Finding relevant biotransformation routes in weighted metabolic networks using atom mapping rules

Proceedings of the German Conference on Bioinformatics, GCB 2007

Volumn , Issue , 2007, Pages 30-44

  Blum, Torsten ^a   Kohlbacher, Oliver ^a  

^a UNIVERSITY OF TÜBINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL ANALYSIS; MAPPING RULES; METABOLIC NETWORK; PATH SEARCH; SYSTEMS BIOLOGY;

BIOINFORMATICS; GRAPH THEORY; MAPPING; METABOLISM;

ATOMS;

EID: 84871232175     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (23)

1. [Ak04] Akutsu,T. (2004) Efficient extraction of mapping rules of atoms from enzymatic reaction data., J. Comput. Biol., 11, 449-62.
2. [Ar00] Arita,M. (2000) Metabolic reconstruction using shortest paths, Simulation Practice and Theory, 8, 109-125.
3. [Ar03] Arita,M. (2003) In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism., Genome Res., 13, 2455-66.
4. [AS06] Aittokallio,T., Schwikowski,B. (2006) Graph-based methods for analysing networks in cell biology, Briefings in Bioinformatics, 7, 243-55.
5. [Ca06] Caspi,R., Foerster,H., Carol,A., Fulcher,A., Hopkinson,R., Ingraham,J., Kaipa,P., Krummenacker, M., Paley,S., Pick,J., Rhee,S.R., Tissier,C., Zhang,P., Karp,P.D. (2006) MetaCyc: A multiorganism database of metabolic pathways and enzymes., Nucl. Acids Res., 34, D511-D516
6. [CCWH06] Croes,D., Couche,F., Wodak,S.J., van Helden,J. (2006) Infering Meaningful Pathways in Weighted Metabolic Networks, J. Mol. Biol., 356, 222-236.
7. [Co99] Cordwell,S.J. (1999) Microbial genomes and "missing" enzymes: redefining biochemical pathways , Arch. Microbiol, 172, 269-279.
8. [Ep98] Eppstein,D. (1998) Finding the k Shortest Paths, SIAM Journal on Computing, 28, 652-673.
9. [HWGW02] van Helden,J., Wernisch,L., Gilbert,D., Wodak,S.J. (2002) Graph-based analysis of metabolic networks., Ernst Schering Res. Found. Workshop, 38, 245-74.
10. [Ka96] Kanehisa,M. (1996) Toward pathway engineering: a new database of genetic and molecular pathways., Science & Technology Japan, 59, 34-38.
11. [Ke05] Keseler,I.M., Collado-Vides,J., Gama-Castro,S., Ingraham,J., Paley,S., Paulsen,I.T., Peralta-Gil, M., Karp,P.D. (2005) EcoCyc: A comprehensive database resource for Escherichia coli, Nucl. Acids Res., 33, D334-7.
12. [KS02] Klamt,S., Stelling,J. (2002) Combinatorial complexity of pathway analysis in metabolic networks., Mol. Biol. Rep., 29, 233-6.
13. [KSGG03] Klamt,S., Stelling,J., Ginkel,M., Gilles,E.D. (2003) FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps., Bioinformatics, 19, 261-9.
14. [KZL00] Küffner,R., Zimmer,R., Lengauer,T. (2000) Pathway analysis in metabolic databases via differential metabolic display (DMD), Bioinformatics, 16, 825-836.
15. [Mo65] Morgan,H.L. (1965) The Generation of a Unique Machine Description for Chemical Structures-A Technique Developed at Chemical Abstracts Service, J. Chem. Doc., 5, 107-113.
16. [PK02] Paley,S., Karp,P.D. (2002) Evaluation of computational metabolic-pathway predictions for H. pylori, Bioinformatics, 18, 715-724.
17. [Ra05] Rahman,S.A., Advani,P., Schunk,R., Schrader,R., Schomburg,D. (2005) Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC), Bioinformatics, 21, 1189-93.
18. [Ro70] Rockafellar,R.T., (1970) Convex analysis, Princeton Landmarks in Mathematics, Princeton University Press.
19. [SCS02] Schomburg,I., Chang,A., Schomburg,D. (2002) BRENDA, enzyme data and metabolic information, Nucl. Acids Res., 30, 47-49.
20. [SDF99] Schuster,S., Dandekar,T., 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.
21. [SLP00] Schilling,C.H., Letscher,D., Palsson,B. (2000) Theory for the Systematic Definition of Metabolic Pathways and their use in Interpreting Metabolic Function from a Pathway-Oriented Perspective, J. Theor. Biol., 203, 229-248.
22. [SS01] Schürmann,M., Sprenger,G. (2001) Fructose-6-phosphate Aldolase is a Novel Class I Aldolase from Escherichia coli and is Related to a Novel Group of Bacterial Transaldolases., J. Biol. Chem., 276, 11055-11061.
23. [WWW89] Weininger,D., Weininger,A., Weininger,J.L. (1989) SMILES. 2. Algorithm for Generation of Unique SMILES Notation, J. Chem. Inf. Comput. Sci., 29, 97-101.