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Advances in Bioinformatics
Volume 2009, Article ID 787128, 9 pages
http://dx.doi.org/10.1155/2009/787128
Research Article

Accurate and Scalable Techniques for the Complex/Pathway Membership Problem in Protein Networks

1Department of Computer Science, University of California, Santa Barbara, CA 93106, USA
2Department of Computer Engineering, Middle East Technical University, 06531 Ankara, Turkey

Received 1 August 2009; Accepted 2 December 2009

Academic Editor: Tamer Kahveci

Copyright © 2009 Orhan Çamoğlu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. L. Lovasz, “Random walks on graphs: a survey,” in Combinatorics, Paul Erdos is Eighty, vol. 2, pp. 353–398, Bolyai Society Mathematical Studies, Budapest, Hungary, 1996. View at Google Scholar
  2. B. Schoelkopf, K. Tsuda, and J.-P. Vert, Eds., Kernel Methods in Computational Biology, MIT Press, Cambridge, Mass, USA, 2004.
  3. S. Letovsky and S. Kasif, “Predicting protein function from protein/protein interaction data: a probabilistic approach,” Bioinformatics, vol. 19, supplement 1, pp. i197–i204, 2003. View at Publisher · View at Google Scholar · View at Scopus
  4. S. Asthana, O. D. King, F. D. Gibbons, and F. P. Roth, “Predicting protein complex membership using probabilistic network reliability,” Genome Research, vol. 14, no. 6, pp. 1170–1175, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  5. E. Nabieva, K. Jim, A. Agarwal, B. Chazelle, and M. Singh, “Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps,” Bioinformatics, vol. 21, supplement 1, pp. i302–i310, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  6. L. G. Valiant, “The complexity of enumeration and reliability problems,” SIAM Journal on Computing, vol. 8, pp. 410–421, 1979. View at Google Scholar
  7. M. T. Dittrich, G. W. Klau, A. Rosenwald, T. Dandekar, and T. Müller, “Identifying functional modules in protein-protein interaction networks: an integrated exact approach,” Bioinformatics, vol. 24, no. 13, pp. i223–i231, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  8. Y. Qi, F. Balem, C. Faloutsos, J. Klein-Seetharaman, and Z. Bar-Joseph, “Protein complex identification by supervised graph local clustering,” Bioinformatics, vol. 24, no. 13, pp. i250–i268, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  9. M. E. Sardiu, L. Florens, and M. P. Washburn, “Evaluation of clustering algorithms for protein complex and protein interaction network assembly,” Journal of Proteome Research, vol. 8, no. 6, pp. 2944–2952, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  10. P. Beltrao and L. Serrano, “Specificity and evolvability in eukaryotic protein interaction networks,” PLoS Computational Biology, vol. 3, no. 2, article e25, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  11. J. Dutkowski and J. Tiuryn, “Identification of functional modules from conserved ancestral protein-protein interactions,” Bioinformatics, vol. 23, no. 13, pp. i149–i158, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  12. T. J. P. van Dam and B. Snel, “Protein complex evolution does not involve extensive network rewiring,” PLoS Computational Biology, vol. 4, no. 7, Article ID e1000132, pp. 1–8, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  13. H. Jeong, S. P. Mason, A.-L. Barabási, and Z. N. Oltvai, “Lethality and centrality in protein networks,” Nature, vol. 411, no. 6833, pp. 41–42, 2001. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  14. M. Kanehisa, S. Goto, S. Kawashima, and A. Nakaya, “Thed KEGG databases at GenomeNet,” Nucleic Acids Research, vol. 30, no. 1, pp. 42–46, 2002. View at Google Scholar · View at Scopus
  15. T. B. Brecht and C. J. Colbourn, “Lower bounds on two-terminal network reliability,” Discrete Applied Mathematics, vol. 21, no. 3, pp. 185–198, 1988. View at Google Scholar · View at Scopus
  16. F. Harary, Graph Theory, Addison-Wesley, Reading, Mass, USA, 1969.
  17. CPLEX, http://www-01.ibm.com/software/websphere/ilog_migration.html.
  18. A. Y. Ng, M. Jordan, and Y. Weiss, “On spectral clustering: analysis and an algorithm,” in Advances in Neural Information Processing Systems 14, 2002. View at Google Scholar
  19. N. Saitou and M. Nei, “The neighbor-joining method: a new method for reconstructing phylogenetic trees,” Molecular Biology and Evolution, vol. 4, no. 4, pp. 406–425, 1987. View at Google Scholar · View at Scopus
  20. N. Beckmann, H.-P. Kriegel, R. Schneider, and B. Seeger, “The R-tree: an efficient and robust access method for points and rectangles,” in Proceedings of the ACM SIGMOD International Conference on Management of Data, pp. 322–331, Atlantic City, NJ, USA, 1990.
  21. P. Uetz, L. Giot, G. Cagney et al., “A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae,” Nature, vol. 403, no. 6770, pp. 623–627, 2000. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  22. T. Ito, T. Chiba, R. Ozawa, M. Yoshida, M. Hattori, and Y. Sakaki, “A comprehensive two-hybrid analysis to explore the yeast protein interactome,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 8, pp. 4569–4574, 2001. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  23. A.-C. Gavin, M. Bösche, R. Krause et al., “Functional organization of the yeast proteome by systematic analysis of protein complexes,” Nature, vol. 415, no. 6868, pp. 141–147, 2002. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  24. Y. Ho, A. Gruhler, A. Heilbut et al., “Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry,” Nature, vol. 415, no. 6868, pp. 180–183, 2002. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus