Subnetwork hierarchies of biochemical pathways

Bioinformatics

Volumn 19, Issue 4, 2003, Pages 532-538

  Holme, Petter ^c   Huss, Mikael ^a   Jeong, Hawoong ^b  

^a ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^b Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^c NONE

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANALYTIC METHOD; ARTICLE; BIOCHEMISTRY; CELL FUNCTION; CLUSTER ANALYSIS; CYTOCHEMISTRY; DATA BASE; GEOMETRY; INFORMATION PROCESSING; METABOLISM; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; STATISTICAL ANALYSIS;

EID: 0037345719     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg033     Document Type: Article

References (24)

1. Albert,R., Jeong,H. and Barabási,A.-L. (2000) Error and attack tolerance of complex networks. Nature, 406, 378-381.
2. Brandes,U. (2001) A faster algorithm for betweenness centrality. J. Math. Sociol., 25, 163-177.
3. Fell,D.A. and Wagner,A. (2000) The small world of metabolism. Nature Biotechnol., 18, 1121-1122.
4. Freeman,M.L. (1977) A set of measures of centrality based upon betweenness. Sociometry, 40, 35-41.
5. Granovetter,M.S. (1973) The strength of weak ties. Am. J. Sociol., 78, 1360-1380.
6. Girvan,M. and Newman,M.E.J. (2002) Community structure in social and biological networks. Proc. Natl Acad. Sci. USA, 99, 7821-7826.
7. Janson,S., Łuczac,T. and Ruciński,A. (2000) Random Graphs. Wiley, New York, pp. 107-126.
8. Jeong,H., Tombor,B., Albert,R., Oltvai,Z.N. and Barabási,A.-L. (2000) The large-scale organization of metabolic networks. Nature, 407, 651-654.
9. Jeong,H., Mason,S.P., Barabási,A.-L. and Oltvai,Z.N. (2001) Lethality and centrality in protein networks. Nature, 411, 41-42.
10. Johnson,S.C. (1976) Hierarchical clustering schemes. Psychometrika, 32, 241-253.
11. Kanehisa,M. and Goto,S. (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30.
12. Karp,P.D. et al. (2000) The EcoCyc and MetaCyc databases. Nucleic Acids Res., 28, 56-59.
13. Lewin,B.M. (1997) Genes VI, 6th edn, Oxford University Press, Oxford.
14. Norris,S.J., Cox,D.L. and Weinstock,G.M. (2001) Biology of Treponema pallidum: correlation of functional activities with genome sequence data. J. Mol. Microb. Biotechnol., 3, 37-62.
15. Overbeek,R. et al. (2000) WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res., 28, 123-125.
16. Patra,S.M. and Vishveshwara,S. (2000) Backbone cluster identification in proteins by a graph theoretical method. Biophys. Chem., 84, 13-25.
17. Principi,N. and Esposito,S. (2001) Emerging role of Mycoplasma pneumoniae and Chlamydia pneumoniae in paediatric respiratory-tract infections. Lancet Infect. Dis., 1, 334-344.
18. Saier,Jr,M.H. (2001) The bacterial phosphotransferase system: structure, function, regulation and evolution. J. Mol. Microbiol. Biotechnol., 3, 325-327.
19. Schilling,C.H. and Palsson,B.Ø. (2000) Assessment of the metabolic capabilities of Haemophilus Influenzae Rd through a genome-scale pathway analysis. J. Theor. Biol., 203, 229-248.
20. Schuster,S. and Hilgetag,C. (1994) On elementary flux modes in biochemical reaction systems at steady state. J. Biol. Syst., 2, 165-182.
21. Schuster,S., Dandekar,T. and Fell,D. (1999) Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol., 17, 53-60.
22. 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.
23. Selkov,E. et al. (1996) The metabolic pathway collection of EMP: the enzymes and metabolic pathway database. Nucleic Acids Res., 24, 26-28.
24. Wagner,A. and Fell,D.A. (2001) The small world inside large metabolical networks. Proc. R. Soc. Lond. B, 268, 1803-1810.