Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms

Bioinformatics

Volumn 19, Issue 2, 2003, Pages 270-277

  Ma, Hongwu ^a,b   Zeng, An Ping ^a  

^a HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^b TIANJIN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARCHAEBACTERIUM; ARTICLE; BACTERIAL GENETICS; CALCULATION; CONTROLLED STUDY; EUKARYOTE; GENE FUNCTION; GENE SEQUENCE; GENE STRUCTURE; GENETIC ANALYSIS; INFORMATION PROCESSING; INFORMATION SYSTEM; MICROBIAL METABOLISM; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN METABOLISM; QUANTITATIVE ANALYSIS; SEQUENCE DATABASE; STRAIN DIFFERENCE;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 0037316239     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/19.2.270     Document Type: Article

References (26)

1. Albert,R. and Barabasi,A.L. (2002) Statistical mechanics of complex networks. Reviews of Modern Physics, 74, 47-97.
2. Albert,R., Barabasi,A.L. and Jeong,H. (2000) Power-law distribution of the World Wide Web. Science, 287, 2115.
3. Batagelj,V. and Mrvar,A. (1998) Pajek - program for large network analysis. Connections, 21, 47-57.
4. Broder,A., Kumar,R., Maghoul,F., Raghavan,P., Rajagopalan,S., Stata,R., Tomkins,A. and Wiener,J. (2000) Graph structure in the web. Computer Networks, 33, 309-320.
5. Edwards,J.S., Covert,M. and Palsson,B. (2002) Metabolic modelling of microbes: the flux-balance approach. Environ. Microbiol., 4, 133-140.
6. Goto,S., Nishioka,T. and Kanehisa,M. (1998) LIGAND: chemical database for enzyme reactions. Bioinformatics, 14, 591-599.
7. Goto,S., Okuno,Y., Hattori,M., Nishioka,T. and Kanehisa,M. (2002) LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res., 30, 402-404.
8. Huynen,M.A. and van Nimwegen,E. (1998) The frequency distribution of gene family sizes in complete genomes. Mol. Biol. Evol., 15, 583-589.
9. Jeong,H., Tombor,B., Albert,R., Oltvai,Z.N. and Barabasi,A.L. (2000) The large-scale organization of metabolic networks. Nature, 407, 651-654.
10. Karp,P.D., Riley,M., Saier,M., Paulsen,I.T., Collado-Vides,J., Paley,S.M., Pellegrini-Toole,A., Bonavides.C. and Gama-Castro,S. (2002) The EcoCyc Database. Nucleic Acids Res., 30, 56-58.
11. Kanehisa,M., Goto,S., Kawashima,S. and Nakaya,A. (2002) The KEGG databases at GenomeNet. Nucleic Acids Res., 30, 42-46.
12. Kuffner,R., Zimmer,R. and Lengauer,T. (2000) Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinformatics, 16, 825-836.
13. Ma,H.W. and Zeng,A.P. (2002) The hierarchical structure giant strong component and centrality of metabolic networks. Bioinformatics, submitted.
14. Neidhardt,F.C., Ingraham,J.L. and Schaechter,M. (1990) Physiology of the Bacterial Cell: a Molecular Approach. Sinauer Associates.
15. Ogata,H., Goto,S., Sato,K., Fujibuchi,W., Bono,H. and Kanehisa,M. (1999) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 27, 29-34.
16. Overbeek,R., Larsen,N., Pusch,G.D., D'Souza,M., Selkov,Jr,E., Kyrpides,N., Fonstein,M., Maltsev,N. and Selkov,E. (2000) WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res., 28, 123-125.
17. Podani,J., Oltvai,Z.N., Jeong,H., Tombor,B., Barabasi,A.L. and Szathmary,E, (2001) Comparable system-level organization of Archaea and Eukaryotes. Nature Genet., 29, 54-56.
18. Price,N.D., Papin,J.A. and Palsson,B.B. (2002) Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome Res., 12, 760-769.
19. Schilling,C.H., Edwards,J.S. and Palsson,B.O. (1999) Toward metabolic phenomics: analysis of genomic data using flux balances. Biotechnol. Prog., 15, 288-295.
20. Schilling,C.H., Letscher,D. and Palsson,B.O. (2000) Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J. Theor Biol., 203, 229-248.
21. Schilling,C.H. and Palsson,B.O. (2000) Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. J Theor. Biol., 203, 249-283.
22. Schilling,C.H., Schuster,S., Palsson,B.O. and Heinrich,R. (1999) Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. Biotechnol. Prog., 15, 296-303.
23. Schuster,S., Dandekar,T. and Fell,D.A. (1999) Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol., 17, 53-60.
24. Schuster,S., Fell,D.A. and Dandekar,T. (2000) A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotechnol., 18, 326-332.
25. Schuster,S., Pfeiffer,T., Moldenhauer,F., Koch,I. and Dandekar,T. (2002) Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics, 18, 351-361.
26. Strogatz,S.H. (2001) Exploring complex networks. Nature, 410, 268-276.