Algorithms to detect multiprotein modularity conserved during evolution

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 6674 LNBI, Issue , 2011, Pages 111-122

  Hodgkinson, Luqman ^a,b,c   Karp, Richard M ^a,b,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c INTERNATIONAL COMPUTER SCIENCE INSTITUTE   (United States)

Author keywords

algorithms; evolution; interactomes; modularity

Indexed keywords

BIOLOGICAL CELLS; EVALUATION MEASURES; EVOLUTION; GRAPH-THEORETIC; INTERACTOMES; LINEAR-TIME ALGORITHMS; MODULARITY; RUNNING TIME;

BIOINFORMATICS; BIOLOGY; CLUSTERING ALGORITHMS; GRAPH THEORY;

EVOLUTIONARY ALGORITHMS;

EID: 79955817260     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-21260-4_14     Document Type: Conference Paper

References (16)

1. Vidal, M.: Interactome modeling. FEBS Letters 579, 1834-1838 (2005)
2. Kelley, B.P., Sharan, R., Karp, R.M., Sittler, T., Root, D.E., Stockwell, B.R., Ideker, T.: Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc. Natl. Acad. Sci. 100(20), 11394-11399 (2003)
3. Sharan, R., Suthram, S., Kelley, R.M., Kuhn, T., McCuine, S., Uetz, P., Sittler, T., Karp, R.M., Ideker, T.: Conserved patterns of protein interaction in multiple species. Proc. Natl. Acad. Sci. 102(6), 1947-1979 (2005)
4. Koyutürk, M., Kim, Y., Topkara, U., Subramaniam, S., Szpankowski, W., Grama, A.: Pairwise alignment of protein interaction networks. Journal of Computational Biology 13(2), 182-199 (2006)
5. Flannick, J., Novak, A., Srinivasan, B.S., McAdams, H.H., Batzoglou, S.: Graemlin: general and robust alignment of multiple large interaction networks. Genome Research 16, 1169-1181 (2006)
6. Narayanan, M., Karp, R.M.: Comparing protein interaction networks via a graph match-and-split algorithm. Journal of Computational Biology 14(7), 892-907 (2007)
7. Beltrao, P., Serrano, L.: Specificity and evolvability in eukaryotic protein interaction networks. PLoS Computational Biology 3(2), e25 (2007)
8. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic local alignment search tool. Journal of Molecular Biology 215(3), 403-410 (1990)
9. Simon, H.A.: The structure of complexity in an evolving world: the role of near decomposability. In: Callebaut, W., Rasskin-Gutman, D. (eds.) Modularity: Understanding the Development and Evolution of Natural Complex Systems. Vienna Series in Theoretical Biology. MIT Press, Cambridge (2005)
10. Li, M., Wang, J., Chen, J., Pan, Y.: Hierarchical organization of functional modules in weighted protein interaction networks using clustering coefficient. In: Mǎndoiu, I., Narasimhan, G., Zhang, Y. (eds.) ISBRA 2009. LNCS (LNBI), vol. 5542, pp. 75-86. Springer, Heidelberg (2009)
11. Andersen, R., Chung, F., Lang, K.: Local graph partitioning using PageRank vectors. In: 47th Annual IEEE Symposium on Foundations of Computer Science (FOCS 2006), pp. 475-486. IEEE Press, New York (2006)
12. Voevodski, K., Teng, S., Xia, Y.: Finding local communities in protein networks. BMC Bioinformatics 10, 297 (2009)
13. Kalaev, M., Bafna, V., Sharan, R.: Fast and accurate alignment of multiple protein networks. In: Vingron, M., Wong, L. (eds.) RECOMB 2008. LNCS (LNBI), vol. 4955, pp. 246-256. Springer, Heidelberg (2008)
14. Razick, S., Magklaras, G., Donaldson, I.M.: iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics 9, 405 (2008)
15. Hodgkinson, L., Karp, R.M.: Algorithms to detect multi-protein modularity conserved during evolution. EECS Department, University of California, Berkeley, Technical Report UCB/EECS-2011-7 (2011)
16. Boyle, E.I., Weng, S., Gollub, J., Jin, H., Botstein, D., Cherry, J.M., Sherlock, G.: Go:termfinder - open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes. Bioinformatics 20(18), 3710-3715 (2004)