Spectral affinity in protein networks

BMC Systems Biology

Volumn 3, Issue , 2009, Pages

  Voevodski, Konstantin ^a   Teng, Shang Hua ^a,b   Xia, Yu ^a,c  

^a BOSTON UNIVERSITY   (United States)

^b MICROSOFT RESEARCH   (United States)

^c Boston University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; BIOLOGY; COMPUTER PROGRAM; METABOLISM; METHODOLOGY; PROTEIN ANALYSIS; THEORETICAL MODEL;

ALGORITHMS; COMPUTATIONAL BIOLOGY; MODELS, THEORETICAL; PROTEIN INTERACTION MAPPING; PROTEINS; SOFTWARE;

EID: 73249127005     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-3-112     Document Type: Article

References (43)

1. Jeong H, Mason S, Barabasi A, Oltvai Z. Lethality and centrality in protein networks. Nature 2001, 411:41-42. 10.1038/35075138, 11333967.
2. Hahn M, Kern A. Comparative Genomics of Centrality and Essentiality in Three Eukaryotic Protein-Interaction Networks. Mol Biol Evol 2005, 22:803-806. 10.1093/molbev/msi072, 15616139.
3. Fowler J. Legislative cosponsorship networks in the US House and Senate. Social Networks 2006, 28:454-465.
4. Gibson D, Kleinberg J, Raghavan P. Inferring Web communities from link topology. Proc ACM Conf on Hypertext and Hypermedia 1998, 225-234.
5. Kumar R, Raghavan P, Rajagopalan S, Tomkins A. Trawling the Web for emerging cyber-communities. Computer Networks 1999, 31:1481-1493.
6. Flake G, Lawrence S, Giles C, Coetzee F. Self-organization and identification of Web communities. Computer 2002, 35:66-70.
7. Palla G, Derenyi I, Farkas I, Vicsek T. Uncovering the overlapping community structure of complex networks in nature and society. Nature 2005, 435:814-818. 10.1038/nature03607, 15944704.
8. Clauset A. Finding local community structure in networks. Phys Rev E Stat Nonlin Soft Matter Phys 2005, 72:026132.
9. Krogan N, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis A, Punna T, Peregrin-Alvarez J, Shales M, Zhang X, Davey M, Robinson M, Paccanaro A, Bray J, Sheung A, Beattie B, Richards D, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete M, Vlasblom J, Wu S, Orsi C, Collins S, Chandran S, Haw R, Rilstone J, Gandi K, Thompson N, Musso G, Onge PS, Ghanny S, Lam M, Butland G, Altaf-U A, Kanaya S, Shilatifard A, O'Shea E, Weissman J, Ingles J, Hughes T, Parkinson J, Gerstein M, Wodak S, Emili A, Greenblatt J. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 2006, 440:637-643. 10.1038/nature04670, 16554755.
10. Anthonisse J. The rush in a directed graph. Tech. rep., Stichting Mathematicsh Centrum 1971,
11. Girvan M, Newman M. Community structure in social and biological networks. Proc Natl Acad Sci USA 2002, 99:7821-7826. 10.1073/pnas.122653799, 122977, 12060727.
12. Newman M, Girvan M. Finding and evaluating community structure in networks. Phys Rev E Stat Nonlin Soft Matter Phys 2004, 69:026113.
13. Przulj N, Wigle D, Jurisica I. Functional topology in a network of protein interactions. Bioinformatics 2004, 20:340-348. 10.1093/bioinformatics/btg415, 14960460.
14. Jansen R, Lan N, Qian J. Integration of genomic datasets to predict protein complexes in yeast. J Struct Funct Genomics 2002, 2:71-81. 10.1023/A:1020495201615, 12836664.
15. von Mering C, Krause R, Snell B, Cornell M, Oliver S, Fields S, Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417:399-403. 10.1038/nature750, 12000970.
16. Amaral L, Scala A, Barthelemyt M, Stanley H. Classes of small-world networks. Proc Natl Acad Sci USA 2000, 97:11149-11152. 10.1073/pnas.200327197, 17168, 11005838.
17. Watts D, Strogatz S. Collective dynamics of 'small-world' networks. Nature 1998, 393:440-442. 10.1038/30918, 9623998.
18. Guare J. Six Degrees of Separation: A Play 1990, Vintate Books.
19. Yip A, Horvath S. Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinformatics 2007, 8(22). 1797055, 17250769.
20. Chua N, Sung W, Wong L. Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics 2006, 22:1623-1630. 10.1093/bioinformatics/btl145, 16632496.
21. Okada K, Kanaya S, Asai K. Accurate extraction of functional associations between proteins based on common interaction partners and common domains. Bioinformatics 2005, 21:2043-2048. 10.1093/bioinformatics/bti305, 15699027.
22. Samanta M, Liang S. Predicting protein functions from redundancies in large-scale protein interaction networks. Proc Natl Acad Sci USA 2003, 100:12579-12583. 10.1073/pnas.2132527100, 240660, 14566057.
23. Goldberg D, Roth F. Assessing experimentally derived interactions in a small world. Proc Natl Acad Sci USA 2003, 100:4372-4376. 10.1073/pnas.0735871100, 404686, 12676999.
24. Li A, Horvath S. Network neighborhood analysis with the multi-node topological overlap measure. Bioinformatics 2007, 23:222-231. 10.1093/bioinformatics/btl581, 17110366.
25. Asthana S, King O, Gibbons F, Roth F. Predicting Protein Complex Membership Using Probabilistic Network Reliability. Genome Res 2004, 14:1170-1175. 10.1101/gr.2203804, 419795, 15140827.
26. Huang H, Zhang L, Roth F, Bader J. Probabilistic Paths for Protein Complex Inference 2007, 4532:14-28. Springer Berlin/Heidelberg.
27. Bader G, Hogue C. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4(2).
28. Spirin V, Mirny L. Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci USA 2003, 100:12123-12128. 10.1073/pnas.2032324100, 218723, 14517352.
29. Chen J, Yuan B. Detecting functional modules in the yeast protein-protein interaction network. Bioinformatics 2006, 22:2283-2290. 10.1093/bioinformatics/btl370, 16837529.
30. King A, Przulj N, Jurisica I. Protein complex prediction via cost-based clustering. Bioinformatics 2004, 20:3013-3020. 10.1093/bioinformatics/bth351, 15180928.
31. Brun C, Chevenet F, Martin D, Wojcik J, Guenoche A, Jacq B. Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network. Genome Biol 2003, 5:R6. 10.1186/gb-2003-5-1-r6, 395738, 14709178.
32. Haveliwala T. Topic-sensitive pagerank: A context-sensitive ranking algorithm for web search. IEEE Trans on Knowledge and Data Engineering 2003, 15:784-796.
33. Fogaras D, Racz B. Towards scaling fully personalized pagerank. Proc Workshop on Algorithms and Models for the Web-Graph 2004, 105-117.
34. Jeh G, Widom J. Scaling personalized web search. Proc World Wide Web Conf 2003, 271-279.
35. Andersen R, Borgs C, Chayes J, Hopcraft J, Mirrokni V, Teng S. Local computation of PageRank contributions. Proc Workshop on Algorithms and Models for the Web-Graph 2007, 150-165.
36. Andersen R, Chung F, Lang K. Local graph partitioning using PageRank vectors. Proc IEEE Foundations of Computer Science 2006, 475-486.
37. Abou A, Karypis G. Multilevel algorithms for partitioning power-law graphs. Proc IEEE Parallel & Distributed Processing Symposium 2006,
38. Batagelj V, Zavernik M. Cores Decomposition of Networks. Recent Trends in Graph Theory, Algebraic Combinatorics, and Graph Algorithms 2001,
39. Qiu H, Hancock E. Clustering and embedding using commute times. IEEE Trans on Pattern Analysis and Machine Intelligence 2007, 29:1873-1890.
40. Mewes H, Amid C, Arnold R, Frishman D, Guldener U, Mannhaupt G, Munsterkotter M, Pagel P, Strack N, Stumpflen V, Warfsmann J, Ruepp A. MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res 2004, 32:D41-44. 10.1093/nar/gkh092, 308826, 14681354.
41. Yu H, Jansen R, Gerstein M. Developing a similarity measure in biological function space. Bioinformatics 2007, 23:2163-2173. 10.1093/bioinformatics/btm291, 17540677.
42. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. BioGRID: a general repository for interaction datasets. Nucleic Acids Res 2006, 34:D535-9. 10.1093/nar/gkj109, 1347471, 16381927.
43. Rodgers JL, Nicewander WA. Thirteen ways to look at the correlation coefficient. Am Stat 1988, 42:59-66.