NeMo: Network module identification in cytoscape

BMC Bioinformatics

Volumn 11, Issue SUPPLL.1, 2010, Pages

  Rivera, Corban G ^a   Vakil, Rachit ^a   Bader, Joel S ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMMUNITY DETECTION; COMMUNITY STRUCTURES; COMPUTATIONAL TOOLS; CONSTRUCTED NETWORKS; DENSELY CONNECTED NETWORKS; GENERALIZATION ERROR; HIERARCHICAL AGGLOMERATIVE CLUSTERING; MODULE IDENTIFICATIONS;

COMPLEX NETWORKS;

ALGORITHM; ARTICLE; CLUSTER ANALYSIS; COMPUTER PROGRAM; METHODOLOGY; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEOMICS;

ALGORITHMS; CLUSTER ANALYSIS; DATABASES, PROTEIN; PROTEIN INTERACTION MAPPING; PROTEOMICS; SOFTWARE;

BIOINFORMATICS;

EID: 75149120711     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-S1-S61     Document Type: Article

References (38)

1. Stumpf MP, Thorne T, de Silva E, Stewart R, An HJ, Lappe M, Wiuf C. Estimating the size of the human interactome. Proc Natl Acad Sci USA 2008, 105(19):6959-6964. 10.1073/pnas.0708078105, 2383957, 18474861.
2. Huang H, Jedynak BM, Bader JS. Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps. PLoS Comput Biol 2007, 3(11):e214. 10.1371/journal.pcbi.0030214, 2082503,2082503, 18039026.
3. Huang H, Bader JS. Precision and recall estimates for two-hybrid screens. Bioinformatics 2009, 25(3):372-378. 10.1093/bioinformatics/btn640, 2639075, 19091773.
4. Hart GT, Ramani AK, Marcotte EM. How complete are current yeast and human protein-interaction networks?. Genome Biol 2006, 7(11):120. 10.1186/gb-2006-7-11-120, 1794583, 17147767.
5. Jagota A. Approximating maximum clique with a Hopfield network. IEEE Trans Neural Netw 1995, 6(3):724-735. 10.1109/72.377977, 18263357.
6. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-2504. 10.1101/gr.1239303, 403769, 14597658.
7. Abou-Rjeili A, Karypis G. Multilevel algorithms for partitioning power-law graphs. Parallel and Distributed Processing Symposium, 2006 IPDPS 2006 20th International: 2006 2006, 10.
8. Karypis G, Kumar V. Multilevel k-way Partitioning Scheme for Irregular Graphs. Journal of Parallel and Distributed Computing 1998, 48(1):96-129.
9. Spielman D, Teng S-H. Nearly-linear time algorithms for graph partitioning, graph sparsification, and solving linear systems. STOC '04: Proceedings of the thirty-sixth annual ACM symposium on Theory of computing: 2004 2004, 81-90. ACM Press.
10. Higham D, Kalna G, Kibble M. Spectral clustering and its use in bioinformatics. Journal of Computational and Applied Mathematics 2007, 204(1):25-37.
11. Newman MEJ. Finding community structure in networks using the eigenvectors of matrices. Physical Review E (Statistical, Nonlinear, and Soft Matter Physics) 2006, 74(3):036104.
12. Barber MJ. Modularity and community detection in bipartite networks. Phys Rev E Stat Nonlin Soft Matter Phys 2007, 76(6 Pt 2):066102.
13. Qi Y, Suhail Y, Lin YY, Boeke JD, Bader JS. Finding friends and enemies in an enemies-only network: a graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions. Genome Res 2008, 18(12):1991-2004. 10.1101/gr.077693.108, 2593582, 18832443.
14. Macropol K, Can T, Singh AK. RRW: repeated random walks on genome-scale protein networks for local cluster discovery. BMC Bioinformatics 2009, 10:283. 10.1186/1471-2105-10-283, 2748087, 19740439.
15. Voevodski K, Teng SH, Xia Y. Finding local communities in protein networks. BMC Bioinformatics 2009, 10:297. 10.1186/1471-2105-10-297, 2755114, 19765306.
16. Karger D, Stein C. A new approach to the minimum cut problem. J ACM 1996, 43(4):601-640.
17. Brandes U, Delling D, Gaertler M, Görke R, Hoefer M, Nikoloski Z, Wagner D. On Finding Graph Clusterings with Maximum Modularity. Graph-Theoretic Concepts in Computer Science 2007, 121-132.
18. Lancichinetti A, Fortunato S. Community detection algorithms: a comparative analysis. 2009,
19. Fortunato S, Barthelemy M. Resolution limit in community detection. Proc Natl Acad Sci USA 2007, 104(1):36-41. 10.1073/pnas.0605965104, 1765466, 17190818.
20. Leicht EA, Newman MEJ. Community Structure in Directed Networks. Physical Review Letters 2008, 100(11). 10.1103/PhysRevLett.100.118703, 18517839.
21. Chung F. The heat kernel as the pagerank of a graph. Proceedings of the National Academy of Sciences 2007,
22. Yoon J, Blumer A, Lee K. An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality. Bioinformatics 2006, 22(24):3106-3108. 10.1093/bioinformatics/btl533, 17060356.
23. Ucar D, Asur S, Catalyurek U, Parthasarathy S. Improving functional modularity in protein-protein interactions graphs using hub-induced subgraphs. Lecture Notes in Computer Science 2006, 4213:371-371.
24. Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4:2. 10.1186/1471-2105-4-2, 149346, 12525261.
25. Lancichinetti A, Fortunato S, Kertesz J. Detecting the overlapping and hierarchical community structure of complex networks. 2009,
26. Altaf-Ul-Amin M, Shinbo Y, Mihara K, Kurokawa K, Kanaya S. Development and implementation of an algorithm for detection of protein complexes in large interaction networks. BMC Bioinformatics 2006, 7:207. 10.1186/1471-2105-7-207, 1473204, 16613608.
27. Clauset A, Newman MEJ, Moore C. Finding community structure in very large networks. 2004,
28. Spirin V, Mirny LA. Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci USA 2003, 100(21):12123-12128. 10.1073/pnas.2032324100, 218723, 14517352.
29. Kumpula J, Kivelä M, Kaski K, Saramäki J. Sequential algorithm for fast clique percolation. Physical Review E (Statistical, Nonlinear, and Soft Matter Physics) 2008, 78(2):026109.
30. Dhillon IS, Guan Y, Kulis B. Weighted graph cuts without eigenvectors a multilevel approach. IEEE Trans Pattern Anal Mach Intell 2007, 29(11):1944-1957. 10.1109/TPAMI.2007.1115, 17848776.
31. Zhang XS, Wang RS, Wang Y, Wang J, Qiu Y, Wang L, Chen L. Modularity optimization in community detection of complex networks. EPL (Europhysics Letters) 2009, 87(3):38002.
32. Ruepp A, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Stransky M, Waegele B, Schmidt T, Doudieu ON, Stumpflen V, et al. CORUM: the comprehensive resource of mammalian protein complexes. Nucleic Acids Res 2008, (36 Database):D646-650. 2238909, 17965090.
33. Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Mark P, Stumpflen V, Mewes HW, et al. The MIPS mammalian protein-protein interaction database. Bioinformatics 2005, 21(6):832-834. 10.1093/bioinformatics/bti115, 15531608.
34. Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A, Santos C, Andrews P, et al. Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res 2007, (35 Database):D566-571. 10.1093/nar/gkl859, 1716720, 17130145.
35. Liu T, Papagiannakopoulos T, Puskar K, Qi S, Santiago F, Clay W, Lao K, Lee Y, Nelson SF, Kornblum HI, et al. Detection of a microRNA signal in an in vivo expression set of mRNAs. PLoS One 2007, 2(8):e804. 10.1371/journal.pone.0000804, 1950084, 17726534.
36. Leonard BE, Myint A. Inflammation and depression: is there a causal connection with dementia?. Neurotox Res 2006, 10(2):149-160. 10.1007/BF03033243, 17062376.
37. Myers JS. Proinflammatory cytokines and sickness behavior: implications for depression and cancer-related symptoms. Oncol Nurs Forum 2008, 35(5):802-807. 10.1188/08.ONF.802-807, 18765326.
38. The Bader Lab. , http://www.baderzone.org