FluxAnalyzer: Exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps

Bioinformatics

Volumn 19, Issue 2, 2003, Pages 261-269

  Klamt, Steffen ^a   Stelling, Jörg ^a   Ginkel, Martin ^a   Gilles, Ernst Dieter ^a  

^a MAX PLANCK INSTITUTE FOR DYNAMICS OF COMPLEX TECHNICAL SYSTEMS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANALYTICAL PARAMETERS; ARTICLE; CALCULATION; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; INFORMATION PROCESSING; MATHEMATICAL MODEL; METABOLISM; PRIORITY JOURNAL; STOICHIOMETRY;

EID: 0037316342     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/19.2.261     Document Type: Article

References (25)

1. Covert,M.W., Schilling,C.H., Famili,I., Edwards,J.S., Goryanin,I.I., Selkov,E. and Palsson,B.O. (2001) Metabolic modeling of microbial strains in silico. Trends Biochem. Sci., 26, 179-186.
2. Edwards,J.S. and Palsson,B.O. (2000) The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc. Natl Acad. Sci. USA, 97, 5528-5533.
3. Happel,J. and Sellers,P.H. (1989) The characterization of complex systems of chemical reactions. Chem. Eng. Comm., 83, 221-240.
4. van der Heijden,R.T.J.M., Heijnen,J.J., Hellinga,C, Romein,B. and Luyben,K.Ch.A.M. (1994a) Linear constraint relations in biochemical reaction systems: I. Classification of the calculability and the balancebility of conversion rates. Biotechnol. Bioeng., 43, 3-10.
5. van der Heijden,R.T.J.M., Romein,B., Heijnen,J.J., Hellinga,C. and Luyben,K.Ch.A.M. (1994b) Linear constraint relations in biochemical reaction systems: II. Diagnosis and estimation of gross errors. Biotechnol. Bioeng., 43, 11-20.
6. Heinrich,R. and Schuster,S. (1996) The Regulation of Cellular Systems. Chapman and Hall, New York.
7. Kitano,H. (2002) Systems biology: a brief overview. Science, 295, 1662-1664.
8. Klamt,S., Schuster,S. and Gilles,E.D. (2002) Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria. Biotechnol. Bioeng., 77, 734-751.
9. Klamt,S. and Stelling,J. (2002) Combinatorial complexity of pathway analysis in metabolic networks. Mol. Biol. Rep., 29, 233-236.
10. Kremling,A., Jahreis,K., Lengeler,J.W. and Gilles,E.D. (2000) The organization of metabolic reaction networks: a signal-oriented approach to cellular models. Metab. Eng., 2, 190-200.
11. Mendes,P. (1997) Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci., 22, 361-363.
12. Neidhardt,F.C., Ingraham,J.L. and Schaechter,M. (1990) Physiology of the Bacterial Cell: A Molecular Approach. Sinauer, Sunderland, MA.
13. Nuño,J.C., Sánchez-Valdenebro,I., Pérez-Iratxeta,C., Meléndez-Hevia,E. and Montero,F. (1997) Network organization of cell metabolism: monosaccharide interconversion. Biochem. J., 324, 104-111.
14. Papin,J.A., Price,N.D., Edwards,J.E. and Palsson,H.O. (2002) The genome scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy. J. Theor. Biol., 215, 67-82.
15. Pfeiffer,T., Sánchez-Valdenebro,I., Nuño,J.C., Montero,F. and Schuster,S. (1999) METATOOL: for studying metabolic networks. Bioinformatics, 15, 251-257.
16. Sauro,H.M. (2000) Jarnac: a system for interactive metabolic analysis. In Hofmeyr,J.-H.S., Rohwer,J.M. and Snoep,J.L. (eds), Animating the cellular Map: Proceedings of the 9th International Meeting on BioThermoKinetics. Stellenbosch University Press.
17. 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.
18. 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.
19. Schuster,S., Fell,D. 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.
20. Schuster,S,, Klamt,S., Weckwerth,W., Moldenhauer,F. and Pfeiffer,T. (2002) Use of network analysis of metabolic systems in bioengineering. Bioproc. Biosyst. Eng., 24, 363-372.
21. Stephanopoulos,G.N., Aristidou,A.A. and Nielsen,J. (1998) Metabolic Engineering. Academic Press, San Diego.
22. Stellling,J., Klamt,S., Bettenbrock,K., Schuster,S. and Gilles,E.D. (2002) Metabolic network structure determines key aspects of functionality and regulation. Nature, 420, 190-193.
23. Tomita,M., Hashimoto,K., Takahashi,K., Shimizu,T.S., Matsuzaki,Y., Miyoshi,F., Saito,K., Tanida,S., Yugi,K., Venter,J.C. and Hutchison,3rd,C.A. (1999) E-CELL: software environment for whole-cell simulation. Bioinformatics, 15, 72-84.
24. 13C metabolic flux analysis. Metab. Eng., 3, 195-206.
25. Wiechert,W. (2002) Modeling and simulation: tools for metabolic engineering. J. Biotechnol., 94, 37-64.