Pathway analyst - Automated metabolic pathway prediction

Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '05

Volumn 2005, Issue , 2005, Pages

  Pireddu, Luca ^a   Poulin, Brett ^a   Szafron, Duane ^a   Lu, Paul ^a   Wishart, David S ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSTS; INFORMATION MANAGEMENT; MARKOV PROCESSES; MATHEMATICAL MODELS; MICROORGANISMS; PROTEINS;

CATALYST PROTEINS; METABOLIC PATHWAYS; SUPPORT VECTOR MACHINES (SVM);

METABOLISM;

EID: 33847260244     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/cibcb.2005.1594924     Document Type: Conference Paper

References (12)

1. M. Ashburner, C. A. Ball, J. A. Blake, D. Botstein, H. Butler, J. M. Cherry, et al., "Gene Ontology: tool for the unification of biology," Nat. Genet., vol. 25, no. 1, pp. 25-29, 2000.
2. C. J. Van Rijsbergen, Information Retrieval, 2nd edition. Dept. of Computer Science, University of Glasgow, 1979. [Online]. Available: citeseer.ist.psu.edu/vanrijsbergen79information.html.
3. M. Kanehisa, S. Goto, S. Kawashima, Y. Okuno, and M. Hattori, "The KEGG resource for deciphering the genome," Nucl. Acids Res., vol. 32, no. 90001, pp. D277-280, 2004.
4. C. J. Krieger, P. Zhang, L. A. Mueller, A. Wang, S. Paley, M. Arnaud, et al., "MetaCyc: a multiorganism database of metabolic pathways and enzymes," Nucl. Acids Res., vol. 32, no. 90001, pp. D438-442, 2004.
5. G. Joshi-Tope, M. Gillespie, I. Vastrik, P. D'Eustachio, E. Schmidt, B. de Bono, et al., "Reactome: a knowledgebase of biological pathways," Nucl. Acids Res., vol. 33, no. suppl. 1, pp. D428-432, 2005.
6. C. Lemer, E. Antezana, F. Couche, F. Fays, X. Santolaria, R. Janky, Y. Deville, J. Richelle, and S. J. Wodak, "The aMAZE lightbench: a web interface to a relational database of cellular processes," Nucl. Acids Res., vol. 32, no. 90001, pp. D443-448, 2004.
7. S. Y. Rhee, W. Beavis, T. Z. Berardini, G. Chen, D. Dixon, A. Doyle, et al., "The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community," Nucl. Acids Res., vol. 31, no. 1, pp. 224-228, 2003. [Online]. Available: http://nar.oxfordjournals.org/cgi/content/ abstract/31/1/224
8. S. Altschul, T. Madden, A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. Lipman, "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs," Nucl. Acids Res., vol. 25, no. 17, pp. 3389-3402, 1997. [Online]. Available: http://nar.oxfordjournals.org/cgi/content/ abstract/25/17/3389
9. J. Thompson, D. Higgins, and T. Gibson., "CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice," Nucleic Acids Research, vol. 22, no. 22, pp. 4673-4680, November 1994.
10. S. Eddy, "HMMER: Profile hidden markov models for biological sequence analysis," http://hmmer.wustl.edu, 2001.
11. A. Bateman, E. Bimey, L. Cerruti, R. Durbin, L. Etwiller, S. R. Eddy, et al., "The Pfam protein families database," Nucl. Acids Res., vol. 30, no. 1, pp. 276-280, 2002. [Online]. Available: http://nar.oxfordjournals.org/ cgi/content/abstract/30/1/276
12. C.-C. Chang and C.-J. Lin. (2001) LIBSVM: a library for support vector machines. Software available at http://www.csie.ntu.edu.tw/cjlin/libsvm.