Deciphering network community structure by surprise

PLoS ONE

Volumn 6, Issue 9, 2011, Pages

  Aldecoa, Rodrigo ^a   Marín, Ignacio ^a  

^a INSTITUTO DE BIOMEDICINA DE VALENCIA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANALYTICAL PARAMETERS; ARTICLE; COMMUNITY STRUCTURE; CONTROLLED STUDY; HUMAN; INTERMETHOD COMPARISON; MATHEMATICAL ANALYSIS; NEWMAN AND GIRVAN'S MODULARITY; PARTITION COEFFICIENT; QUALITATIVE ANALYSIS; QUALITY CONTROL; SOCIAL NETWORK; SURPRISE PARAMETER; COMMUNITY CARE; METABOLISM; SACCHAROMYCES CEREVISIAE; THEORETICAL MODEL;

SACCHAROMYCES CEREVISIAE PROTEIN;

ALGORITHMS; COMMUNITY NETWORKS; MODELS, THEORETICAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 80052366868     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0024195     Document Type: Article

References (29)

1. Barabási AL, Oltvai ZN, (2004) Network biology: Understanding the cell's functional organization. Nat Rev Genet 5: 101-113.
2. Wasserman S, Faust K, (1994) Social network analysis: Methods and applications. Cambridge University Press, Cambridge, U.K.
3. Strogatz SH, (2001) Exploring complex networks. Nature 410: 268-276.
4. Costa LD, Rodrigues FA, Travieso G, Boas PRV, (2007) Characterization of complex networks: A survey of measurements. Adv Phys 56: 167-242.
5. Newman MEJ, (2010) Networks: An introduction. Oxford University Press, Oxford. U.K.
6. Fortunato S, (2010) Community detection in graphs. Phys Rep 486: 75-174.
7. Newman MEJ, Girvan M, (2004) Finding and evaluating community structure in networks. Phys Rev E 69: 026113.
8. Fortunato S, Barthélemy M, (2007) Resolution limit in community detection. Proc Natl Acad Sci USA 104: 36-41.
9. Arnau V, Mars S, Marín I, (2005) Iterative cluster analysis of protein interaction data. Bioinformatics 21: 364-378.
10. Lancichinetti A, Fortunato S, Radicchi F, (2008) Benchmark graphs for testing community detection algorithms. Phys Rev E 78: 046110.
11. Watts DJ, (1999) in Small worlds. The dynamics of networks between order and randomness. Princeton University Press, Princeton, N.J.
12. Girvan M, Newman MEJ, (2002) Community structure in social and biological networks. Proc Natl Acad Sci USA 99: 7821-7826.
13. Aldecoa R, Marín I, (2010) Jerarca: Efficient analysis of complex networks using hierarchical clustering. PLoS ONE 5: e11585.
14. Danon L, Díaz-Guilera A, Duch J, Arenas A, (2005) Comparing community structure identification. J Stat Mech P09008.
15. Lancichinetti A, Fortunato S, (2009) Community detection algorithms: a comparative analysis. Phys Rev E 80: 056117.
16. Meilǎ M, (2007) Comparing clusterings - an information based distance. J Multivar Anal 98: 873-895.
17. Pielou EC, (1966) The measurement of diversity in different types of biological collections. J Theor Biol 13: 131-144.
18. Pu SY, Wong J, Turner B, Cho E, Wodak SJ, (2009) Up-to-date catalogues of yeast protein complexes. Nucl Acids Res 37: 825-831.
19. Zachary WW, (1977) Information-flow model for conflict and fission in small-groups. J Anthropol Res 33: 452-473.
20. Freeman LC, (1993) Finding groups with a simple genetic algorithm. J Math Sociol 17: 227-241.
21. Lucas JI, Arnau V, Marín I, (2006) Comparative genomics and protein domain graph analyses link ubiquitination and RNA metabolism. J Mol Biol 357: 9-17.
22. Marco A, Marín I, (2009) Interactome and Gene Ontology provide congruent yet subtly different views of a eukaryotic cell. BMC Syst Biol 3: 69.
23. Rosvall M, Bergstrom CT, (2008) Maps of random walks on complex networks reveal community structure. Proc Natl Acad Sci USA 105: 1118-1123.
24. Ronhovde P, Nussinov Z, (2009) Multiresolution community detection for megascale networks by information-based replica correlations. Phys Rev E 80: 016109.
25. Blondel VD, Guillaume JL, Lambiotte R, Lefebvre E, (2008) Fast unfolding of communities in large networks. J Stat Mech P10008.
26. Duch J, Arenas A, (2005) Community detection in complex networks using Extremal Optimization. Phys Rev E 72: 027104.
27. MacArthur RH, (1957) On the relative abundance of bird species. Proc Nat Acad Sci USA 43: 293-295.
28. Newman MEJ, (2006) Modularity and community structure in networks. Proc Natl Acad Sci USA 103: 8577-8582.
29. Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, et al. (2008) The BioGRID interaction database: 2008 update. Nucl Acids Res 36: D637-D640.