Multi-functional Protein Clustering in PPI Networks

1. Adamcsek, B., Palla, G., Farkas, I.J., Dernyi, I., Vicsek, T.: Cfinder: locating cliques and overlapping modules in biological networks. Bioinformatics 22(8), 1021–1023 (2006)

   Article  Google Scholar 

2. Arnau, V., Mars, S., Marìn, I.: Iterative cluster analysis of protein interaction data. Bioinformatics 21(3), 364–378 (2004)

   Article  Google Scholar 

3. Asur, S., Ucar, D., Parthasarathy, S.: An ensemble framework for clustering protein-protein interaction networks. Bioinformatics 40, i29–i40 (2007)

   Article  Google Scholar 

4. Bader, G., Hogue, H.: An automated method for finding molecular complexes in large protein-protein interaction networks. BMC Bioinformatics 4(2) (2003)

   Google Scholar 

5. Blatt, M., Wiseman, S., Domany, E.: Superparamagnetic clustering of data. Phisical Review Letters 76(18), 3251–3254 (1996)

   Article  Google Scholar 

6. Brohèe, S., van Helden, J.: Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 7, 488 (2006)

   Article  Google Scholar 

7. Cheng, Y., Church, G.M.: Biclustering of expression data. In: Proceedings of the 8th International Conference On Intelligent Systems for Molecular Biology (ISMB 2000), pp. 93–103 (2000)

   Google Scholar 

8. Cho, Y.-R., Hwang, W., Ramanathan, M., Zhang, A.: Semantic integration to identify overlapping functional modules in protein interaction networks. BMC Bioinformatics 8, 265 (2007)

   Article  Google Scholar 

9. Derenyi, I., et al.: Clique percolation in random networks. Physical Review Letters 94, 160–202 (2005)

   Article  Google Scholar 

10. Enright, A.J., Dongen, S.V., Ouzounis, C.A.: An efficient algorithm for large-scale detection of protein families. Nucleid Acids Res 30(7), 1575–1584 (2002)

    Article  Google Scholar 

11. Asburner, S., et al.: Gene ontology: tool for the unification of biology. the gene ontology consortium 25, 25–29 (2000)

    Google Scholar 

12. Hartuv, E., Shamir, R.: Clustering algorithm based graph connectivity. Information Processing Letters 76, 175–181 (2000)

    Article  MATH  MathSciNet  Google Scholar 

13. Jeong, H., Barabasi, A.L., Oltvai, Z.N.: Lethality and centrality in protein networks. Nature 411, 41–42 (2001)

    Article  Google Scholar 

14. King, A.D., Przulj, N., Jurisica, I.: Protein complex prediction via cost-based clustering. Bioinformatics 20(17), 3013–3020 (2004)

    Article  Google Scholar 

15. Lin, C., Cho, Y., Hwang, W., Pei, P., Zhang, A.: Clustering methods in protein-protein interaction network. In: Knowledge Discovery in Bioinformatics: Techniques, Methods and Application, John Wiley & Sons,Inc., Chichester (2006)

    Google Scholar 

16. Madeira, S.C., Oliveira, A.L.: Biclustering algorithms for biological data analysis: A survey. IEEE Transactions on Computational Biology and Bioinformatics 1(1), 24–45 (2004)

    Article  Google Scholar 

17. Orlev, N., Shamir, R., Shiloh, Y.: Pivot: Protein interaction visualization tool. Bioinformatics 20(3), 424–425 (2004)

    Article  Google Scholar 

18. Pei, P., Zhang, A.: A two-step approach for clustering proteins based on protein interaction profiles. In: IEEE Int. Symposium on Bioinformatics and Bioengeneering (BIBE 2005), pp. 201–209 (2005)

    Google Scholar 

19. Pereira, J.B., Enright, A.J., Ouzounis, C.A.: Detection of functional modules from protein interaction networks. Proteins: Structure, Fuctions, and Bioinformatics (20), 49–57 (2004)

    Article  Google Scholar 

20. Pizzuti, C., Rombo, S.: Pincoc: a co-clustering based approach to analyze protein-protein interaction networks. In: Proceedings of the 8th International Conference on Intelligent Data Engineering and Automated Learning (IDEAL 2007) (2007)

    Google Scholar 

21. Salwinski, L., Miller, C.S., Smith, A.J., Pettit, F.K., Bowie, J.U., Eisenberg, D.: The database of interacting proteins: 2004 update. Nucleic Acids Research 32(Database issue), D449–D451 (2004)

    Article  Google Scholar 

22. Samantha, M.P., Liang, S.: Redundancies in large-scale protein interaction networks. In: Proceedings of the National Academy of Science, USA, 100, pp. 12579–12583 (2003)

    Google Scholar 

23. Spirin, V., Mirny, L.A.: Protein complexes and and functional modules in molecular networks. In: Proceedings of the National Academy of Science, USA, 100, pp. 12123–12128 (2003)

    Google Scholar 

24. Ucar, D., Asur, S., Çatalyürek, Ü.V., Parthasarathy, S.: Improving functional modularity in protein-protein interactions graphs using hub-induced subgraphs. In: Fürnkranz, J., Scheffer, T., Spiliopoulou, M. (eds.) PKDD 2006. LNCS (LNAI), vol. 4213, pp. 371–382. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

25. von Mering, D., Krause, C., et al.: Comparative assessment of a large-scale data sets of protein-protein interactions. Nature 31, 399–403 (2002)

    Article  Google Scholar 

26. Watt, D.J.: Small worlds. Princeton University Press, Princeton (1999)

    Google Scholar 

Download references