Randomizing genome-scale metabolic networks

PLoS ONE

Volumn 6, Issue 7, 2011, Pages

  Samal, Areejit ^a,b   Martin, Olivier C ^a,c  

^a UNIVERSITÉ PARIS SUD   (France)

^b MAX PLANCK INSTITUTE FOR MATHEMATICS IN THE SCIENCES   (Germany)

^c UNIVERSITÉ PARIS SACLAY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOCHEMISTRY; CHEMICAL REACTION; DATA BASE; GENETIC VARIABILITY; GENOTYPE; GLYCOLYSIS; INFORMATION PROCESSING; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; METABOLISM; MONTE CARLO METHOD; PROBABILITY; SOCIAL NETWORK; BIOLOGICAL MODEL; GENETICS; GENOME; THEORETICAL MODEL;

GENOME; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; MODELS, THEORETICAL;

EID: 79960329623     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0022295     Document Type: Article

References (36)

1. Watts DJ, Strogatz SH, (1998) Collective dynamics of 'small-world' networks. Nature 393: 440-442.
2. Milgram S, (1967) The Small World Problem. Psychology Today 1.
3. Pauly D, Christensen VV, Dalsgaard J, Froese R, Torres F Jr, (1998) Fishing down marine food webs. Science 279: 860-863.
4. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, et al. (2002) Network motifs: simple building blocks of complex networks. Science 298: 824-827.
5. Albert R, Barabasi AL, (2002) Statistical mechanics of complex networks. Rev Mod Phys 74: 47-97.
6. Barabasi AL, Oltvai ZN, (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101-113.
7. Newman M, (2003) The structure and function of complex networks. Siam Review 45: 167-256.
8. Maslov S, Sneppen K, (2002) Specificity and stability in topology of protein networks. Science 296: 910-913.
9. Guimera R, Sales-Pardo M, Amaral LA, (2007) Classes of complex networks defined by role-to-role connectivity profiles. Nat Phys 3: 63-69.
10. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL, (2000) The large-scale organization of metabolic networks. Nature 407: 651-654.
11. Wagner A, Fell DA, (2001) The small world inside large metabolic networks. Proc Biol Sci 268: 1803-1810.
12. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL, (2002) Hierarchical organization of modularity in metabolic networks. Science 297: 1551-1555.
13. Ma H, Zeng AP, (2003) Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 19: 270-277.
14. Tanaka R, (2005) Scale-rich metabolic networks. Phys Rev Lett 94: 168101.
15. Rodrigues JFM, Wagner A, (2009) Evolutionary plasticity and innovations in complex metabolic reaction networks. PLoS Comput Biol in Press.
16. Kanehisa M, Goto S, (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research pp. 27-30.
17. Reed JL, Vo TD, Schilling CH, Palsson BO, (2003) An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biology 4: R54.
18. Clauset A, Shalizi CR, Newman MEJ, (2009) Power-Law Distributions in Empirical Data. Siam Review 51: 661-703.
19. Newman M, (2005) Power laws, Pareto distributions and Zipf's law. Contemporary Physics 46: 323-351.
20. Tanaka R, Csete M, Doyle J, (2005) Highly optimised global organisation of metabolic networks. Syst Biol (Stevenage) 152: 179-184.
21. Burgard AP, Nikolaev EV, Schilling CH, Maranas CD, (2004) Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res 14: 301-312.
22. Schuster S, Schuster R, (1991) Detecting strictly detailed balanced subnetworks in open chemical reaction networks. J Math Chem 6: 17-40.
23. Feist AM, Palsson BO, (2008) The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol 26: 659-667.
24. Price ND, Reed JL, Palsson BO, (2004) Genome-scale models of microbial cells: evaluating the consequences of constraints. Nature Reviews Microbiology 2: 886-897.
25. Kauffman KJ, Prakash P, Edwards JS, (2003) Advances in flux balance analysis. Curr Opin Biotechnol 14: 491-496.
26. Samal A, Rodrigues JFM, Jost J, Martin OC, Wagner A, (2010) Genotype networks in metabolic reaction spaces. BMC Syst Biol.
27. Broder A, Kumar R, Maghoul F, Raghavan P, Rajagopalan S, et al. (2000) Graph structure in the web. Computer Networks 33: 309-320.
28. Wagner A, (2007) Gene networks and natural selection. In: Pagel M, Pomiankowski A, editors. Evolutionary Genomics and Proteomics Sunderland, MA Sinauer Associates Inc.
29. Papp B, Teusink B, Notebaart RA, (2009) A critical view of metabolic network adaptations. HFSP J 3: 24-35.
30. Wasserman S, Faust K, (1994) Social network analysis: methods and applications. Cambridge Cambridge University Press.
31. Csardi G, Nepusz T, (2006) The igraph software package for complex network research. InterJournal Complex Systems.
32. Harary F, (1969) Graph Theory: Addison-Wesley Publishing Company.
33. Csete M, Doyle J, (2004) Bow ties, metabolism and disease. Trends Biotechnol 22: 446-450.
34. Ma HW, Zeng AP, (2003) The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics 19: 1423-1430.
35. Edwards JS, Ibarra RU, Palsson BO, (2001) In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 19: 125-130.
36. Segrè D, Vitkup D, Church GM, (2002) Analysis of optimality in natural and perturbed metabolic networks. Proceedings of the National Academy of Sciences of the United States of America 99: 15112-15117.