-
1
-
-
0742305866
-
Network biology: understanding the cell's functional organization
-
10.1038/nrg1272, 14735121
-
Barabási A, Oltvai Z. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5(2):101-113. 10.1038/nrg1272, 14735121.
-
(2004)
Nat Rev Genet
, vol.5
, Issue.2
, pp. 101-113
-
-
Barabási, A.1
Oltvai, Z.2
-
2
-
-
0036726314
-
Yeast genomic databases and the challenge of the post-genomic era
-
10.1007/s10142-002-0061-7, 23483083
-
Garrels J. Yeast genomic databases and the challenge of the post-genomic era. Funct & Integr genomics 2002, 2(4):212-237. 10.1007/s10142-002-0061-7, 23483083.
-
(2002)
Funct & Integr genomics
, vol.2
, Issue.4
, pp. 212-237
-
-
Garrels, J.1
-
3
-
-
0037306721
-
Protein complexes and proteome organization from yeast to man
-
10.1016/S1367-5931(02)00007-8, 12547422
-
Gavin A, Superti-Furga G. Protein complexes and proteome organization from yeast to man. Curr Opin Chem Biol 2003, 7:21. 10.1016/S1367-5931(02)00007-8, 12547422.
-
(2003)
Curr Opin Chem Biol
, vol.7
, pp. 21
-
-
Gavin, A.1
Superti-Furga, G.2
-
4
-
-
54349096842
-
Modifying the DPClus algorithm for identifying protein complexes based on new topological structures
-
10.1186/1471-2105-9-398, 2570695, 18816408
-
Li M, Chen J, Wang J, Hu B, Chen G. Modifying the DPClus algorithm for identifying protein complexes based on new topological structures. BMC bioinformatics 2008, 9:398. 10.1186/1471-2105-9-398, 2570695, 18816408.
-
(2008)
BMC bioinformatics
, vol.9
, pp. 398
-
-
Li, M.1
Chen, J.2
Wang, J.3
Hu, B.4
Chen, G.5
-
5
-
-
84873707527
-
Single-gene and whole-genome duplications and the evolution of protein-protein interaction networks
-
Hoboken: Wiley-Blackwell, Gustavo Caetano-Anollés
-
Amoutzias G, de Peer YV. Single-gene and whole-genome duplications and the evolution of protein-protein interaction networks. Evolutionary Genomics and Systems Biology 2010, 413-429. Hoboken: Wiley-Blackwell, Gustavo Caetano-Anollés.
-
(2010)
Evolutionary Genomics and Systems Biology
, pp. 413-429
-
-
Amoutzias, G.1
de Peer, Y.V.2
-
6
-
-
78649679994
-
Recent advances in clustering methods for protein interaction networks
-
10.1186/1471-2164-11-S3-S10, 3045793, 21210966
-
Wang J, Li M, Deng Y, Pan Y. Recent advances in clustering methods for protein interaction networks. BMC genomics 2010, 11(Suppl 3):S10. 10.1186/1471-2164-11-S3-S10, 3045793, 21210966.
-
(2010)
BMC genomics
, vol.11
, Issue.SUPPL. 3
-
-
Wang, J.1
Li, M.2
Deng, Y.3
Pan, Y.4
-
7
-
-
0034515528
-
A clustering algorithm based on graph connectivity
-
Hartuv E, Shamir R. A clustering algorithm based on graph connectivity. Inf Process Lett 2000, 76(4):175-181.
-
(2000)
Inf Process Lett
, vol.76
, Issue.4
, pp. 175-181
-
-
Hartuv, E.1
Shamir, R.2
-
9
-
-
0142059836
-
Protein complexes and functional modules in molecular networks
-
Spirin V, Mirny L. Protein complexes and functional modules in molecular networks. Proceedings of the National Academy of Sciences 2003, 100(21):12123-12128.
-
(2003)
Proceedings of the National Academy of Sciences
, vol.100
, Issue.21
, pp. 12123-12128
-
-
Spirin, V.1
Mirny, L.2
-
10
-
-
10244264813
-
Protein complex prediction via cost-based clustering
-
10.1093/bioinformatics/bth351, 15180928
-
King A, Pržulj N, Jurisica I. Protein complex prediction via cost-based clustering. Bioinformatics 2004, 20(17):3013-3020. 10.1093/bioinformatics/bth351, 15180928.
-
(2004)
Bioinformatics
, vol.20
, Issue.17
, pp. 3013-3020
-
-
King, A.1
Pržulj, N.2
Jurisica, I.3
-
11
-
-
1542357701
-
Defining and identifying communities in networks
-
10.1073/pnas.0400054101, 365677, 14981240
-
Radicchi F, Castellano C, Cecconi F, Loreto V, Parisi D. Defining and identifying communities in networks. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(9):2658-2663. 10.1073/pnas.0400054101, 365677, 14981240.
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.9
, pp. 2658-2663
-
-
Radicchi, F.1
Castellano, C.2
Cecconi, F.3
Loreto, V.4
Parisi, D.5
-
12
-
-
42749100809
-
Fast algorithm for detecting community structure in networks
-
Newman M. Fast algorithm for detecting community structure in networks. Phys Rev E 2004, 69(6):066133.
-
(2004)
Phys Rev E
, vol.69
, Issue.6
, pp. 066133
-
-
Newman, M.1
-
13
-
-
14644444197
-
Analyzing protein complexes in Drosophila with tandem affinity purification-mass spectrometry
-
10.1002/dvdy.20272, 15704125
-
Veraksa A, Bauer A, Artavanis-Tsakonas S. Analyzing protein complexes in Drosophila with tandem affinity purification-mass spectrometry. Dev Dyn 2005, 232(3):827-834. 10.1002/dvdy.20272, 15704125.
-
(2005)
Dev Dyn
, vol.232
, Issue.3
, pp. 827-834
-
-
Veraksa, A.1
Bauer, A.2
Artavanis-Tsakonas, S.3
-
14
-
-
33645830948
-
CFinder: locating cliques and overlapping modules in biological networks
-
10.1093/bioinformatics/btl039, 16473872
-
Adamcsek B, Palla G, Farkas I, Derényi I, Vicsek T. CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics 2006, 22(8):1021-1023. 10.1093/bioinformatics/btl039, 16473872.
-
(2006)
Bioinformatics
, vol.22
, Issue.8
, pp. 1021-1023
-
-
Adamcsek, B.1
Palla, G.2
Farkas, I.3
Derényi, I.4
Vicsek, T.5
-
15
-
-
33748579201
-
Interaction graph mining for protein complexes using local clique merging
-
Li X, Tan S, Foo C, Ng S. Interaction graph mining for protein complexes using local clique merging. GENOME INFORM SER 2005, 16(2):260-269.
-
(2005)
GENOME INFORM SER
, vol.16
, Issue.2
, pp. 260-269
-
-
Li, X.1
Tan, S.2
Foo, C.3
Ng, S.4
-
16
-
-
33744805096
-
Development and implementation of an algorithm for detection of protein complexes in large interaction networks
-
10.1186/1471-2105-7-207, 1473204, 16613608
-
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, 7:207-219. 10.1186/1471-2105-7-207, 1473204, 16613608.
-
(2006)
BMC bioinformatics
, vol.7
, pp. 207-219
-
-
Altaf-Ul-Amin, M.1
Shinbo, Y.2
Mihara, K.3
Kurokawa, K.4
Kanaya, S.5
-
17
-
-
38849128078
-
Identifying protein complexes directly from high-throughput TAP data with Markov random fields
-
10.1186/1471-2105-8-482, 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. 10.1186/1471-2105-8-482, 2222659, 18093306.
-
(2007)
BMC bioinformatics
, vol.8
, pp. 482
-
-
Rungsarityotin, W.1
Krause, R.2
Schödl, A.3
Schliep, A.4
-
18
-
-
34548511546
-
Semantic integration to identify overlapping functional modules in protein interaction networks
-
10.1186/1471-2105-8-265, 1971074, 17650343
-
Cho Y, Hwang W, Ramanathan M, Zhang A. Semantic integration to identify overlapping functional modules in protein interaction networks. BMC bioinformatics 2007, 8:265. 10.1186/1471-2105-8-265, 1971074, 17650343.
-
(2007)
BMC bioinformatics
, vol.8
, pp. 265
-
-
Cho, Y.1
Hwang, W.2
Ramanathan, M.3
Zhang, A.4
-
19
-
-
33846681448
-
Modular organization of protein interaction networks
-
10.1093/bioinformatics/btl562, 17092991
-
Luo F, Yang Y, Chen C, Chang R, Zhou J, Scheuermann R. Modular organization of protein interaction networks. Bioinformatics 2007, 23(2):207-214. 10.1093/bioinformatics/btl562, 17092991.
-
(2007)
Bioinformatics
, vol.23
, Issue.2
, pp. 207-214
-
-
Luo, F.1
Yang, Y.2
Chen, C.3
Chang, R.4
Zhou, J.5
Scheuermann, R.6
-
20
-
-
33751166180
-
Identification of overlapping community structure in complex networks using fuzzy c-means clustering
-
Zhang S, Wang R, Zhang X. Identification of overlapping community structure in complex networks using fuzzy c-means clustering. Physica A: Stat Mech Appl 2007, 374:483-490.
-
(2007)
Physica A: Stat Mech Appl
, vol.374
, pp. 483-490
-
-
Zhang, S.1
Wang, R.2
Zhang, X.3
-
21
-
-
59649099220
-
Predicting protein complexes from PPI data: a core-attachment approach
-
10.1089/cmb.2008.01TT, 19193141
-
Leung H, Xiang Q, Yiu S, Chin F. Predicting protein complexes from PPI data: a core-attachment approach. J Comput Biol 2009, 16(2):133-144. 10.1089/cmb.2008.01TT, 19193141.
-
(2009)
J Comput Biol
, vol.16
, Issue.2
, pp. 133-144
-
-
Leung, H.1
Xiang, Q.2
Yiu, S.3
Chin, F.4
-
22
-
-
67650735594
-
Complex discovery from weighted PPI networks
-
10.1093/bioinformatics/btp311, 19435747
-
Liu G, Wong L, Chua H. Complex discovery from weighted PPI networks. Bioinformatics 2009, 25(15):1891-1897. 10.1093/bioinformatics/btp311, 19435747.
-
(2009)
Bioinformatics
, vol.25
, Issue.15
, pp. 1891-1897
-
-
Liu, G.1
Wong, L.2
Chua, H.3
-
23
-
-
64549145094
-
Detecting the overlapping and hierarchical community structure in complex networks
-
Lancichinetti A, Fortunato S, Kertész J. Detecting the overlapping and hierarchical community structure in complex networks. New J Phys 2009, 11(3):033015.
-
(2009)
New J Phys
, vol.11
, Issue.3
, pp. 033015
-
-
Lancichinetti, A.1
Fortunato, S.2
Kertész, J.3
-
24
-
-
78149344632
-
Identifying protein complexes from interaction networks based on clique percolation and distance restriction
-
10.1186/1471-2164-11-S2-S10, 3045793, 21210966
-
Wang J, Liu B, Li M, Pan Y. Identifying protein complexes from interaction networks based on clique percolation and distance restriction. BMC Genomics 2010, 11(Suppl 2):S10. 10.1186/1471-2164-11-S2-S10, 3045793, 21210966.
-
(2010)
BMC Genomics
, vol.11
, Issue.SUPPL. 2
-
-
Wang, J.1
Liu, B.2
Li, M.3
Pan, Y.4
-
25
-
-
77951967208
-
SPICi: a fast clustering algorithm for large biological networks
-
10.1093/bioinformatics/btq078, 2853685, 20185405
-
Jiang P, Singh M. SPICi: a fast clustering algorithm for large biological networks. Bioinformatics 2010, 26(8):1105-1111. 10.1093/bioinformatics/btq078, 2853685, 20185405.
-
(2010)
Bioinformatics
, vol.26
, Issue.8
, pp. 1105-1111
-
-
Jiang, P.1
Singh, M.2
-
26
-
-
79952841798
-
A fast hierarchical clustering algorithm for functional modules discovery in protein interaction networksDavid00
-
Wang J, Li M, Chen J, Pan Y. A fast hierarchical clustering algorithm for functional modules discovery in protein interaction networksDavid00. Comput Biol Bioinformatics, IEEE/ACM Transactions on 2011, 8(3):607-620.
-
(2011)
Comput Biol Bioinformatics, IEEE/ACM Transactions on
, vol.8
, Issue.3
, pp. 607-620
-
-
Wang, J.1
Li, M.2
Chen, J.3
Pan, Y.4
-
28
-
-
84872678695
-
Identifying protein complexes in protein-protein interaction networks by using clique seeds and graph entropy
-
10.1002/pmic.201200336, 23112006
-
Chen B, Shi J, Zhang S, Wu F. Identifying protein complexes in protein-protein interaction networks by using clique seeds and graph entropy. Proteomics 2013, 13(2):269-277. 10.1002/pmic.201200336, 23112006.
-
(2013)
Proteomics
, vol.13
, Issue.2
, pp. 269-277
-
-
Chen, B.1
Shi, J.2
Zhang, S.3
Wu, F.4
-
29
-
-
20444504323
-
Uncovering the overlapping community structure of complex networks in nature and society
-
10.1038/nature03607, 15944704
-
Palla G, Derényi I, Farkas I, Vicsek T. Uncovering the overlapping community structure of complex networks in nature and society. Nature 2005, 435(7043):814-818. 10.1038/nature03607, 15944704.
-
(2005)
Nature
, vol.435
, Issue.7043
, pp. 814-818
-
-
Palla, G.1
Derényi, I.2
Farkas, I.3
Vicsek, T.4
-
30
-
-
2942552459
-
An automated method for finding molecular complexes in large protein interaction networks
-
10.1186/1471-2105-4-2, 149346, 12525261
-
Bader G, Hogue C. 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.
-
(2003)
BMC bioinformatics
, vol.4
, pp. 2
-
-
Bader, G.1
Hogue, C.2
-
31
-
-
0034660322
-
Protein function in the post-genomic era
-
10.1038/35015694, 10866208
-
Eisenberg D, Marcotte E, Xenarios I, Yeates T. Protein function in the post-genomic era. NATURE-LONDON- 2000, 405:823-826. 10.1038/35015694, 10866208.
-
(2000)
NATURE-LONDON-
, vol.405
, pp. 823-826
-
-
Eisenberg, D.1
Marcotte, E.2
Xenarios, I.3
Yeates, T.4
-
32
-
-
1342330546
-
Functional topology in a network of protein interactions
-
10.1093/bioinformatics/btg415, 14960460
-
Pržulj N, Wigle D, Jurisica I. Functional topology in a network of protein interactions. Bioinformatics 2004, 20(3):340-348. 10.1093/bioinformatics/btg415, 14960460.
-
(2004)
Bioinformatics
, vol.20
, Issue.3
, pp. 340-348
-
-
Pržulj, N.1
Wigle, D.2
Jurisica, I.3
-
33
-
-
13244284551
-
Dynamic complex formation during the yeast cell cycle
-
de Lichtenberg U, Jensen L, Brunak S, Bork P. Dynamic complex formation during the yeast cell cycle. Sci Signal 2005, 307(5710):724-727.
-
(2005)
Sci Signal
, vol.307
, Issue.5710
, pp. 724-727
-
-
de Lichtenberg, U.1
Jensen, L.2
Brunak, S.3
Bork, P.4
-
34
-
-
34247464637
-
Revealing static and dynamic modular architecture of the eukaryotic protein interaction network
-
1865589, 17453049
-
Komurov K, White M. Revealing static and dynamic modular architecture of the eukaryotic protein interaction network. Mol Syst Biol 2007, 3:110. 1865589, 17453049.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 110
-
-
Komurov, K.1
White, M.2
-
36
-
-
63349085550
-
Up-to-date catalogues of yeast protein complexes
-
10.1093/nar/gkn1005, 2647312, 19095691
-
Pu S, Wong J, Turner B, Cho E, Wodak S. Up-to-date catalogues of yeast protein complexes. Nucleic Acids Res 2009, 37(3):825-831. 10.1093/nar/gkn1005, 2647312, 19095691.
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.3
, pp. 825-831
-
-
Pu, S.1
Wong, J.2
Turner, B.3
Cho, E.4
Wodak, S.5
-
37
-
-
0036088133
-
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
-
10.1093/nar/30.1.303, 99070, 11752321
-
Xenarios I, Salwinski L, Duan X, Higney P, Kim S, Eisenberg D. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 2002, 30:303-305. 10.1093/nar/30.1.303, 99070, 11752321.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 303-305
-
-
Xenarios, I.1
Salwinski, L.2
Duan, X.3
Higney, P.4
Kim, S.5
Eisenberg, D.6
-
38
-
-
27944487902
-
Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes
-
10.1126/science.1120499, 16254148
-
Tu B, Kudlicki A, Rowicka M, McKnight S. Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science 2005, 310(5751):1152-1158. 10.1126/science.1120499, 16254148.
-
(2005)
Science
, vol.310
, Issue.5751
, pp. 1152-1158
-
-
Tu, B.1
Kudlicki, A.2
Rowicka, M.3
McKnight, S.4
-
39
-
-
84872735831
-
Construction and application of dynamic protein interaction network based on time course gene expression data
-
10.1002/pmic.201200277, 23225755
-
Wang J, Peng X, Li M, Pan Y. Construction and application of dynamic protein interaction network based on time course gene expression data. Proteomics 2013, 13(2):301-312. 10.1002/pmic.201200277, 23225755.
-
(2013)
Proteomics
, vol.13
, Issue.2
, pp. 301-312
-
-
Wang, J.1
Peng, X.2
Li, M.3
Pan, Y.4
-
40
-
-
0005924596
-
Graph clustering by flow simulation
-
University of Utrecht 2000
-
van Dongen S. Graph clustering by flow simulation. PhD thesis University of Utrecht 2000.
-
PhD thesis
-
-
van Dongen, S.1
-
41
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
10.1093/nar/30.7.1575, 101833, 11917018
-
Enright A, Van Dongen S, Ouzounis C. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002, 30(7):1575-1584. 10.1093/nar/30.7.1575, 101833, 11917018.
-
(2002)
Nucleic Acids Res
, vol.30
, Issue.7
, pp. 1575-1584
-
-
Enright, A.1
Van Dongen, S.2
Ouzounis, C.3
|