An efficient algorithm for detecting frequent subgraphs in biological networks

Bioinformatics

Volumn 20, Issue SUPPL. 1, 2004, Pages

  Koyutürk, Mehmet ^a   Grama, Ananth ^a   Szpankowski, Wojciech ^a  

^a Purdue University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BIOLOGICAL MODEL; CONFERENCE PAPER; DATA BASE; METABOLISM; MOLECULAR BIOLOGY; PRIORITY JOURNAL; PROTEIN INTERACTION;

EID: 14844305006     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth919     Document Type: Conference Paper

References (19)

1. Agrawal, R. and Srikant, R. (1994) Fast algorithms for mining association rules. Proceedings of the 20th International Conference on Very Large Data Bases (VLDB'94), Santiaogo di Chile, Chile, September, pp. 487-499.
2. Akutsu, T., Kuhara, S., Maruyama, O. and Miyano, S. (1998) Identification of gene regulatory networks by strategic gene disruptions and gene overexpressions. Proceedings of the Ninth Annual ACM-SIAM Symposium on Discrete Algorithms, San Francisco, CA, January, pp. 695-702.
3. Altschul, S.F, Madden, T.L., Scheffer, A.A., Zhang, Z., Zhang, J., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
4. Cook, D.J. and Holder, L.B. (2000) Graph-based data mining. IEEE Intell. Syst., 15, 32-41.
5. Goto, S., Bono, H., Ogata, H., Fujibuchi, W., Sato, K. and Kanehisa, M. (1997) Organizing and computing metabolic pathway data in terms of binary relations. Pacific Symp. Biocomput., 175-186.
6. Gouda, K. and Zaki, M.J. (2001) Efficiently mining maximal frequent itemsets. IEEE International Conference on Data Mining (ICDM'01), San Jose, CA, November, pp. 163-170.
7. Hartwell, L.H., Hopfield, J.J., Leibler, S. and Murray, A.W. (1999) From molecular to modular cell biology. Nature, 402, C47-C51.
8. Ho, Y., Grahler, A., Heilbut, A., Bader, G.D., Moore, L., Adams, S.L., Millar, A., Taylor, P., Bennett, K., Boutilier, K. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisae by mass spectrometry. Nature, 415, 180-183.
9. Inokuchi, A., Washio, T., Okada, T. and Motoda, H. (2001) Applying the a priori-based graph mining method to mutagenesis data analysis. J. Comput. Aided Chem., 2, 87-92.
10. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M. and Sakaki, Y. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci., USA, 98, 4569-4574.
11. Karp, P.D. and Mavrovouniotis, M.L. (1994) Representing, analysing, and synthesizing biochemical pathways. IEEE Expert, 11-21.
12. Krishnamurthy, L., Nadeau, J., Özsoyoǧlu, G., Özsoyoǧlu, M., Schaeffer, G., Taşan, M. and Xu, W. (2003) Pathways database system: an integrated system for biological pathways. Bioinformatics, 19, 930-937.
13. Kuramochi, M. and Karypis, G. (2001) Frequent subgraph discovery. IEEE International Conference on Data Mining (ICDM'01), San Jose, CA, November, pp. 313-320.
14. Olken, F. (2003) Biopathways and protein interaction databases. A lecture in Bioinformatics Tools for Comparative Genomics: A short course, Berkeley, CA, February.
15. Oltvai, Z.N. and Barabasi, A.L. (2002) Life's complexity pyramid. Science, 298, 763-764.
16. Rives, A.W. and Galitski, T. (2003) Modular organization of cellular networks, Proc. Natl Acad. Sci., USA, 100, 1128-1133.
17. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL-W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
18. Tohsato, Y., Matsuda, H. and Hashimoto, A. (2000) A multiple alignment algorithm for metabolic pathway analysis using enzyme hierarchy. Eighth International Conference Intelligent Systems for Molecular Biology (ISMB'00), La Jolla, CA, August, pp. 376-383.
19. Yan, X. and Han, J. (2002) gSpan: graph-based substructure pattern mining. IEEE International Conference on Data Mining (ICDM'02), Maebashi City, Japan, December, pp. 721-724.