D. J. Watts and S. H. Strogatz, Collective dynamics of 'small-world' networks, Nature, vol.393, pp.440-442, 1998.

S. Milgram, The Small World Problem. Psychology Today, vol.1, 1967.

D. Pauly, V. V. Christensen, J. Dalsgaard, R. Froese, F. Torres et al., Fishing down marine food webs, Science, vol.279, pp.860-863, 1998.

R. Milo, S. Shen-orr, S. Itzkovitz, N. Kashtan, and D. Chklovskii, Network motifs: simple building blocks of complex networks, Science, vol.298, pp.824-827, 2002.

R. Albert and A. L. Barabasi, Statistical mechanics of complex networks, Rev Mod Phys, vol.74, pp.47-97, 2002.

A. L. Barabasi and Z. N. Oltvai, Network biology: understanding the cell's functional organization, Nat Rev Genet, vol.5, pp.101-113, 2004.

M. Newman, The structure and function of complex networks, Siam Review, vol.45, pp.167-256, 2003.

S. Maslov and K. Sneppen, Specificity and stability in topology of protein networks, Science, vol.296, pp.910-913, 2002.

R. Guimera, M. Sales-pardo, and L. A. Amaral, Classes of complex networks defined by role-to-role connectivity profiles, Nat Phys, vol.3, pp.63-69, 2007.

H. Jeong, B. Tombor, R. Albert, Z. N. Oltvai, and A. L. Barabasi, The large-scale organization of metabolic networks, Nature, vol.407, pp.651-654, 2000.

A. Wagner and D. A. Fell, The small world inside large metabolic networks, Proc Biol Sci, vol.268, pp.1803-1810, 2001.

E. Ravasz, A. L. Somera, D. A. Mongru, Z. N. Oltvai, and A. L. Barabasi, Hierarchical organization of modularity in metabolic networks, Science, vol.297, pp.1551-1555, 2002.

H. Ma and A. P. Zeng, Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms, Bioinformatics, vol.19, pp.270-277, 2003.

R. Tanaka, Scale-rich metabolic networks, Phys Rev Lett, vol.94, p.168101, 2005.

J. Rodrigues and A. Wagner, Evolutionary plasticity and innovations in complex metabolic reaction networks, PLoS Comput Biol in Press, 2009.

M. Kanehisa and S. Goto, KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Research, pp.27-30, 2000.

J. L. Reed, T. D. Vo, C. H. Schilling, and B. O. Palsson, An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR), Genome Biology, vol.4, p.54, 2003.

A. Clauset, C. R. Shalizi, and M. Newman, Power-Law Distributions in Empirical Data, Siam Review, vol.51, pp.661-703, 2009.

M. Newman, Power laws, Pareto distributions and Zipf's law, Contemporary Physics, vol.46, pp.323-351, 2005.

R. Tanaka, M. Csete, and J. Doyle, Highly optimised global organisation of metabolic networks, Syst Biol (Stevenage), vol.152, pp.179-184, 2005.

A. P. Burgard, E. V. Nikolaev, C. H. Schilling, and C. D. Maranas, Flux coupling analysis of genome-scale metabolic network reconstructions, Genome Res, vol.14, pp.301-312, 2004.

S. Schuster and R. Schuster, Detecting strictly detailed balanced subnetworks in open chemical reaction networks, J Math Chem, vol.6, pp.17-40, 1991.

A. M. Feist and B. O. Palsson, The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli, Nat Biotechnol, vol.26, pp.659-667, 2008.

N. D. Price, J. L. Reed, and B. O. Palsson, Genome-scale models of microbial cells: evaluating the consequences of constraints, Nature Reviews Microbiology, vol.2, pp.886-897, 2004.

K. J. Kauffman, P. Prakash, and J. S. Edwards, Advances in flux balance analysis, Curr Opin Biotechnol, vol.14, pp.491-496, 2003.

A. Samal, J. Rodrigues, J. Jost, O. C. Martin, and A. Wagner, Genotype networks in metabolic reaction spaces, BMC Syst Biol, vol.30, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00544012

A. Broder, R. Kumar, F. Maghoul, P. Raghavan, and S. Rajagopalan, Graph structure in the web, Computer Networks, vol.33, pp.309-320, 2000.

A. Wagner, Gene networks and natural selection, Evolutionary Genomics and Proteomics, 2007.

B. Papp, B. Teusink, and R. A. Notebaart, A critical view of metabolic network adaptations, HFSP J, vol.3, pp.24-35, 2009.

S. Wasserman and K. Faust, Social network analysis : methods and applications, vol.825, 1994.

G. Csardi and T. Nepusz, The igraph software package for complex network research. InterJournal Complex Systems, vol.1695, 2006.

F. Harary, Graph Theory, 1969.

M. Csete and J. Doyle, Bow ties, metabolism and disease, Trends Biotechnol, vol.22, pp.446-450, 2004.

H. W. Ma and A. P. Zeng, The connectivity structure, giant strong component and centrality of metabolic networks, Bioinformatics, vol.19, pp.1423-1430, 2003.

J. S. Edwards, R. U. Ibarra, and B. O. Palsson, In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data, Nat Biotechnol, vol.19, pp.125-130, 2001.

D. Segrè, D. Vitkup, and G. M. Church, Analysis of optimality in natural and perturbed metabolic networks, Proceedings of the National Academy of Sciences of the United States of America, vol.99, pp.15112-15117, 2002.