Reconstruction of metabolic networks from genome information and its structural and functional analysis

Computational Systems Biology

Volumn , Issue , 2006, Pages 169-189

  Ma, Hong Wu ^a   Zeng, An Ping ^a  

^a HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84882299374     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-012088786-6/50028-9     Document Type: Chapter

References (46)

1. Albert R., Jeong H., Barabasi A.L. Error and attack tolerance of complex networks. Nature 2000, 406:378-382.
2. Almaas E., Kovacs B., Vicsek T., Oltvai Z.N., Barabasi A.L. Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 2004, 427:839-843.
3. Arita M. In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. Genome Res. 2003, 13:2455-2466.
4. Batagelj V., Mrvar A. Pajek: Program for large network analysis. Connections 1998, 21:47-57.
5. Bray D. Molecular networks: The top-down view. Science 2003, 301:1864-1865.
6. Broder A., Kumar R., Maghoul F., Raghavan P., Rajagopalan S., Stata R., Tomkins A., wiener J. Graph structure in the Web. Computer Networks 2000, 33:309-320.
7. Covert M.W., Knight E.M., Reed J.L., Herrgard M.J., Palsson B.O. Integrating high-throughput and computational data elucidates bacterial networks. Nature 2004, 429:92-96.
8. Csete M., Doyle J. Bow-ties, metabolism, and disease. Trends Biotechnol. 2004, 22:446-450.
9. Edwards J.S., Ibarra R.U., Palsson B.O. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol. 2001, 19:125-130.
10. Edwards J.S., Covert M., Palsson B. Metabolic modelling of microbes: The flux-balance approach. Environ. Microbiol. 2002, 4:133-140.
11. Famili I., Forster J., Nielsen J., Palsson B.O. Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc. Natl. Acad. Sci. USA 2003, 100:13134-13139.
12. Forster J., Famili I., Fu P., Palsson B.O., Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 2003, 13:244-253.
13. Gagneur J., Jackson D.B., Casari G. Hierarchical analysis of dependency in metabolic networks. Bioinformatics 2003, 19:1027-1034.
14. Gasteiger E., Gattiker A., Hoogland C., Ivanyi I., Appel R.D., Bairoch A. ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucl. Acids. Res. 2003, 31:3784-3788.
15. Goto S., Okuno Y., Hattori M., Nishioka T., Kanehisa M. LIGAND: Database of chemical compounds and reactions in biological pathways. Nucleic Acids Res. 2002, 30:402-404.
16. Hartwell L.H., Hopfield J.J., Leibler S., Murray A.W. From molecular to modular cell biology. Nature 1999, 402:C47-C52.
17. Hatzimanikatis V., Li C., Ionita J.A., Broadbelt L.J. Metabolic networks: Enzyme function and metabolite structure. Curr. Opin. Struct. Biol. 2004, 14:300-306.
18. Ibarra R.U., Edwards J.S., Palsson B.O. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 2002, 420:186-189.
19. Jeong H., Tombor B., Albert R., Oltvai Z.N., Barabasi A.L. The large-scale organization of metabolic networks. Nature 2000, 407:651-654.
20. Jeong H., Mason S.P., Barabasi A.L., Oltvai Z.N. Lethality and centrality in protein networks. Nature 2001, 411:41-42.
21. Kanehisa M., Goto S., Kawashima S., Okuno Y., Hattori M. The KEGG resource for deciphering the genome. Nucl. Acids. Res. 2004, 32:D277-D280.
22. Karp P.D. Call for an enzyme genomics initiative. Genome Biology 2004, 5:401.
23. Karp P.D., Riley M., Saier M., Paulsen I.T., Paley S.M., Pellegrini-Toole A. The EcoCyc and MetaCyc databases. Nucleic Acids Res 2000, 28:56-59.
24. Kitano H. Biological robustness. Nat. Rev. Genet. 2004, 5:826-837.
25. Klamt S., Stelling J. Combinatorial complexity of pathway analysis in metabolic networks. Mol. Biol. Rep. 2002, 29:233-236.
26. Klamt S., Stelling J. Two approaches for metabolic pathway analysis?. Trends Biotechnol. 2003, 21:64-69.
27. Luscombe N.M., Babu M.M., Yu H., Snyder M., Teichmann S.A., Gerstein M. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 2004, 431:308-312.
28. Ma H.W., Zeng A.P. Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 2003, 19:270-277.
29. Ma H.W., Zeng A.P. The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics 2003, 19:1423-1430.
30. Ma H.W., Zeng A.P. Phylogenetic comparasion of metabolic capacities of organisms at genome level. Molecular Phylogenetics and Evolution 2004, 31:204-213.
31. Ma H.W., Kumar B., Ditges U., Gunzer F., Buer J., Zeng A.P. An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic Acids Res. 2004, 32:6643-6649.
32. Ma H.W., Zhao X.M., Yuan Y.J., Zeng A.P. Decomposition of metabolic network based on the global connectivity structure of reaction graph. Bioinformatics 2004, 20:1870-1876.
33. Palsson B.O., Price N.D., Papin J.A. Development of network-based pathway definitions: The need to analyze real metabolic networks. Trends Biotechnol. 2003, 21:195-198.
34. Papin J.A., Stelling J., Price N.D., Klamt S., Schuster S., Palsson B.O. Comparison of network-based pathway analysis methods. Trends Biotechnol. 2004, 22:400-405.
35. Price N.D., Papin J.A., Palsson B.B. Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome Res. 2002, 12:760-769.
36. Ravasz E., Somera A.L., Mongru D.A., Oltvai Z.N., Barabasi A.L. Hierarchical organization of modularity in metabolic networks. Science 2002, 297:1551-1555.
37. Salgado H., Gama-Castro S., Martinez-Antonio A., Diaz-Peredo E., Sanchez-Solano F., Peralta-Gil M., Garcia-Alonso D., Jimenez-Jacinto V., Santos-Zavaleta A., Bonavides-Martinez C., Collado-Vides J. RegulonDB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res. 2004, 32:D303-D306.
38. Schilling C.H., Covert M.W., Famili I., Church G.M., Edwards J.S., Palsson B.O. Genome-scale metabolic model of Helicobacter pylori 26695. J. Bacteriol. 2002, 184:4582-4593.
39. Schomburg I., Chang A., Ebeling C., Gremse M., Heldt C., Huhn G., Schomburg D. BRENDA, the enzyme database: Updates and major new developments. Nucleic Acids Res. 2004, 32:D431-D433.
40. Schuster S., Dandekar T., Fell D.A. Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering. Trends Biotechnol. 1999, 17:53-60.
41. Schuster S., Pfeiffer T., Moldenhauer F., Koch I., Dandekar T. Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics 2002, 18:351-361.
42. Stelling J., Klamt S., Bettenbrock K., Schuster S., Gilles E.D. Metabolic network structure determines key aspects of functionality and regulation. Nature 2002, 420:190-193.
43. Strogatz S.H. Exploring complex networks. Nature 2001, 410:268-276.
44. Sun J., Zeng A.P. IdentiCS: Identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence. BMC Bioinformatics 2004, 5:112.
45. Wagner A., Fell D.A. The small world inside large metabolic networks. Proc. R. Soc. Lond. B. Biol. Sci. 2001, 268:1803-1810.
46. Wolf Y.I., Karev G., Koonin E.V. Scale-free networks in biology: New insights into the fundamentals of evolution?. Bioessays 2002, 24:105-109.