3, pp.1044-1055, 1999.

P. Buchner, Endosymbiosis of animals with plant microorganisms, 1965.

S. Shigenobu, H. Watanabe, M. Hattori, Y. Sakaki, and H. Ishikawa, Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp, Nature, vol.407, issue.6800, pp.81-87, 2000.

R. Caspi, H. Foerster, C. Fulcher, P. Kaipa, M. Krummenacker et al., The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases, Nucleic Acids Res, vol.36, pp.623-631, 2008.

M. Arita, The metabolic world of Escherichia coli is not small, Proc Natl Acad Sci, vol.101, issue.6, pp.1543-1547, 2004.

T. Handorf, N. Christian, O. Ebenhoh, and D. Kahn, An environmental perspective on metabolism, J Theor Biol, vol.252, issue.3, pp.530-537, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00428159

F. Picard, J. J. Daudin, M. Koskas, S. Schbath, and S. Robin, Assessing the exceptionality of network motifs, J Comput Biol, vol.15, pp.1-20, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01197515

M. Mariadassou and S. Robin, Uncovering latent structure in valued graphs: a variational approach, Tech Rep 10 SSB, 2007.
URL : https://hal.archives-ouvertes.fr/hal-01197514

U. Alon-webpage,

P. D. Karp, S. Paley, and P. Romero, The Pathway Tools software. Bioinformatics, vol.18, pp.225-232, 2002.

D. Vallenet, MaGe: a microbial genome annotation system supported by synteny results, Nucleic Acids Res, vol.34, pp.53-65, 2006.

A. Antoniadis, J. Bigot, V. Sachs, and R. , A multiscale approach for statistical characterization of functional images, Journal of Computational and Graphical Statistics, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00627384

F. Picard, S. Robin, M. Lavielle, C. Vaisse, and J. J. Daudin, A statistical approach for CGH microarray data analysis, BMC Bioinformatics, vol.6, p.27, 2005.
URL : https://hal.archives-ouvertes.fr/inria-00071444

, ARPACK

A. Martinez-antonio and J. Collado-vides, Identifying global regulators in transcriptional regulatory networks in bacteria, Curr Opin Microbiol, vol.6, issue.5, pp.482-489, 2003.

A. Martinez-antonio, S. Jangra, and D. Thieffry, Functional organization of Escherichia Coli transcriptional regulatory network, J Mol Biol, vol.381, pp.238-247, 2008.