-
1
-
-
0037161731
-
Comparative assessment of large-scale data sets of protein-protein interactions
-
12000970
-
von Mering C, Krause R, Sne B, et al. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417(6887):399-403. 12000970.
-
(2002)
Nature
, vol.417
, Issue.6887
, pp. 399-403
-
-
von Mering, C.1
Krause, R.2
Sne, B.3
-
2
-
-
34249945479
-
Specificity in protein interactions and its relationship with sequence diversity and coevolution
-
1876561, 17468399
-
Hakes L, Lovell SC, Oliver SG, et al. Specificity in protein interactions and its relationship with sequence diversity and coevolution. PNAS 2007, 104(19):7999-8004. 1876561, 17468399.
-
(2007)
PNAS
, vol.104
, Issue.19
, pp. 7999-8004
-
-
Hakes, L.1
Lovell, S.C.2
Oliver, S.G.3
-
4
-
-
0035799707
-
Lethality and centrality in protein networks
-
Jeong H, Mason S, Barabási AL, et al. Lethality and centrality in protein networks. Nature 2001, 411(6833):41-42.
-
(2001)
Nature
, vol.411
, Issue.6833
, pp. 41-42
-
-
Jeong, H.1
Mason, S.2
Barabási, A.L.3
-
5
-
-
0345600247
-
A protein interaction map of Drosophila melanogaster
-
Giot L, et al. A protein interaction map of Drosophila melanogaster. Science 2003, 302:1727-1736.
-
(2003)
Science
, vol.302
, pp. 1727-1736
-
-
Giot, L.1
-
6
-
-
9144264169
-
A map of the interactome network of the metazoan
-
1698949, 14704431
-
Li S, Armstrong C, Bertin N. A map of the interactome network of the metazoan. Science 2004, 303(5657):540-543. 1698949, 14704431.
-
(2004)
Science
, vol.303
, Issue.5657
, pp. 540-543
-
-
Li, S.1
Armstrong, C.2
Bertin, N.3
-
7
-
-
0034887573
-
Scale-free behavior in protein domain networks
-
Wuchty S. Scale-free behavior in protein domain networks. Mollecular Biology and Evolution 2001, 18(9):1694-1702.
-
(2001)
Mollecular Biology and Evolution
, vol.18
, Issue.9
, pp. 1694-1702
-
-
Wuchty, S.1
-
8
-
-
12944331889
-
Small-world network approach to identify key residues in protein-protein interaction
-
del Sol A, O'Meara P. Small-world network approach to identify key residues in protein-protein interaction. Proteins 2004, 58(3):672-682.
-
(2004)
Proteins
, vol.58
, Issue.3
, pp. 672-682
-
-
del Sol, A.1
O'Meara, P.2
-
9
-
-
17444396776
-
Topology of small-world networks of protein-protein complex structures
-
del Sol A, Fujihashi H, O'Meara P. Topology of small-world networks of protein-protein complex structures. Bioinformatics 2005, 21(8):1311-131.
-
(2005)
Bioinformatics
, vol.21
, Issue.8
, pp. 1311-2131
-
-
del Sol, A.1
Fujihashi, H.2
O'Meara, P.3
-
10
-
-
33751255087
-
Evaluation of clustering algorithms for protein-protein interaction networks
-
1397874, 16448555
-
Brohée S, van Helden J. Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 2006, 7:48. 1397874, 16448555.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 48
-
-
Brohée, S.1
van Helden, J.2
-
11
-
-
0142059836
-
Protein complexes and functional modules in molecular networks
-
218723, 14517352
-
Spirin V, Mirny LA. Protein complexes and functional modules in molecular networks. PNAS 2003, 100:12123-12128. 218723, 14517352.
-
(2003)
PNAS
, vol.100
, pp. 12123-12128
-
-
Spirin, V.1
Mirny, L.A.2
-
12
-
-
0038074373
-
Topological structure analysis of the protein-protein interaction network in budding yeast
-
154226, 12711690
-
Bu D, Zhao Y, Cai L, et al. Topological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Research 2003, 31(9):2443-2450. 154226, 12711690.
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.9
, pp. 2443-2450
-
-
Bu, D.1
Zhao, Y.2
Cai, L.3
-
13
-
-
42949105070
-
An Algorithm for Finding Functional Modules and Protein Complexes in Protein-Protein Interaction Networks
-
doi:10.1155/2008/86027
-
Cui G, Chen Y, Huang DS, Han K. An Algorithm for Finding Functional Modules and Protein Complexes in Protein-Protein Interaction Networks. Journal of Biomedicine and Biotechnology 2008, 1-10. doi:10.1155/2008/86027.
-
(2008)
Journal of Biomedicine and Biotechnology
, pp. 1-10
-
-
Cui, G.1
Chen, Y.2
Huang, D.S.3
Han, K.4
-
14
-
-
15944412875
-
Identification of functional modules in protein complexes via hyperclique pattern discovery
-
Xiong H, He X, Ding C, et al. Identification of functional modules in protein complexes via hyperclique pattern discovery. Pacific Symposium on Biocomputing 2005, 10:221-232.
-
(2005)
Pacific Symposium on Biocomputing
, vol.10
, pp. 221-232
-
-
Xiong, H.1
He, X.2
Ding, C.3
-
15
-
-
2942552459
-
An Automated method for finding molecular complexes in large protein interaction networks
-
149346, 12525261
-
Bader GD, Hogue CW. An Automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4:2. 149346, 12525261.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 2
-
-
Bader, G.D.1
Hogue, C.W.2
-
16
-
-
33845955474
-
Inferring topology from clustering coefficients in protein-protein interaction networks
-
1361790, 16401345
-
Friedel C, Zimmer R. Inferring topology from clustering coefficients in protein-protein interaction networks. BMC Bioinformatics 2006, 7-519. 1361790, 16401345.
-
(2006)
BMC Bioinformatics
, pp. 7-519
-
-
Friedel, C.1
Zimmer, R.2
-
17
-
-
78649679358
-
-
http://www.cytoscape.org/
-
-
-
-
18
-
-
33749541272
-
Prediction of protein complexes based on protein interaction data and functional annotation data using kernel methods
-
Zhang S, Ning X, Liu H, Zhang X. Prediction of protein complexes based on protein interaction data and functional annotation data using kernel methods. ICIC 2006, Lecture Notes in Bioinformatics 4115:514-524.
-
ICIC 2006, Lecture Notes in Bioinformatics
, vol.4115
, pp. 514-524
-
-
Zhang, S.1
Ning, X.2
Liu, H.3
Zhang, X.4
-
19
-
-
38449101120
-
Integration of biological networks and gene expression data using Cytoscape
-
Cline MS, Smoot M, Cerami E, et al. Integration of biological networks and gene expression data using Cytoscape. NatProtoc 2007, 2(10):2366-2382.
-
(2007)
NatProtoc
, vol.2
, Issue.10
, pp. 2366-2382
-
-
Cline, M.S.1
Smoot, M.2
Cerami, E.3
-
20
-
-
38849128078
-
Identifying protein complexes directly from high-throughput TAP data with Markov random fields
-
2222659, 18093306
-
Rungsarityotin W, Krause R, Schödl A, Schliep A. Identifying protein complexes directly from high-throughput TAP data with Markov random fields. BMC Bioinformatics 2007, 8:482. 2222659, 18093306.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 482
-
-
Rungsarityotin, W.1
Krause, R.2
Schödl, A.3
Schliep, A.4
-
21
-
-
33744805096
-
Development and implementation of an algorithm for detection of protein complexes in large interaction networks
-
1473204, 16613608
-
Altaf-UI-Amin M, Shinbo Y, Mihara K, et al. Development and implementation of an algorithm for detection of protein complexes in large interaction networks. BMC Bioinformatics 2006, 7:207. 1473204, 16613608.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 207
-
-
Altaf-UI-Amin, M.1
Shinbo, Y.2
Mihara, K.3
-
22
-
-
54349096842
-
Modifying the DPClus algorithm for identifying protein complexes based on new topological structures
-
2570695, 18816408
-
Li M, Chen J, Wang JX, et al. Modifying the DPClus algorithm for identifying protein complexes based on new topological structures. BMC Bioinformatics 2008, 9:398. 2570695, 18816408.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 398
-
-
Li, M.1
Chen, J.2
Wang, J.X.3
-
23
-
-
1842580761
-
A Functional and topological characterization of protein interaction networks
-
Yook S, Oltvai Z, Barabási. A Functional and topological characterization of protein interaction networks. Proteomics 2004, 4(4):928-942.
-
(2004)
Proteomics
, vol.4
, Issue.4
, pp. 928-942
-
-
Yook, S.1
Oltvai, Z.2
Barabási3
-
24
-
-
33144462588
-
Hierarchical Structure of the Protein-Protein Interaction Networks
-
Ng K, Lee P, Huang C, Fang J, Hsiao H, Tsai J. Hierarchical Structure of the Protein-Protein Interaction Networks. CHINESE JOURNAL OF PHYSICS 2006, 44(1):67-77.
-
(2006)
CHINESE JOURNAL OF PHYSICS
, vol.44
, Issue.1
, pp. 67-77
-
-
Ng, K.1
Lee, P.2
Huang, C.3
Fang, J.4
Hsiao, H.5
Tsai, J.6
-
25
-
-
0037442317
-
The topology of the transcriptional regulatory network in the yeast
-
Farkas I, Jeong H, Viscek T, Barabasi A, Oltvai Z. The topology of the transcriptional regulatory network in the yeast. S. cerevisiae. Physica A 2003, 318:601-612.
-
(2003)
S. cerevisiae. Physica A
, vol.318
, pp. 601-612
-
-
Farkas, I.1
Jeong, H.2
Viscek, T.3
Barabasi, A.4
Oltvai, Z.5
-
26
-
-
78649649061
-
The betweenness centrality of biological networks. Master of Science in Computer Science
-
September 16
-
Narayanan S. The betweenness centrality of biological networks. Master of Science in Computer Science. Virginia Polytechnic Institute and State University 2005, September 16.
-
(2005)
Virginia Polytechnic Institute and State University
-
-
Narayanan, S.1
-
27
-
-
0037062448
-
Community structure in social and biological networks
-
122977, 12060727
-
Girvan M, Newman M. Community structure in social and biological networks. PNAS 2002, 99:7821-7826. 122977, 12060727.
-
(2002)
PNAS
, vol.99
, pp. 7821-7826
-
-
Girvan, M.1
Newman, M.2
-
28
-
-
37649028224
-
Finding and evaluating community structure in networks
-
Newman M, Girvan M. Finding and evaluating community structure in networks. Physical Review E 2004, 69(2):1-16.
-
(2004)
Physical Review E
, vol.69
, Issue.2
, pp. 1-16
-
-
Newman, M.1
Girvan, M.2
-
29
-
-
1542357701
-
Defining and identifying communities in networks
-
365677, 14981240
-
Radicchi F, Castellano C, Cecconi F. Defining and identifying communities in networks. PNAS 2004, 101(9):2658-2663. 365677, 14981240.
-
(2004)
PNAS
, vol.101
, Issue.9
, pp. 2658-2663
-
-
Radicchi, F.1
Castellano, C.2
Cecconi, F.3
-
30
-
-
33748701649
-
Detecting functional modules in the yeast protein-protein interaction network
-
Chen JC, Yuan B. Detecting functional modules in the yeast protein-protein interaction network. Bioinformatics 2006, 22(18):2283-229.
-
(2006)
Bioinformatics
, vol.22
, Issue.18
, pp. 2283-3229
-
-
Chen, J.C.1
Yuan, B.2
-
31
-
-
33846681448
-
Modular organization of protein interaction networks
-
Luo F, Yang Y, Chen CF, et al. Modular organization of protein interaction networks. Bioinformatics 2007, 23(2):207-214.
-
(2007)
Bioinformatics
, vol.23
, Issue.2
, pp. 207-214
-
-
Luo, F.1
Yang, Y.2
Chen, C.F.3
-
32
-
-
25444490121
-
The use of edge-betweenness clustering to investigate biological function in protein interaction networks
-
555937, 15740614
-
Ruth D, Frank D, Christopher M. The use of edge-betweenness clustering to investigate biological function in protein interaction networks. BMC Bioinformatics 2005, 6:39. 555937, 15740614.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 39
-
-
Ruth, D.1
Frank, D.2
Christopher, M.3
-
33
-
-
43049151837
-
Hierarchical structure and the prediction of missing links in networks
-
Clauset A, Moore C, Newman M. Hierarchical structure and the prediction of missing links in networks. Nature 2008, 453:98-101.
-
(2008)
Nature
, vol.453
, pp. 98-101
-
-
Clauset, A.1
Moore, C.2
Newman, M.3
-
34
-
-
38049081211
-
Betweenness-based decomposition methods for social and biological networks
-
Leeds, Leeds University Press, Barber S, Baxter PD, Mardia KV, &Walls RE
-
Pinney J, Westhead D. Betweenness-based decomposition methods for social and biological networks. Interdisciplinary Statistics and Bioinformatics 2006, 87-90. Leeds, Leeds University Press, Barber S, Baxter PD, Mardia KV, &Walls RE.
-
(2006)
Interdisciplinary Statistics and Bioinformatics
, pp. 87-90
-
-
Pinney, J.1
Westhead, D.2
-
36
-
-
38049036713
-
A parallel edge-betweenness clustering tool for protein-protein interaction networks
-
Yang Q, Lonardi S. A parallel edge-betweenness clustering tool for protein-protein interaction networks. International Journal of Data Mining and Bioinformatics 2007, 1(3):241-247.
-
(2007)
International Journal of Data Mining and Bioinformatics
, vol.1
, Issue.3
, pp. 241-247
-
-
Yang, Q.1
Lonardi, S.2
-
37
-
-
17444396776
-
Topology of small-world networks of protein-protein complex structures
-
del Sol A, Fujihashi H, O'Meara P. Topology of small-world networks of protein-protein complex structures. Bioinformatics 2005, 21(8):1311-1315.
-
(2005)
Bioinformatics
, vol.21
, Issue.8
, pp. 1311-1315
-
-
del Sol, A.1
Fujihashi, H.2
O'Meara, P.3
-
38
-
-
33947619951
-
Graph theory and networks in biology
-
Mason O, Verwoerd M. Graph theory and networks in biology. IET Systems Biology 2006, 1(2):89-119.
-
(2006)
IET Systems Biology
, vol.1
, Issue.2
, pp. 89-119
-
-
Mason, O.1
Verwoerd, M.2
-
40
-
-
67650160441
-
Hierarchical organization of functional modules in weighted protein interaction networks using clustering coefficient
-
LNBI 5542
-
Li M, Wang JX, Chen J, Pan Y. Hierarchical organization of functional modules in weighted protein interaction networks using clustering coefficient. ISBRA2009 75-86. LNBI 5542.
-
ISBRA2009
, pp. 75-86
-
-
Li, M.1
Wang, J.X.2
Chen, J.3
Pan, Y.4
-
41
-
-
40449109730
-
Consistent dissection of the protein interaction network by combining global and local metrics
-
2246273, 18154653
-
Wang C, Ding C, Yang Q, Holbrook SR. Consistent dissection of the protein interaction network by combining global and local metrics. Genome Biology 2007, 8:R271. 2246273, 18154653.
-
(2007)
Genome Biology
, vol.8
-
-
Wang, C.1
Ding, C.2
Yang, Q.3
Holbrook, S.R.4
-
42
-
-
0034515528
-
A clustering algorithm based graph connectivity
-
Hartuv E, Shamir R. A clustering algorithm based graph connectivity. Information Processing Letters 2000, 76:175-181.
-
(2000)
Information Processing Letters
, vol.76
, pp. 175-181
-
-
Hartuv, E.1
Shamir, R.2
-
43
-
-
1342330546
-
Functional topology in a network of protein interactions
-
Pržulj N, Wigle DA, Jurisica I. Functional topology in a network of protein interactions. Bioinformatics 2004, 20(3):340-348.
-
(2004)
Bioinformatics
, vol.20
, Issue.3
, pp. 340-348
-
-
Pržulj, N.1
Wigle, D.A.2
Jurisica, I.3
-
44
-
-
13844264514
-
Iterative cluster analysis of protein interaction data
-
Arnau V, Mars S, Marín I. Iterative cluster analysis of protein interaction data. Bioinformatics 2005, 21:364-378.
-
(2005)
Bioinformatics
, vol.21
, pp. 364-378
-
-
Arnau, V.1
Mars, S.2
Marín, I.3
-
45
-
-
4444281384
-
The interactome as a tree: an attempt to visualize the protein-protein interaction network in yeast,
-
519110, 15356297
-
Lu H, Zhu X, Liu H, Skogerbo G, Zhang J, Zhang Y, Cai L, Zhao Y, Sun S, Xu J, Bu D, Chen R. The interactome as a tree: an attempt to visualize the protein-protein interaction network in yeast,. Nucleic Acids Res 2004, 32(No. 16):4804-4811. 519110, 15356297.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.16
, pp. 4804-4811
-
-
Lu, H.1
Zhu, X.2
Liu, H.3
Skogerbo, G.4
Zhang, J.5
Zhang, Y.6
Cai, L.7
Zhao, Y.8
Sun, S.9
Xu, J.10
Bu, D.11
Chen, R.12
-
46
-
-
55949137146
-
Clustering complex networks and biological networks by nonnegative matrix factorization with various similarity measures
-
Wang RS, Zhang SH, Wang Y, et al. Clustering complex networks and biological networks by nonnegative matrix factorization with various similarity measures. Neurocomputing 2008, 72:134-141.
-
(2008)
Neurocomputing
, vol.72
, pp. 134-141
-
-
Wang, R.S.1
Zhang, S.H.2
Wang, Y.3
-
47
-
-
67349144761
-
On the similarity metric and the distance metric
-
Chen S, Ma B, Zhang K. On the similarity metric and the distance metric. Theoretical Computer Science 2009, 410:2365-2376.
-
(2009)
Theoretical Computer Science
, vol.410
, pp. 2365-2376
-
-
Chen, S.1
Ma, B.2
Zhang, K.3
-
48
-
-
34548511546
-
Semantic integration to identify overlapping functional modules in protein interaction networks
-
1971074, 17650343
-
Cho YR, Hwang W, Ramanmathan M, Zhang AD. Semantic integration to identify overlapping functional modules in protein interaction networks. BMC Bioinformatics 2007, 8:265. 1971074, 17650343.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 265
-
-
Cho, Y.R.1
Hwang, W.2
Ramanmathan, M.3
Zhang, A.D.4
-
49
-
-
10244264813
-
Protein complex prediction via cost-based clustering
-
King AD, Pržulj N, Jurisica I. Protein complex prediction via cost-based clustering. Bioinformatics 2004, 20(17):3013-302.
-
(2004)
Bioinformatics
, vol.20
, Issue.17
, pp. 3013-3302
-
-
King, A.D.1
Pržulj, N.2
Jurisica, I.3
-
50
-
-
14644396645
-
Functional cartography of complex metabolic networks
-
2175124, 15729348
-
Guimera R, Amaral Nunes LA. Functional cartography of complex metabolic networks. Nature 2005, 433:895-900. 2175124, 15729348.
-
(2005)
Nature
, vol.433
, pp. 895-900
-
-
Guimera, R.1
Amaral Nunes, L.A.2
-
51
-
-
26244464025
-
Comparing community structure identification
-
P09008, 2151742, 18159217
-
Danon L, Díaz-Guilera A, Duch J, Arenas A. Comparing community structure identification. Journal of Statistical Mechanics 2005, 2005(9). P09008, 2151742, 18159217.
-
(2005)
Journal of Statistical Mechanics
, vol.2005
, Issue.9
-
-
Danon, L.1
Díaz-Guilera, A.2
Duch, J.3
Arenas, A.4
-
52
-
-
36348985751
-
Maximizing Modularity is hard
-
e-print arXiv:physics/0608255
-
Brandes U, Delling D, Gaertler M, et al. Maximizing Modularity is hard. e-print arXiv:physics/0608255.
-
-
-
Brandes, U.1
Delling, D.2
Gaertler, M.3
-
53
-
-
41349117788
-
Finding community structure in very large networks
-
066111
-
Clauset A, Newman M, Moore C. Finding community structure in very large networks. Phys. Rev. E 2004, 70. 066111.
-
(2004)
Phys. Rev. E
, vol.70
-
-
Clauset, A.1
Newman, M.2
Moore, C.3
-
54
-
-
27244441304
-
Community detection in complex networks using extreme optimization
-
027104
-
Duch J, Arenas A. Community detection in complex networks using extreme optimization. Physical Review E 2005, 72. 027104.
-
(2005)
Physical Review E
, vol.72
-
-
Duch, J.1
Arenas, A.2
-
55
-
-
33745012299
-
Modularity and community structure in networks
-
1482622, 16723398
-
Newman. Modularity and community structure in networks. PNAS 2006, 103(23):8577-8582. 1482622, 16723398.
-
(2006)
PNAS
, vol.103
, Issue.23
, pp. 8577-8582
-
-
Newman1
-
57
-
-
78649648529
-
Identifying network communities with high resolution
-
Ruan JH, Zhang WX. Identifying network communities with high resolution. Physical Review E 2007, 4:1-14.
-
(2007)
Physical Review E
, vol.4
, pp. 1-14
-
-
Ruan, J.H.1
Zhang, W.X.2
-
58
-
-
34248397539
-
A novel functional module detection algorithm for protein-protein interaction networks
-
1764415, 17147822
-
Hwang W, Cho Y, Zhang A. A novel functional module detection algorithm for protein-protein interaction networks. Algorithms for Molecular Biology 2006, 1:24. 1764415, 17147822.
-
(2006)
Algorithms for Molecular Biology
, vol.1
, pp. 24
-
-
Hwang, W.1
Cho, Y.2
Zhang, A.3
-
59
-
-
39749149026
-
CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions
-
2253513, 18230159
-
Hwang W, Cho Y, Zhang A. CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions. BMC Bioinformatics 2008, 9:64. 2253513, 18230159.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 64
-
-
Hwang, W.1
Cho, Y.2
Zhang, A.3
-
61
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
101833, 11917018
-
Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Research 2002, 30(7):1575-1584. 101833, 11917018.
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.7
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
62
-
-
0346156102
-
Detection of functional modules from protein interaction networks
-
Pereira-Leal J, Enright A, Ouzounis C. Detection of functional modules from protein interaction networks. PROTEINS: Structure, Function, and Bioinformatics 2004, 54:49-57.
-
(2004)
PROTEINS: Structure, Function, and Bioinformatics
, vol.54
, pp. 49-57
-
-
Pereira-Leal, J.1
Enright, A.2
Ouzounis, C.3
-
63
-
-
65849100458
-
Markov clustering versus affinity propagation for the partitioning of protein interaction graphs
-
2682798, 19331680
-
Vlasblom J, Wodak SJ. Markov clustering versus affinity propagation for the partitioning of protein interaction graphs. BMC Bioinformatics 2009, 10:99. 2682798, 19331680.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 99
-
-
Vlasblom, J.1
Wodak, S.J.2
-
65
-
-
49649104565
-
A structural approach for finding functional modules from large biological networks
-
Mete M, Tang F, Xu X, Yuruk N. A structural approach for finding functional modules from large biological networks. BMC Bioinformatics 2008 9(Suppl 9):S19.
-
BMC Bioinformatics 2008
, vol.9
, Issue.SUPPL 9
-
-
Mete, M.1
Tang, F.2
Xu, X.3
Yuruk, N.4
-
66
-
-
65449131622
-
Core and periphery structures in protein interaction networks
-
2681073, 19426456
-
Luo F, Li B, Wan XF, Scheuermann RH. Core and periphery structures in protein interaction networks. BMC Bioinformatics 2009, 10(Suppl 4):S8. 2681073, 19426456.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.SUPPL 4
-
-
Luo, F.1
Li, B.2
Wan, X.F.3
Scheuermann, R.H.4
-
69
-
-
20444504323
-
Uncoverring the overlapping community structure of complex networks in nature and society
-
Palla G, Dernyi I, Farkas I, et al. Uncoverring the overlapping community structure of complex networks in nature and society. Nature 2005, 435(7043):814-818.
-
(2005)
Nature
, vol.435
, Issue.7043
, pp. 814-818
-
-
Palla, G.1
Dernyi, I.2
Farkas, I.3
-
70
-
-
33645830948
-
CFinder: locating cliques and overlapping modules in biological networks
-
Adamcsek B, Palla G, Farkas I, et al. CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics 2006, 22(8):1021-1023.
-
(2006)
Bioinformatics
, vol.22
, Issue.8
, pp. 1021-1023
-
-
Adamcsek, B.1
Palla, G.2
Farkas, I.3
-
71
-
-
30644463216
-
Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastatis
-
Jonsson P, Cavanna T, Zicha D, Bates P. Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastatis. BMC Bioinformmatics 2006, 7:2.
-
(2006)
BMC Bioinformmatics
, vol.7
, pp. 2
-
-
Jonsson, P.1
Cavanna, T.2
Zicha, D.3
Bates, P.4
-
72
-
-
33751229605
-
Identification of functional modules in a PPI network by clique percolation clustering
-
Zhang S, Ning X, Zhang X. Identification of functional modules in a PPI network by clique percolation clustering. Computational Biology and Chemistry 2006, 30:445-451.
-
(2006)
Computational Biology and Chemistry
, vol.30
, pp. 445-451
-
-
Zhang, S.1
Ning, X.2
Zhang, X.3
-
74
-
-
33645761859
-
Fast and accurate method for identifying high-quality protein-interaction modules by clique merging and its application to yeast
-
Zhang C, Liu S, Zhou Y. Fast and accurate method for identifying high-quality protein-interaction modules by clique merging and its application to yeast. J Proteome Res 2006, 5(4):801-7.
-
(2006)
J Proteome Res
, vol.5
, Issue.4
, pp. 801-807
-
-
Zhang, C.1
Liu, S.2
Zhou, Y.3
-
75
-
-
33748579201
-
Interaction Graph mining for protein complexes using local clique merging
-
Li XL, Tan SH, Foo CS, et al. Interaction Graph mining for protein complexes using local clique merging. Genome Informatics 2005, 16:260-269.
-
(2005)
Genome Informatics
, vol.16
, pp. 260-269
-
-
Li, X.L.1
Tan, S.H.2
Foo, C.S.3
-
76
-
-
38449114820
-
Discovering protein complexes in dense reliable neighborhoods of protein interaction networks
-
August
-
Li XL, Foo CS, Ng SK. Discovering protein complexes in dense reliable neighborhoods of protein interaction networks. Proc LSS Comput Syst Bioinform Conf 2007, 6:157-168. August.
-
(2007)
Proc LSS Comput Syst Bioinform Conf
, vol.6
, pp. 157-168
-
-
Li, X.L.1
Foo, C.S.2
Ng, S.K.3
-
77
-
-
34248396293
-
Decomposition of overlapping protein complexes a graph theoretical method for analyzing static and dynamic protein association
-
1481596, 16722537
-
Zotenko E, Guimarães K, Jothi R. Decomposition of overlapping protein complexes a graph theoretical method for analyzing static and dynamic protein association. Algorithms for Molecular Biology 2006, 1:7. 1481596, 16722537.
-
(2006)
Algorithms for Molecular Biology
, vol.1
, pp. 7
-
-
Zotenko, E.1
Guimarães, K.2
Jothi, R.3
-
78
-
-
41549118299
-
The intersection graphs of subtrees in trees are exactly the chordal graphs
-
Gavril F. The intersection graphs of subtrees in trees are exactly the chordal graphs. Journal of Combinatorial Theory (B) 1974, 16:47-56.
-
(1974)
Journal of Combinatorial Theory (B)
, vol.16
, pp. 47-56
-
-
Gavril, F.1
-
81
-
-
33947109414
-
A seed-refine algorithm for detecting protein complexes from protein interaction data
-
Pei P, Zhang A. A seed-refine algorithm for detecting protein complexes from protein interaction data. IEEE Transactions on Nanobioscience 2007, 6(1):43-50.
-
(2007)
IEEE Transactions on Nanobioscience
, vol.6
, Issue.1
, pp. 43-50
-
-
Pei, P.1
Zhang, A.2
-
83
-
-
13444282425
-
The Stanford Microarray Database accommodates additional microarray platforms and data formats
-
Ball CA, et al. The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acid Research 2005, 33:D580-D582.
-
(2005)
Nucleic Acid Research
, vol.33
-
-
Ball, C.A.1
-
85
-
-
33751166180
-
Identification of overlapping community structure in complex networks using fuzzy c-means clustering
-
Zhang S, Wang RS, Zhang XS. Identification of overlapping community structure in complex networks using fuzzy c-means clustering. PHYSICA 374(1).
-
PHYSICA
, vol.374
, Issue.1
-
-
Zhang, S.1
Wang, R.S.2
Zhang, X.S.3
-
86
-
-
59449103335
-
Detect overlapping and hierarchical community structure in networks
-
Shen H, Cheng X, Cai K, Hu MB. Detect overlapping and hierarchical community structure in networks. Physica A 2009, 388:1706-1712.
-
(2009)
Physica A
, vol.388
, pp. 1706-1712
-
-
Shen, H.1
Cheng, X.2
Cai, K.3
Hu, M.B.4
-
87
-
-
64549145094
-
Detecting the overlapping and hierarchical community structure in complex networks
-
Lancichinetti A, Fortunato S, Kertesz J. Detecting the overlapping and hierarchical community structure in complex networks. New Journal of Physics 2009, 11:1-17.
-
(2009)
New Journal of Physics
, vol.11
, pp. 1-17
-
-
Lancichinetti, A.1
Fortunato, S.2
Kertesz, J.3
-
89
-
-
25444434087
-
AVID: an integrative framework for discovering functional relationships among proteins
-
1177925, 15929793
-
Jiang T, Keating AE. AVID: an integrative framework for discovering functional relationships among proteins. BMC Bioinformatics 2005, 6:136. 1177925, 15929793.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 136
-
-
Jiang, T.1
Keating, A.E.2
-
90
-
-
39649083998
-
Integration of genomic data for inferring protein complexes from global protein-protein interaction networks
-
Man AND Cybernetics-Part B
-
Zheng H, Wang H, Glass DH. Integration of genomic data for inferring protein complexes from global protein-protein interaction networks. IEEE Transactions on Systems 2008, 38(1):5-16. Man AND Cybernetics-Part B.
-
(2008)
IEEE Transactions on Systems
, vol.38
, Issue.1
, pp. 5-16
-
-
Zheng, H.1
Wang, H.2
Glass, D.H.3
-
91
-
-
41349108025
-
From pull-down data to protein interaction networks and complexes with biological relevance
-
Zhang B, Park BH, Karpinets T, Samatova NF. From pull-down data to protein interaction networks and complexes with biological relevance. 2008, 24(7):979-986.
-
(2008)
, vol.24
, Issue.7
, pp. 979-986
-
-
Zhang, B.1
Park, B.H.2
Karpinets, T.3
Samatova, N.F.4
-
92
-
-
46249128543
-
Identifying functional modules in protein-protein interaction networks: an integrated exact approach
-
Jul 1, 2718639, 18586718
-
Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Müller T. Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics 2008, 24(13):i223-31. Jul 1, 2718639, 18586718.
-
(2008)
Bioinformatics
, vol.24
, Issue.13
-
-
Dittrich, M.T.1
Klau, G.W.2
Rosenwald, A.3
Dandekar, T.4
Müller, T.5
-
93
-
-
67649568100
-
Protein complex prediction based on mutually exclusive interactions in protein interaction network
-
Jung SH, Jang W, Hur H, Hyun B, Han D. Protein complex prediction based on mutually exclusive interactions in protein interaction network. Genome Informatics 2008, 21:77-88.
-
(2008)
Genome Informatics
, vol.21
, pp. 77-88
-
-
Jung, S.H.1
Jang, W.2
Hur, H.3
Hyun, B.4
Han, D.5
-
94
-
-
0036141992
-
Relating whole-genome expression data with protein-protein interactions
-
155252, 11779829
-
Jansen R, Greenbaum D, Gerstein M. Relating whole-genome expression data with protein-protein interactions. Genome Research 2002, 12:37-46. 155252, 11779829.
-
(2002)
Genome Research
, vol.12
, pp. 37-46
-
-
Jansen, R.1
Greenbaum, D.2
Gerstein, M.3
-
96
-
-
0000801240
-
Discovering regulatory and signalling circuits in molecular interaction networks
-
Ideker T, Ozier O, Schwikowski B, Siegel AF. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 2002, 18:S233-S240.
-
(2002)
Bioinformatics
, vol.18
-
-
Ideker, T.1
Ozier, O.2
Schwikowski, B.3
Siegel, A.F.4
-
97
-
-
34548742517
-
Identification of functional modules using network topology and high-throughput data
-
1839897, 17408515
-
Ulitsky I, Shamir R. Identification of functional modules using network topology and high-throughput data. BMC Systems Biology 2007, 1:8. 1839897, 17408515.
-
(2007)
BMC Systems Biology
, vol.1
, pp. 8
-
-
Ulitsky, I.1
Shamir, R.2
-
98
-
-
0842309161
-
Discovering molecular pathways from protein interaction and gene expression data
-
Segal E, Wang H, Koller D. Discovering molecular pathways from protein interaction and gene expression data. Bioinformatics 2003, 19(Suppl 1):i264-71.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL 1
-
-
Segal, E.1
Wang, H.2
Koller, D.3
-
99
-
-
41149147660
-
Growing functional modules from a seed protein via integration of protein interaction and gene expression data
-
2233647, 17956603
-
Maraziotis IA, Dimitrakopoulou K, Bezerianos A. Growing functional modules from a seed protein via integration of protein interaction and gene expression data. BMC Bioinformatics 2007, 8:408. 2233647, 17956603.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 408
-
-
Maraziotis, I.A.1
Dimitrakopoulou, K.2
Bezerianos, A.3
-
101
-
-
33646437012
-
Integrated analysis of multiple data sources reveals modular structure of biological networks
-
Lu H, Shi B, Wu G, et al. Integrated analysis of multiple data sources reveals modular structure of biological networks. Biochem Biophys Res Commun 2006, 345(1):302-9.
-
(2006)
Biochem Biophys Res Commun
, vol.345
, Issue.1
, pp. 302-309
-
-
Lu, H.1
Shi, B.2
Wu, G.3
-
102
-
-
65449141657
-
Identifying functional modules using expression profiles and confidence-scored protein interactions
-
1 May
-
Ulitsky I, Shamir R. Identifying functional modules using expression profiles and confidence-scored protein interactions. Bioinformatics 2009, 25:1158-1164. 1 May.
-
(2009)
Bioinformatics
, vol.25
, pp. 1158-1164
-
-
Ulitsky, I.1
Shamir, R.2
-
103
-
-
33748464764
-
Combining functional and topological properties to identify core modules in protein interaction networks
-
Sep 1
-
Lubovac Z, Gamalielsson J, Olsson B. Combining functional and topological properties to identify core modules in protein interaction networks. Proteins. 2006, 64(4):948-59. Sep 1.
-
(2006)
Proteins.
, vol.64
, Issue.4
, pp. 948-959
-
-
Lubovac, Z.1
Gamalielsson, J.2
Olsson, B.3
-
104
-
-
46749134436
-
Discovering functional interaction patterns in protein-protein interaction networks
-
2442100, 18547430
-
Turanalp ME, Can T. Discovering functional interaction patterns in protein-protein interaction networks. BMC Bioinformatics 2008, 9:276. 2442100, 18547430.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 276
-
-
Turanalp, M.E.1
Can, T.2
-
105
-
-
78649667284
-
-
http://psimap.com/index.php/
-
-
-
-
106
-
-
0033518234
-
From molecular to modular cell biology
-
Hartwell LH, Hopfield JJ, Leibler S, Murray AW. From molecular to modular cell biology. Nature 1999, 402(6761 Suppl).
-
(1999)
Nature
, vol.402
, Issue.6761 SUPPL
-
-
Hartwell, L.H.1
Hopfield, J.J.2
Leibler, S.3
Murray, A.W.4
-
107
-
-
47849096998
-
Inferring modules of functionally interacting proteins using the Bond Energy Algorithm
-
2474619, 18559112
-
Watanabe RL, Morett E, Vallejo EE. Inferring modules of functionally interacting proteins using the Bond Energy Algorithm. BMC Bioinformatics 2008, 9:285. 2474619, 18559112.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 285
-
-
Watanabe, R.L.1
Morett, E.2
Vallejo, E.E.3
-
108
-
-
0036931833
-
Cluster ensembles - a knowledge reuse framework for combining partitionings
-
AAAI
-
Strehl A, Ghosh J. Cluster ensembles - a knowledge reuse framework for combining partitionings. 2002, 93-98. AAAI.
-
(2002)
, pp. 93-98
-
-
Strehl, A.1
Ghosh, J.2
-
109
-
-
34547852262
-
An ensemble framework for clustering protein-protein interaction networks
-
Asur S, Ucar D, Parthasarathy S. An ensemble framework for clustering protein-protein interaction networks. Bioinformatics 2007, 23(13):i29-i40.
-
(2007)
Bioinformatics
, vol.23
, Issue.13
-
-
Asur, S.1
Ucar, D.2
Parthasarathy, S.3
-
110
-
-
48249087654
-
Ensemble non-negative matrix factorization methods for clustering protein-protein interactions
-
Greene D, Cagney G, Krogan N, Cunningham P. Ensemble non-negative matrix factorization methods for clustering protein-protein interactions. Bioinformatics 2008, 24(15):1722-1728.
-
(2008)
Bioinformatics
, vol.24
, Issue.15
, pp. 1722-1728
-
-
Greene, D.1
Cagney, G.2
Krogan, N.3
Cunningham, P.4
-
111
-
-
0033592606
-
Learning the parts of objects by nonnegative matrix factorization
-
Lee DD, Seung HS. Learning the parts of objects by nonnegative matrix factorization. Nature 1999, 401:788-91.
-
(1999)
Nature
, vol.401
, pp. 788-791
-
-
Lee, D.D.1
Seung, H.S.2
-
112
-
-
55949137146
-
Clustering complex networks and biological networks by non-negative matrix factorization with various similarity measures
-
Wang R, Zhang S, Wang Y, Zhang XS, Chen L. Clustering complex networks and biological networks by non-negative matrix factorization with various similarity measures. Neurocomputing 2008, 72:134-141.
-
(2008)
Neurocomputing
, vol.72
, pp. 134-141
-
-
Wang, R.1
Zhang, S.2
Wang, Y.3
Zhang, X.S.4
Chen, L.5
-
113
-
-
9144242935
-
MIPS: analysis and annotation of proteins from whole genomes
-
308826, 14681354
-
Mewes HW, Amid C, Arnold R, et al. MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Research 2004, 32:D41-D44. 308826, 14681354.
-
(2004)
Nucleic Acids Research
, vol.32
-
-
Mewes, H.W.1
Amid, C.2
Arnold, R.3
-
114
-
-
78649679890
-
-
http://www.geneontology.org/
-
-
-
-
115
-
-
34548407017
-
Discovering functions and revealing mechanisms at molecular level from biological networks
-
Zhang S, Jin G, Zhang XS, Chen L. Discovering functions and revealing mechanisms at molecular level from biological networks. Proteomics 2007, 7:2856-2869.
-
(2007)
Proteomics
, vol.7
, pp. 2856-2869
-
-
Zhang, S.1
Jin, G.2
Zhang, X.S.3
Chen, L.4
-
116
-
-
78649652691
-
Comparison of protein complexes predicted from PPI networks by DPClus and Newman clustering algorithms
-
Tuji H, Altaf-Ul-Amin M, Arita M, et al. Comparison of protein complexes predicted from PPI networks by DPClus and Newman clustering algorithms. IPSJDigital Courier 2006, 2:674-684.
-
(2006)
IPSJDigital Courier
, vol.2
, pp. 674-684
-
-
Tuji, H.1
Altaf-Ul-Amin, M.2
Arita, M.3
-
117
-
-
33947252154
-
Network-based prediction of protein function
-
1847944, 17353930
-
Sharan R, Ulitsky I, Shamir R. Network-based prediction of protein function. Molecular Systems Biology 2007, 3:88. 1847944, 17353930.
-
(2007)
Molecular Systems Biology
, vol.3
, pp. 88
-
-
Sharan, R.1
Ulitsky, I.2
Shamir, R.3
-
118
-
-
0242268461
-
Predicting protein functions from redundancies in large-scale protein interaction networks
-
240660, 14566057
-
Samanta MP, Liang S. Predicting protein functions from redundancies in large-scale protein interaction networks. PNAS 2003, 100(22):12579-12583. 240660, 14566057.
-
(2003)
PNAS
, vol.100
, Issue.22
, pp. 12579-12583
-
-
Samanta, M.P.1
Liang, S.2
-
119
-
-
47649107210
-
Protein function prediction from interaction networks using a random walk ranking algorithm
-
Freschi V. Protein function prediction from interaction networks using a random walk ranking algorithm. Bioinformatics and Bioengineering 2007, 42-48.
-
(2007)
Bioinformatics and Bioengineering
, pp. 42-48
-
-
Freschi, V.1
-
120
-
-
48349138497
-
Computational methods for predicting protein-protein interactions
-
Pitre S, Alamgir M, Green JR, Dumontier M, Dehne F, Golshani A. Computational methods for predicting protein-protein interactions. Adv Biochem Eng Biotechnol. 2008, 110:247-67.
-
(2008)
Adv Biochem Eng Biotechnol.
, vol.110
, pp. 247-267
-
-
Pitre, S.1
Alamgir, M.2
Green, J.R.3
Dumontier, M.4
Dehne, F.5
Golshani, A.6
-
121
-
-
57549085034
-
Prediction of protein-protein interaction networks
-
Jun; Chapter 8:Unit 8.2
-
Gomez SM, Choi K, Wu Y. Prediction of protein-protein interaction networks. Curr Protoc Bioinformatics 2008, Jun; Chapter 8:Unit 8.2.
-
(2008)
Curr Protoc Bioinformatics
-
-
Gomez, S.M.1
Choi, K.2
Wu, Y.3
-
122
-
-
33645319955
-
Predicting interactions in protein networks by completing defective cliques
-
Yu H, Paccanaro A, Trifonov V, Gerstein M. Predicting interactions in protein networks by completing defective cliques. Bioinformatics 2006, 22(7):823-9.
-
(2006)
Bioinformatics
, vol.22
, Issue.7
, pp. 823-829
-
-
Yu, H.1
Paccanaro, A.2
Trifonov, V.3
Gerstein, M.4
-
123
-
-
51549118673
-
An Improved Method Based on Maximal Clique for Predicting Interactions in Protein Interaction Networks
-
Jianxin W, Zhao C, Min L. An Improved Method Based on Maximal Clique for Predicting Interactions in Protein Interaction Networks. BMEI2008 IEEE press 2008, 62-66.
-
(2008)
BMEI2008 IEEE press
, pp. 62-66
-
-
Jianxin, W.1
Zhao, C.2
Min, L.3
-
124
-
-
34248347402
-
Dynamical systems for discovering protein complexes and functional modules from biological networks
-
Li W, Liu Y, Huang HC, Peng Y, Lin Y, Ng WK, Ong KL. Dynamical systems for discovering protein complexes and functional modules from biological networks. IEEE/ACM Trans Comput Biol Bioinform 2007, 4(2):233-50.
-
(2007)
IEEE/ACM Trans Comput Biol Bioinform
, vol.4
, Issue.2
, pp. 233-250
-
-
Li, W.1
Liu, Y.2
Huang, H.C.3
Peng, Y.4
Lin, Y.5
Ng, W.K.6
Ong, K.L.7
-
125
-
-
61949358848
-
Identifying dynamic network modules with temporal and spatial con-straints
-
Jin R, McCallen S, Liu CC, Xiang Y, Almaas E, Zhou XJ. Identifying dynamic network modules with temporal and spatial con-straints. Pac Symp Biocomput 2009, 203:14.
-
(2009)
Pac Symp Biocomput
, vol.203
, pp. 14
-
-
Jin, R.1
McCallen, S.2
Liu, C.C.3
Xiang, Y.4
Almaas, E.5
Zhou, X.J.6
|