The multiple alignment algorithm for metabolic pathways without abstraction

Proceedings - IEEE International Conference on Data Mining, ICDM

Volumn , Issue , 2010, Pages 669-678

  Chen, Wenbin ^a,b   Rocha, Andrea M ^c   Hendrix, William ^a,b   Schmidt, Matthew ^a,b   Samatova, Nagiza F ^a,b  

^a North Carolina State University   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

^c University of South Florida   (United States)

Author keywords

Alignment; K partite graph matching; Pathway

Indexed keywords

COMPUTATIONAL BIOLOGY; COMPUTATIONAL PROBLEM; K-PARTITE GRAPH; K-PARTITE GRAPH MATCHING; K-PARTITE MATCHING; METABOLIC PATHWAYS; MULTIPLE ALIGNMENT; MULTIPLE PATHWAYS; PATHWAY; SIMILARITY SCORES; SUB-NETWORK; TOPOLOGICAL STRUCTURE;

ALIGNMENT; BIOINFORMATICS; CATALYSTS; DATA MINING; ENZYMES; HEURISTIC ALGORITHMS; METABOLISM; TOPOLOGY;

PATTERN MATCHING;

EID: 79951759652     PISSN: 15504786     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICDMW.2010.21     Document Type: Conference Paper

References (26)

1. F. Ay, T. Kahveci, Valerie de Crecy-Lagard. Consistent alignment of metabolic pathways without any abstraction in modeling, CSB, 2008.
2. Bono, H., Ogata, H., Goto, S. and Kanehisa, M. Reconstruction of Amino Acid Biosynthesis Pathways from the Complete Genome Sequence. Genome Research, 8(3):203- 210, 1998. (Pubitemid 28177232)
3. 13CNMR spectroscopy." Microbiology 140: 2085- 2092. 1994. (Pubitemid 24259045)
4. Dandekar, T., Schuster, S., Snel, B., Huynen, M. and Bork, P. Pathway Alignment: Application to the Comparative Analysis of Glycolytic Enzymes, Biochemical J., 343(1): 115-124, 1999. (Pubitemid 29473885)
5. M.L. Fredman and R.E. Tarjan. Fibonacci Heaps and Their Uses in Improved Network Optimization Algorithms, FOCS, 338-346, 1984.
6. M. R. Garey and D. S. Johnson. Computers and Intractability. Freeman, 1979.
7. G. He, J. Liu, C. Zhao. Approximation algorithms for some graph partitioning problems. Journal of Graph Algorithms and Applications. vol. 4, no. 2, pp. 1-11 (2000). (Pubitemid 39064646)
8. Hattori M, Okuno Y, Goto S, and Kanehisa M. Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J Am Chem Soc, 125(39):11853C11865, 2003. (Pubitemid 37175419)
9. Karlin, S., J. Theriot and J. Mrázek. "Comparative analysis of gene expression among low G+C gram-positive genomes." Proceedings of the National Academy of Sciences of the United States of America 101(16): 6182-6187. 2004. (Pubitemid 38520548)
10. B. P. Kelley, R. Sharan, R. M. Karp, T. Sittler, D. E. Root, B. R. Stockwell, and T. Ideker. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proceedings of the National Academy of Sciences, 100(20):11394-11399, 2003. (Pubitemid 37205946)
11. M. Koyutürk, A. Grama, and W. Szpankowski. An efficient algorithm for detecting frequent subgraphs in biological networks. Bioinformatics, 20(1):200-207, 2004.
12. Y. Li, D. de Ridder, M. de Groot, and M. Reinders. Metabolic pathway alignment between species using a comprehensive and flexible similarity measure. BMC Systems Biology, 2(1):111, 2008.
13. H. Ogata, W. Fujibuchi, S. Goto, and M. Kanehisa. A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. Nucl. Acids Res., 28(20):4021-4028, Oct. 2000.
14. Pevsner, J [Ed]. Bioinformatics and Functional Genomics (2nd ed.). Wiley-Blackwell, 2009.
15. Pinter RY, Rokhlenko O, Yeger-Lotem E, and Ziv-Ukelson M. Alignment of metabolic pathways. Bioinformatics, 21(16):3401C8, 2005.
16. Seo, J.-S., H. Chong, H.S. Park. K.-O. Yoon, C. Jung, J.J. Kim, J.H. Hong, H. Kim, J.-H. Kim, J.-I. Kil, C.J. Park, H.- M. Oh, J.-S. Lee, S.-J. Jin, H.-W. Um, H.-J. Lee, S.-J. Oh, J.Y. Kim, H.L. Kang, S.Y. Lee, K.J. Lee, and H.S. Kang. "The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4." Nat Biotech 23(1): 63-68. 2005. (Pubitemid 41724626)
17. R. Sharan and T. Ideker. Modeling cellular machinery through biological network comparison. Nature Biotechnology, 24(4):427-433, 2006.
18. R. Singh, J.B Xu, and B. Berger. Global Alignment of Multiple Protein Interaction Networks. Pacific Symposium on Biocomputing. 303-314, 2008.
19. P. Sridhar P, T. Kahveci, and S. Ranka. An iterative algorithm for metabolic network-based drug target identification. In PSB, volume 12, pages 88C99, 2007.
20. W. Tian and N. F. Samatova. Pairwise alignment of interaction networks by fast identification of maximal conserved patterns. In Pacific Symposium on Biocomputing., page 99, 2009.
21. Tohsato Y, Matsuda H, and Hashimoto A. A Multiple Alignment Algorithm for Metabolic Pathway Analysis Using Enzyme Hierarchy. In ISMB, pages 376C383, 2000.
22. Y. Tohsato and Y. Nishimura. Metabolic Pathway Alignment Based on Similarity between Chemical Structures. IPSJ Digital Courier, 3, 2007.
23. S. Wernicke and F. Rasche. Simple and fast alignment of metabolic pathways by exploiting local diversity. Bioinformatics, 23(15):1978-1985, Aug. 2007. (Pubitemid 47299839)
24. Douglas B. West. Introduction to Graph Theory, Second Edition. China Machine Press, 2004.
25. White, D. The physiology and biochemistry of prokaryotes. New York: Oxford University Press, 2007.
26. H. Yu, N. M. Luscombe, H. X. Lu, X. Zhu, Y. Xia, J. J. Han, N. Bertin, S. Chung, M. Vidal, and M. Gerstein. Annotation transfer between genomes: Protein-Protein interologs and Protein-DNA regulogs. Genome Research, 14(6):1107-1118, June 2004. (Pubitemid 38811547)