-
1
-
-
33645830948
-
Cfinder: locating cliques and overlapping modules in biological networks
-
Adamcsek,B. et al. (2006) Cfinder: locating cliques and overlapping modules in biological networks. Bioinformatics, 22, 1021-1023.
-
(2006)
Bioinformatics
, vol.22
, pp. 1021-1023
-
-
Adamcsek, B.1
-
2
-
-
77955518815
-
Link communities reveal multiscale complexity in networks
-
Ahn,Y.Y. et al. (2010) Link communities reveal multiscale complexity in networks. Nature, 466, 761-764.
-
(2010)
Nature
, vol.466
, pp. 761-764
-
-
Ahn, Y.Y.1
-
3
-
-
33744805096
-
Development and implementation of an algorithm for detection of protein complexes in large interaction networks
-
Altaf-Ul-Amin,M. et al. (2006) Development and implementation of an algorithm for detection of protein complexes in large interaction networks. BMC Bioinformatics, 7, 207.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 207
-
-
Altaf-Ul-Amin, M.1
-
4
-
-
0034069495
-
Gene ontology: tool for the unification of biology
-
Ashburner,M. et al. (2000) Gene ontology: tool for the unification of biology. Nat Genet., 25, 25-29.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
-
5
-
-
34547852262
-
An ensemble framework for clustering protein-protein interaction networks
-
Asur,S. et al. (2007) An ensemble framework for clustering protein-protein interaction networks. Bioinformatics, 23, i29-i40.
-
(2007)
Bioinformatics
, vol.23
-
-
Asur, S.1
-
6
-
-
2942552459
-
An automated method for finding molecular complexes in large protein interaction networks
-
Bader,G. and Hogue,C. (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics, 4, 2.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 2
-
-
Bader, G.1
Hogue, C.2
-
7
-
-
33751255087
-
Evaluation of clustering algorithms for protein-protein interaction networks
-
Brohee,S. and Helden,J.V. (2006) Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics, 7, 488.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 488
-
-
Brohee, S.1
Helden, J.V.2
-
8
-
-
75149164017
-
A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles
-
Chin,C.H. et al. (2010) A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles. BMC Bioinformatics, 11(Suppl 1), S25.
-
(2010)
BMC Bioinformatics
, vol.11
, Issue.SUPPL. 1
-
-
Chin, C.H.1
-
9
-
-
0005924596
-
Graph clustering by flow simulation
-
PhD thesis, University of Utrecht, Netherlands
-
Dongen,S.V. (2000) Graph clustering by flow simulation. PhD thesis, University of Utrecht, Netherlands.
-
(2000)
-
-
Dongen, S.V.1
-
10
-
-
74049087026
-
Community detection in graphs
-
Fortunato,S. (2010) Community detection in graphs. Phys. Reports, 486, 75-174.
-
(2010)
Phys. Reports
, vol.486
, pp. 75-174
-
-
Fortunato, S.1
-
11
-
-
70349212097
-
Bootstrapping the interactome: unsupervised identification of protein complexes in yeast
-
Friedel,C.C. et al. (2009) Bootstrapping the interactome: unsupervised identification of protein complexes in yeast. J. Comput. Biol., 16, 971-987.
-
(2009)
J. Comput. Biol
, vol.16
, pp. 971-987
-
-
Friedel, C.C.1
-
12
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
Gavin,A.C. et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature, 440, 631-636.
-
(2006)
Nature
, vol.440
, pp. 631-636
-
-
Gavin, A.C.1
-
13
-
-
63549103226
-
Enumeration of condition-dependent dense modules in protein interaction networks
-
Georgii,E. et al. (2009) Enumeration of condition-dependent dense modules in protein interaction networks. Bioinformatics, 25, 933-940.
-
(2009)
Bioinformatics
, vol.25
, pp. 933-940
-
-
Georgii, E.1
-
14
-
-
65549157835
-
Finding overlapping communities using disjoint community detection algorithms
-
Complex Networks, Springer-Verlag, Berlin, Heidelberg
-
Gregory,S. (2009) Finding overlapping communities using disjoint community detection algorithms. Complex Networks, Springer-Verlag, Berlin, Heidelberg, 47-61.
-
(2009)
, pp. 47-61
-
-
Gregory, S.1
-
15
-
-
77951967208
-
Spici: a fast clustering algorithm for large biological networks
-
Jiang,P. and Singh,M. (2010) Spici: a fast clustering algorithm for large biological networks. Bioinformatics, 26, 1105-1111.
-
(2010)
Bioinformatics
, vol.26
, pp. 1105-1111
-
-
Jiang, P.1
Singh, M.2
-
16
-
-
33947712535
-
Wiphi: a weighted yeast interactome enriched for direct physical interactions
-
Kiemer,L. et al. (2007)Wiphi: a weighted yeast interactome enriched for direct physical interactions. Proteomics, 7, 932-943.
-
(2007)
Proteomics
, vol.7
, pp. 932-943
-
-
Kiemer, L.1
-
17
-
-
10244264813
-
Protein complex prediction via cost-based clustering
-
King,A.D. et al. (2004) Protein complex prediction via cost-based clustering. Bioinformatics, 20, 3013-3020.
-
(2004)
Bioinformatics
, vol.20
, pp. 3013-3020
-
-
King, A.D.1
-
18
-
-
33645453254
-
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
-
Krogan,N.J. et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature, 440, 637-643.
-
(2006)
Nature
, vol.440
, pp. 637-643
-
-
Krogan, N.J.1
-
19
-
-
59649099220
-
Predicting protein complexes from ppi data: a coreattachment approach
-
Leung,H.C.M. et al. (2009) Predicting protein complexes from ppi data: a coreattachment approach. J. Comput. Biol., 16, 133-144.
-
(2009)
J. Comput. Biol
, vol.16
, pp. 133-144
-
-
Leung, H.C.M.1
-
20
-
-
77954768699
-
The function of communities in protein interaction networks at multiple scales
-
Lewis,A. et al. (2010) The function of communities in protein interaction networks at multiple scales. BMC Syst. Biol., 4, 100.
-
(2010)
BMC Syst. Biol
, vol.4
, pp. 100
-
-
Lewis, A.1
-
21
-
-
54349096842
-
Modifying the dpclus algorithm for identifying protein complexes based on new topological structures
-
Li, M. et al. (2008) Modifying the dpclus algorithm for identifying protein complexes based on new topological structures. BMC Bioinformatics, 9, 398.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 398
-
-
Li, M.1
-
22
-
-
76749150479
-
Computational approaches for detecting protein complexes from protein interaction networks: a survey
-
Li,X. et al. (2010) Computational approaches for detecting protein complexes from protein interaction networks: a survey. BMC Genomics, 11(Suppl 1), S3.
-
(2010)
BMC Genomics
, vol.11
, Issue.SUPPL. 1
-
-
Li, X.1
-
23
-
-
38449114820
-
Discovering protein complexes in dense reliable neighborhoods of protein interaction networks
-
Li,X.L. et al. (2007) Discovering protein complexes in dense reliable neighborhoods of protein interaction networks. In Computational Systems Bioinformatics Conference, Vol. 6, pp. 157-168.
-
(2007)
In Computational Systems Bioinformatics Conference
, vol.6
, pp. 157-168
-
-
Li, X.L.1
-
24
-
-
33846681448
-
Modular organization of protein interaction networks
-
Luo,F. (2007) Modular organization of protein interaction networks. Bioinformatics, 23, 207.
-
(2007)
Bioinformatics
, vol.23
, pp. 207
-
-
Luo, F.1
-
25
-
-
70349754527
-
RRW: repeated random walks on genome-scale protein networks for local cluster discovery
-
Macropol,K. (2009) RRW: repeated random walks on genome-scale protein networks for local cluster discovery. BMC bioinformatics, 10, 283.
-
(2009)
BMC bioinformatics
, vol.10
, pp. 283
-
-
Macropol, K.1
-
26
-
-
80054022389
-
NWE: node-weighted expansion for protein complex prediction using random walk distances
-
Maruyama,O. and Chihara,A. (2011) NWE: node-weighted expansion for protein complex prediction using random walk distances. Proteome Sci., 9(Suppl 1), S14.
-
(2011)
Proteome Sci.
, vol.9
, Issue.SUPPL. 1
-
-
Maruyama, O.1
Chihara, A.2
-
28
-
-
33745957596
-
Inferring protein-protein interactions using interaction network topologies
-
Paccanaro,A. et al. (2005) Inferring protein-protein interactions using interaction network topologies. In IJCNN, Vol.1, pp. 161-166.
-
(2005)
In IJCNN
, vol.1
, pp. 161-166
-
-
Paccanaro, A.1
-
29
-
-
0346156102
-
Detection of functional modules from protein interaction networks
-
PereiraLeal,J.B. et al. (2004) Detection of functional modules from protein interaction networks. PROTEINS: Struct Funct Bioinform, 54, 49-57.
-
(2004)
PROTEINS: Struct Funct Bioinform
, vol.54
, pp. 49-57
-
-
PereiraLeal, J.B.1
-
30
-
-
0347755535
-
The database of interacting proteins: 2004 update
-
Salwinski,L. et al. (2004) The database of interacting proteins: 2004 update. Nucleic Acids Res., 32(Suppl 1), D449-D451.
-
(2004)
Nucleic Acids Res.
, vol.32
, Issue.SUPPL. 1
-
-
Salwinski, L.1
-
31
-
-
70350647698
-
Scalable graph clustering using stochastic flows: applications to community discovery
-
Satuluri,V. and Parthasarathy,S. (2009) Scalable graph clustering using stochastic flows: applications to community discovery. In Proceedings of SIGKDD, ACM, pp. 737-746.
-
(2009)
In Proceedings of SIGKDD, ACM
, pp. 737-746
-
-
Satuluri, V.1
Parthasarathy, S.2
-
33
-
-
77952994540
-
Refining markov clustering for protein complex prediction by incorporating core-attachment structure
-
Srihari,S. et al. (2009) Refining markov clustering for protein complex prediction by incorporating core-attachment structure. Genome Inform. Series, 23, 159-168.
-
(2009)
Genome Inform. Series
, vol.23
, pp. 159-168
-
-
Srihari, S.1
-
34
-
-
78651328883
-
The biogrid interaction database: 2011 update
-
Stark,C. et al. (2011) The biogrid interaction database: 2011 update. Nucleic Acids Res., 39(Suppl 1), D698.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.SUPPL. 1
-
-
Stark, C.1
-
35
-
-
33750325308
-
Improving functional modularity in protein-protein interactions graphs using hub-induced subgraphs
-
Ucar,D. et al. (2006) Improving functional modularity in protein-protein interactions graphs using hub-induced subgraphs. In PKDD, pp. 371-382.
-
(2006)
In PKDD
, pp. 371-382
-
-
Ucar, D.1
-
36
-
-
65849100458
-
Markov clustering versus affinity propagation for the partitioning of protein interaction graphs
-
Vlasblom,J. andWodak,S. (2009) Markov clustering versus affinity propagation for the partitioning of protein interaction graphs. BMC Bioinformatics, 10, 99.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 99
-
-
Vlasblom, J.1
Wodak, S.2
-
37
-
-
79952841798
-
A fast hierarchical clustering algorithm for functional modules discovery in protein interaction networks
-
Wang,J. et al. (2011) A fast hierarchical clustering algorithm for functional modules discovery in protein interaction networks. IEEE/ACM Trans. Comput. Biol. Bioinformatics, 8, 607-620.
-
(2011)
IEEE/ACM Trans. Comput. Biol. Bioinformatics
, vol.8
, pp. 607-620
-
-
Wang, J.1
-
38
-
-
67649518162
-
A core-attachment based method to detect protein complexes in ppi networks
-
Wu,M. et al. (2009) A core-attachment based method to detect protein complexes in ppi networks. BMC Bioinformatics, 10, 169.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 169
-
-
Wu, M.1
|