Web-based information retrieval system for the prediction of metabolic pathways

Chen M, Hofestädt R (2004)
IEEE TRANSACTIONS ON NANOBIOSCIENCE 3(3): 192-199.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
Abstract / Bemerkung
Analysis of metabolic pathways is a central topic in understanding the relationship between genotype and phenotype. The rapid accumulation of biological data provides the possibility of studying metabolic pathways both at the genomic and metabolic levels. Our motivation is to develop a conceptual framework and computational system that will allow retrieval of metabolic information and prediction of metabolic pathways. In this paper, we introduce a metabolic pathway prediction framework that extracts metabolic information from biological databases via the Internet, and builds metabolic pathways with data sources of genes, sequences, enzymes, metabolites, etc. It provides an easy-to-use interface to retrieve, display, and manipulate metabolic information. The system has been implemented into PathAligner, available at http://bibiserv.techfak.uni-bielefeld. de/pathaligner/.
Erscheinungsjahr
Zeitschriftentitel
IEEE TRANSACTIONS ON NANOBIOSCIENCE
Band
3
Ausgabe
3
Seite(n)
192-199
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PUB-ID

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Chen M, Hofestädt R. Web-based information retrieval system for the prediction of metabolic pathways. IEEE TRANSACTIONS ON NANOBIOSCIENCE. 2004;3(3):192-199.
Chen, M., & Hofestädt, R. (2004). Web-based information retrieval system for the prediction of metabolic pathways. IEEE TRANSACTIONS ON NANOBIOSCIENCE, 3(3), 192-199. doi:10.1109/TNB.2004.833691
Chen, M., and Hofestädt, R. (2004). Web-based information retrieval system for the prediction of metabolic pathways. IEEE TRANSACTIONS ON NANOBIOSCIENCE 3, 192-199.
Chen, M., & Hofestädt, R., 2004. Web-based information retrieval system for the prediction of metabolic pathways. IEEE TRANSACTIONS ON NANOBIOSCIENCE, 3(3), p 192-199.
M. Chen and R. Hofestädt, “Web-based information retrieval system for the prediction of metabolic pathways”, IEEE TRANSACTIONS ON NANOBIOSCIENCE, vol. 3, 2004, pp. 192-199.
Chen, M., Hofestädt, R.: Web-based information retrieval system for the prediction of metabolic pathways. IEEE TRANSACTIONS ON NANOBIOSCIENCE. 3, 192-199 (2004).
Chen, Ming, and Hofestädt, Ralf. “Web-based information retrieval system for the prediction of metabolic pathways”. IEEE TRANSACTIONS ON NANOBIOSCIENCE 3.3 (2004): 192-199.

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FNTM: a server for predicting functional networks of tissues in mouse.
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PMID: 25940632

32 References

Daten bereitgestellt von Europe PubMed Central.


AUTHOR UNKNOWN, 0
TRANSFAC: transcriptional regulation, from patterns to profiles.
Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Munch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E., Nucleic Acids Res. 31(1), 2003
PMID: 12520026
TRANSPATH: an integrated database on signal transduction and a tool for array analysis.
Krull M, Voss N, Choi C, Pistor S, Potapov A, Wingender E., Nucleic Acids Res. 31(1), 2003
PMID: 12519957
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction.
Overbeek R, Larsen N, Pusch GD, D'Souza M, Selkov E Jr, Kyrpides N, Fonstein M, Maltsev N, Selkov E., Nucleic Acids Res. 28(1), 2000
PMID: 10592199
The EcoCyc Database.
Karp PD, Riley M, Saier M, Paulsen IT, Collado-Vides J, Paley SM, Pellegrini-Toole A, Bonavides C, Gama-Castro S., Nucleic Acids Res. 30(1), 2002
PMID: 11752253
A minimal gene set for cellular life derived by comparison of complete bacterial genomes.
Mushegian AR, Koonin EV., Proc. Natl. Acad. Sci. U.S.A. 93(19), 1996
PMID: 8816789
PathFinder: reconstruction and dynamic visualization of metabolic pathways.
Goesmann A, Haubrock M, Meyer F, Kalinowski J, Giegerich R., Bioinformatics 18(1), 2002
PMID: 11836220
Representation of function: the next step.
Overbeek R, Larsen N, Smith W, Maltsev N, Selkov E., Gene 191(1), 1997
PMID: 9210599
A reconstruction of the metabolism of Methanococcus jannaschii from sequence data.
Selkov E, Maltsev N, Olsen GJ, Overbeek R, Whitman WB., Gene 197(1-2), 1997
PMID: 9332394
Genome-scale Gene Expression Analysis and Pathway Reconstruction in KEGG.
Nakao M, Bono H, Kawashima S, Kamiya T, Sato K, Goto S, Kanehisa M., Genome Inform Ser Workshop Genome Inform 10(), 1999
PMID: 11072346
Metabolic modeling of microbial strains in silico.
Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BO., Trends Biochem. Sci. 26(3), 2001
PMID: 11246024
representing and analysing molecular and cellular function using the computer
van, Chemistry & Biology 381(), 2000
Computation with the KEGG pathway database.
Ogata H, Goto S, Fujibuchi W, Kanehisa M., BioSystems 47(1-2), 1998
PMID: 9715755
PIR: a new resource for bioinformatics.
McGarvey PB, Huang H, Barker WC, Orcutt BC, Garavelli JS, Srinivasarao GY, Yeh LS, Xiao C, Wu CH., Bioinformatics 16(3), 2000
PMID: 10869023
computer-assisted prediction of metabolism
wipke, Structure-Activity Correlations as Predictive Tools in Toxicology (), 1983
BRENDA, enzyme data and metabolic information.
Schomburg I, Chang A, Schomburg D., Nucleic Acids Res. 30(1), 2002
PMID: 11752250
Use of computerized methods to predict metabolic pathways and metabolites.
Spann ML, Chu KC, Wipke WT, Ouchi G., J Environ Pathol Toxicol 2(1), 1978
PMID: 722215

AUTHOR UNKNOWN, 0
The Protein Data Bank.
Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C., Acta Crystallogr. D Biol. Crystallogr. 58(Pt 6 No 1), 2002
PMID: 12037327

AUTHOR UNKNOWN, 0
The KEGG databases at GenomeNet.
Kanehisa M, Goto S, Kawashima S, Nakaya A., Nucleic Acids Res. 30(1), 2002
PMID: 11752249
Reconstruction of amino acid biosynthesis pathways from the complete genome sequence.
Bono H, Ogata H, Goto S, Kanehisa M., Genome Res. 8(3), 1998
PMID: 9521924
The EBI SRS server-new features.
Zdobnov EM, Lopez R, Apweiler R, Etzold T., Bioinformatics 18(8), 2002
PMID: 12176845
reconstruction of metabolic networks using incomplete information
gaasterland, Proc 3rd Int Conf Intelligent Systems Molecular Biology (), 1995

collado-vides, Gene Regulation and Metabolism— Post Genomic Computational Approaches (), 2002
PathMiner: predicting metabolic pathways by heuristic search.
McShan DC, Rao S, Shah I., Bioinformatics 19(13), 2003
PMID: 12967966
automated metabolic reconstruction for methanococcus jannaschii
sophia, Arachaea 1(), 2003
chapter 1: introduction to biochemistry
lehninger, Principles of Biochemistry (), 1993
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.
Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M., Nucleic Acids Res. 31(1), 2003
PMID: 12520024
GenBank.
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL., Nucleic Acids Res. 31(1), 2003
PMID: 12519940

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