Homomorphisms of multisource trees into networks with applications to metabolic pathways

Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

Volumn , Issue , 2007, Pages 350-357

  Cheng, Qiong ^a   Harrison, Robert ^a   Zelikovsky, Alexander ^a  

^a GEORGIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; CONFORMAL MAPPING; ENZYMES; ESCHERICHIA COLI; FUNCTIONS; SYSTEMS ENGINEERING; TREES (MATHEMATICS);

BIOLOGICAL NETWORKS; CEREVISIAE; COMPLEX NETWORKS; DIRECTED ACYCLIC GRAPHS; DYNAMIC PROGRAMMING ALGORITHMS; E. COLI; GENERAL NETWORKS; METABOLIC PATHWAYS; MINIMUM COSTS; MULTISOURCE; NETWORK MAPPINGS; SUBTILIS; TREE NETWORKS;

METROPOLITAN AREA NETWORKS;

EID: 47649104018     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBE.2007.4375587     Document Type: Conference Paper

References (17)

1. http://www.biocyc.org/.
2. M. Chen and R. Hofest. An algorithm for linear metabolic pathway alignment. In silico biology (In silico biol.) ISSN, 1386-6338: 111-128, 2005.
3. Q. Cheng and A. Zelikovsky. Optimal mapping of multi source trees into dag in biological network. ISBRA'07Poster, May 2007.
4. T. Dandekar, S. Schuster, B. Snel, M. Huynen, and P. Bork. Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochem. J., 1: 115-124, 1999.
5. C. V. Forst and K. Schulten. Evolution of metabolisms: a new method for the comparison of metabolic pathways using genomics information. J. Comput. Biol., 6: 343-360, 1999.
6. M. L. Green and P. D. Karp. A bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics, Sep. 2004.
7. B. P. Kelly, R. Sharan, R. M. Karp, T. Sittler, D. E. Root, and B. R. Stockwell. Pathblast: a tool for alignment of protein interaction networks. Nucleic Acids Research, Vol.32: W83-W88, 2004.
8. B. P. Kelly, R. Sharan, R. M. Karp, T. Sittler, D. E. Root, and B. R. Stockwell. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. PNAS, 11394-11399, Sep. 30 2003.
9. I. M. Keseler, V. J. Collado, C. S. Gama, J. Ingraham, S. Paley, I. T. Paulsen, M. Peralta-Gil, and P. D. Karp. Ecocyc: a comprehensive database resource for escherichia coli. Nucleic Acids Research, 33(1):D334-337, 2006.
10. C. J. Krieger, P. Zhang, L. A. Mueller, A. Wang, S. Paley, M. Arnaud, J. Pick, S. Rhee, and P. Karp. Metacyc: a multi-organism database of metabolic pathways and enzymes. Nucleic Acids Research, 32(1):D438-42, 2006.
11. Z. Li, Y. Wang, S. Zhang, X.-S. Zhang, and L. Chen. Alignment of protein interaction networks by integer quadratic programming. EMBS '06. 28th Annual International Conference of the IEEE, 5527-5530, Aug. 2006.
12. R. Pinter, O. Rokhlenko, D. Tsur, and M. Ziv-Ukelson. Approximate labeled subtree homeomorphism. In Proceedings of 15th Annual Symposium of Combinatorial Pattern Matching.
13. R. Y. Pinter, O. Rokhlenko, E. Yeger-Lotem, and M. Ziv-Ukelson. Alignment of metabolic pathways. Bioinformatics.
14. R. Sharan, S. Suthram, R. M. Kelley, T. Kuhn, S. McCuine, P. Uetz, T. Sittler, R. M. Karp, and T. Ideker. Conserved patterns of protein interaction in multiple species. PNAS, Vol.102: 1974-1979, 2005.
15. Y. Tohsato, H. Matsuda, and A. Hashimoto. A multiple alignment algorithm for metabolic pathway analysis using enzyme hierarchy. Proc. 8th International Conference on Intelligent Systems for Molecular Biology, 376-383, ISMB 2000.
16. S. Wernicke. Combinatorial algorithms to cope with the complexity of biological networks. Dissertation, December 2006.
17. Q. Yang and S.-H. Sze. Path macting and graph matching in biological networks. Journal of Computational Biology, Vol. 14, No. 1: 56-67: 5527-5530, 2007.