Fast and accurate alignment of multiple protein networks

Journal of Computational Biology

Volumn 16, Issue 8, 2009, Pages 989-999

  Kalaev, Maxim ^a   Bafna, Vineet ^b   Sharan, Roded ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Combinatorial proteomics; Computational molecular biology; Gene expression; Gene networks; Genetic variation; Sequence analysis

Indexed keywords

ALGORITHM; BACTERIAL STRAIN; CONFERENCE PAPER; EUKARYOTE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; QUALITY CONTROL;

ALGORITHMS; ANIMALS; BACTERIAL PROTEINS; FUNGAL PROTEINS; PROTEIN INTERACTION MAPPING; PROTEINS; PROTEOMICS; TIME FACTORS;

EID: 70349193233     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2009.0136     Document Type: Conference Paper

References (20)

1. Aebersold, R., and Mann, M. 2003. Mass spectrometry-based proteomics. Nature 422, 198-207.
2. Ashburner, M., et al. 2000. The gene ontology consortium. gene ontology: tool for the unification of biology. Nat. Genet. 25, 25-29.
3. Benjamini, Y., and Hochberg, Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Statist. Soc. 57, 289-300.
4. Boyle, E., Weng, S., Gollub, J., et al. 2004. 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, 3710-3715.
5. Dutkowski, J., and Tiuryn, J. 2007. Identification of functional modules from conserved ancestral protein-protein interactions. Bioinformatics 23, 149-158.
6. Flannick, J., et al. 2006. Graemlin: general and robust alignment of multiple large interaction networks. Genome Res. 16, 1169-1181.
7. Gavin, A., et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147.
8. Hirsh, E., and Sharan, R. 2006. Identification of conserved protein complexes based on a model of protein network evolution. Bioinformatics.
9. Ho, Y., et al. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183.
10. Ito, T., Chiba, T., and Yoshida, M. 2001a. Exploring the yeast protein interactome using comprehensive two-hybrid projects. Trends Biotechnol. 19, 23-27.
11. Ito, T., et al. 2001b. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 98, 4569-4574.
12. Kelley, B., et al. 2003. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc. Natl. Acad. Sci. USA 100, 11394-11399.
13. Koyuturk, M., et al. 2006. Pairwise local alignment of protein interaction networks guided by models of evolution.
14. J. Comput. Biol. 13, 182-199.
15. Pellegrini, M., Marcotte, E., Thompson, M., et al. 1999. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA 96, 4285-4288.
16. Shamir, R., Sharan, R., and Tsur, D. 2004. Cluster graph modification problems. Discrete Appl. Math. 144, 173-182.
17. Sharan, R., Ideker, T., Kelley, B., et al. 2005a. Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. J. Comput. Biol. 12, 835-846.
18. Sharan, R., et al. 2005b. Conserved patterns of protein interaction in multiple species. Proc. Natl. Acad. Sci. USA 102, 1974-1979.
19. Stelzl, U., et al. 2005. A human protein-protein interaction network: a resource for annotating the proteome. Cell 122, 830-832.
20. Uetz, P., et al. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627.