-
1
-
-
0742305866
-
Network biology: understanding the cell's functional organization
-
10.1038/nrg1272, 14735121
-
Barabasi A-L, Oltvai ZN. 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
-
-
Barabasi, A.-.L.1
Oltvai, Z.N.2
-
2
-
-
0037417817
-
Modular organization of cellular networks
-
10.1073/pnas.0237338100, 298738, 12538875
-
Rives AW, Galitski T. Modular organization of cellular networks. Proceedings of the National Academy of Sciences of the United States of America 2003, 100(3):1128-1133. 10.1073/pnas.0237338100, 298738, 12538875.
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.3
, pp. 1128-1133
-
-
Rives, A.W.1
Galitski, T.2
-
3
-
-
25444490121
-
The use of edge-betweenness clustering to investigate biological function in protein interaction networks
-
10.1186/1471-2105-6-39, 555937, 15740614
-
Dunn R, Dudbridge F, Sanderson CM. The use of edge-betweenness clustering to investigate biological function in protein interaction networks. BMC Bioinformatics 2005, 6:39. 10.1186/1471-2105-6-39, 555937, 15740614.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 39
-
-
Dunn, R.1
Dudbridge, F.2
Sanderson, C.M.3
-
4
-
-
20444504323
-
Uncovering the overlapping community structure of complex networks in nature and society
-
10.1038/nature03607, 15944704
-
Palla G, Derenyi 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
Derenyi, I.2
Farkas, I.3
Vicsek, T.4
-
5
-
-
33751229605
-
Identification of functional modules in a PPI network by clique percolation clustering
-
10.1016/j.compbiolchem.2006.10.001, 17098476
-
Zhang S, Ning X, Zhang X-S. Identification of functional modules in a PPI network by clique percolation clustering. Computational Biology and Chemistry 2006, 30(6):445-451. 10.1016/j.compbiolchem.2006.10.001, 17098476.
-
(2006)
Computational Biology and Chemistry
, vol.30
, Issue.6
, pp. 445-451
-
-
Zhang, S.1
Ning, X.2
Zhang, X.-.S.3
-
6
-
-
49649104565
-
A structural approach for finding functional modules from large biological networks
-
10.1186/1471-2105-9-S9-S19, 2537570, 18793464
-
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. 10.1186/1471-2105-9-S9-S19, 2537570, 18793464.
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.SUPPL 9
-
-
Mete, M.1
Tang, F.2
Xu, X.3
Yuruk, N.4
-
7
-
-
67649518162
-
A core-attachment based method to detect protein complexes in PPI networks
-
10.1186/1471-2105-10-169, 2701950, 19486541
-
Wu M, Li X, Kwoh CK, Ng SK. A core-attachment based method to detect protein complexes in PPI networks. BMC Bioinformatics 2009, 10:169. 10.1186/1471-2105-10-169, 2701950, 19486541.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 169
-
-
Wu, M.1
Li, X.2
Kwoh, C.K.3
Ng, S.K.4
-
8
-
-
67650735594
-
Complex discovery from weighted PPI networks
-
10.1093/bioinformatics/btp311, 19435747
-
Liu G, Wong L, Chua HN. 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.N.3
-
9
-
-
59649099220
-
Predicting protein complexes from PPI data: a core-attachment approach
-
10.1089/cmb.2008.01TT, 19193141
-
Leung HC, Xiang Q, Yiu SM, Chin FY. 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.C.1
Xiang, Q.2
Yiu, S.M.3
Chin, F.Y.4
-
10
-
-
33846681448
-
Modular organization of protein interaction networks
-
10.1093/bioinformatics/btl562, 17092991
-
Luo F, Yang Y, Chen CF, Chang R, Zhou J, Scheuermann RH. 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.F.3
Chang, R.4
Zhou, J.5
Scheuermann, R.H.6
-
11
-
-
0005924596
-
Graph Clustering by Flow Simulation
-
University of Utrecht, The Netherlands
-
Dongen S. Graph Clustering by Flow Simulation. 2000, University of Utrecht, The Netherlands.
-
(2000)
-
-
Dongen, S.1
-
12
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
10.1093/nar/30.7.1575, 101833, 11917018
-
Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucl Acids Res 2002, 30(7):1575-1584. 10.1093/nar/30.7.1575, 101833, 11917018.
-
(2002)
Nucl Acids Res
, vol.30
, Issue.7
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
13
-
-
34548742517
-
Identification of functional modules using network topology and high-throughput data
-
10.1186/1752-0509-1-8, 1839897, 17408515
-
Ulitsky I, Shamir R. Identification of functional modules using network topology and high-throughput data. BMC Syst Biol 2007, 1:8. 10.1186/1752-0509-1-8, 1839897, 17408515.
-
(2007)
BMC Syst Biol
, vol.1
, pp. 8
-
-
Ulitsky, I.1
Shamir, R.2
-
14
-
-
65449141657
-
Identifying functional modules using expression profiles and confidence-scored protein interactions
-
10.1093/bioinformatics/btp118, 19297352
-
Ulitsky I, Shamir R. Identifying functional modules using expression profiles and confidence-scored protein interactions. Bioinformatics 2009, 25(9):1158-1164. 10.1093/bioinformatics/btp118, 19297352.
-
(2009)
Bioinformatics
, vol.25
, Issue.9
, pp. 1158-1164
-
-
Ulitsky, I.1
Shamir, R.2
-
15
-
-
68549122904
-
Identifying the topology of protein complexes from affinity purification assays
-
10.1093/bioinformatics/btp353, 2723003, 19505940
-
Friedel CC, Zimmer R. Identifying the topology of protein complexes from affinity purification assays. Bioinformatics 2009, 25(16):2140-2146. 10.1093/bioinformatics/btp353, 2723003, 19505940.
-
(2009)
Bioinformatics
, vol.25
, Issue.16
, pp. 2140-2146
-
-
Friedel, C.C.1
Zimmer, R.2
-
16
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
10.1038/nature04532, 16429126
-
Gavin A-C, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dumpelfeld B, et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 2006, 440(7084):631-636. 10.1038/nature04532, 16429126.
-
(2006)
Nature
, vol.440
, Issue.7084
, pp. 631-636
-
-
Gavin, A.-.C.1
Aloy, P.2
Grandi, P.3
Krause, R.4
Boesche, M.5
Marzioch, M.6
Rau, C.7
Jensen, L.J.8
Bastuck, S.9
Dumpelfeld, B.10
-
17
-
-
33747586075
-
A direct comparison of protein interaction confidence assignment schemes
-
10.1186/1471-2105-7-360, 1550431, 16872496
-
Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T. A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics 2006, 7:360. 10.1186/1471-2105-7-360, 1550431, 16872496.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 360
-
-
Suthram, S.1
Shlomi, T.2
Ruppin, E.3
Sharan, R.4
Ideker, T.5
-
18
-
-
0037161731
-
Comparative assessment of large-scale data sets of protein-protein interactions
-
10.1038/nature750, 12000970
-
von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417(6887):399-403. 10.1038/nature750, 12000970.
-
(2002)
Nature
, vol.417
, Issue.6887
, pp. 399-403
-
-
von Mering, C.1
Krause, R.2
Snel, B.3
Cornell, M.4
Oliver, S.G.5
Fields, S.6
Bork, P.7
-
19
-
-
34147121646
-
Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae
-
Collins SR, Kemmeren P, Zhao XC, Greenblatt JF, Spencer F, Holstege FC, Weissman JS, Krogan NJ. Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics 2007, 6(3):439-450.
-
(2007)
Mol Cell Proteomics
, vol.6
, Issue.3
, pp. 439-450
-
-
Collins, S.R.1
Kemmeren, P.2
Zhao, X.C.3
Greenblatt, J.F.4
Spencer, F.5
Holstege, F.C.6
Weissman, J.S.7
Krogan, N.J.8
-
20
-
-
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. Proc Natl Acad Sci USA 2004, 101(9):2658-2663. 10.1073/pnas.0400054101, 365677, 14981240.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.9
, pp. 2658-2663
-
-
Radicchi, F.1
Castellano, C.2
Cecconi, F.3
Loreto, V.4
Parisi, D.5
-
21
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
10.1038/75556, 10802651
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25(1):25-29. 10.1038/75556, 10802651.
-
(2000)
Nat Genet
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
-
22
-
-
12344269924
-
GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
-
10.1093/bioinformatics/bth456, 15297299
-
Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G. GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 2004, 20(18):3710-3715. 10.1093/bioinformatics/bth456, 15297299.
-
(2004)
Bioinformatics
, vol.20
, Issue.18
, pp. 3710-3715
-
-
Boyle, E.I.1
Weng, S.2
Gollub, J.3
Jin, H.4
Botstein, D.5
Cherry, J.M.6
Sherlock, G.7
-
23
-
-
33748335463
-
A new measure for functional similarity of gene products based on Gene Ontology
-
10.1186/1471-2105-7-302, 1559652, 16776819
-
Schlicker A, Domingues FS, Rahnenfuhrer J, Lengauer T. A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics 2006, 7:302. 10.1186/1471-2105-7-302, 1559652, 16776819.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 302
-
-
Schlicker, A.1
Domingues, F.S.2
Rahnenfuhrer, J.3
Lengauer, T.4
-
24
-
-
70349212097
-
Bootstrapping the interactome: unsupervised identification of protein complexes in yeast
-
10.1089/cmb.2009.0023, 19630542
-
Friedel CC, Krumsiek J, Zimmer R. Bootstrapping the interactome: unsupervised identification of protein complexes in yeast. J Comput Biol 2009, 16(8):971-987. 10.1089/cmb.2009.0023, 19630542.
-
(2009)
J Comput Biol
, vol.16
, Issue.8
, pp. 971-987
-
-
Friedel, C.C.1
Krumsiek, J.2
Zimmer, R.3
-
25
-
-
0033967852
-
TRIPLES: a database of gene function in Saccharomyces cerevisiae
-
10.1093/nar/28.1.81, 102388, 10592187
-
Kumar A, Cheung KH, Ross-Macdonald P, Coelho PS, Miller P, Snyder M. TRIPLES: a database of gene function in Saccharomyces cerevisiae. Nucleic Acids Res 2000, 28(1):81-84. 10.1093/nar/28.1.81, 102388, 10592187.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 81-84
-
-
Kumar, A.1
Cheung, K.H.2
Ross-Macdonald, P.3
Coelho, P.S.4
Miller, P.5
Snyder, M.6
-
26
-
-
9144242935
-
MIPS: analysis and annotation of proteins from whole genomes
-
Database, 10.1093/nar/gkh092, 308826, 14681354
-
Mewes HW, Amid C, Arnold R, Frishman D, Guldener U, Mannhaupt G, Munsterkotter M, Pagel P, Strack N, Stumpflen V, et al. MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res 2004, (32 Database):D41-44. 10.1093/nar/gkh092, 308826, 14681354.
-
(2004)
Nucleic Acids Res
, Issue.32
-
-
Mewes, H.W.1
Amid, C.2
Arnold, R.3
Frishman, D.4
Guldener, U.5
Mannhaupt, G.6
Munsterkotter, M.7
Pagel, P.8
Strack, N.9
Stumpflen, V.10
-
27
-
-
12144290243
-
Structure-based assembly of protein complexes in yeast
-
10.1126/science.1092645, 15044803
-
Aloy P, Bottcher B, Ceulemans H, Leutwein C, Mellwig C, Fischer S, Gavin AC, Bork P, Superti-Furga G, Serrano L, et al. Structure-based assembly of protein complexes in yeast. Science 2004, 303(5666):2026-2029. 10.1126/science.1092645, 15044803.
-
(2004)
Science
, vol.303
, Issue.5666
, pp. 2026-2029
-
-
Aloy, P.1
Bottcher, B.2
Ceulemans, H.3
Leutwein, C.4
Mellwig, C.5
Fischer, S.6
Gavin, A.C.7
Bork, P.8
Superti-Furga, G.9
Serrano, L.10
-
28
-
-
34548550573
-
Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process
-
10.1093/bioinformatics/btm309, 17553854
-
Elo LL, Jarvenpaa H, Oresic M, Lahesmaa R, Aittokallio T. Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process. Bioinformatics 2007, 23(16):2096-2103. 10.1093/bioinformatics/btm309, 17553854.
-
(2007)
Bioinformatics
, vol.23
, Issue.16
, pp. 2096-2103
-
-
Elo, L.L.1
Jarvenpaa, H.2
Oresic, M.3
Lahesmaa, R.4
Aittokallio, T.5
-
29
-
-
48449102450
-
Hubba: hub objects analyzer--a framework of interactome hubs identification for network biology
-
Web Server, 10.1093/nar/gkn257, 2447731, 18503085
-
Lin CY, Chin CH, Wu HH, Chen SH, Ho CW, Ko MT. Hubba: hub objects analyzer--a framework of interactome hubs identification for network biology. Nucleic Acids Res 2008, (36 Web Server):W438-443. 10.1093/nar/gkn257, 2447731, 18503085.
-
(2008)
Nucleic Acids Res
, Issue.36
-
-
Lin, C.Y.1
Chin, C.H.2
Wu, H.H.3
Chen, S.H.4
Ho, C.W.5
Ko, M.T.6
-
30
-
-
0033518234
-
From molecular to modular cell biology
-
10.1038/35011540, 10591225
-
Hartwell LH, Hopfield JJ, Leibler S, Murray AW. From molecular to modular cell biology. Nature 1999, 402(6761 Suppl):C47-52. 10.1038/35011540, 10591225.
-
(1999)
Nature
, vol.402
, Issue.6761 SUPPL
-
-
Hartwell, L.H.1
Hopfield, J.J.2
Leibler, S.3
Murray, A.W.4
-
31
-
-
48249103199
-
Structure of eukaryotic RNA polymerases
-
10.1146/annurev.biophys.37.032807.130008, 18573085
-
Cramer P, Armache KJ, Baumli S, Benkert S, Brueckner F, Buchen C, Damsma GE, Dengl S, Geiger SR, Jasiak AJ, et al. Structure of eukaryotic RNA polymerases. Annu Rev Biophys 2008, 37:337-352. 10.1146/annurev.biophys.37.032807.130008, 18573085.
-
(2008)
Annu Rev Biophys
, vol.37
, pp. 337-352
-
-
Cramer, P.1
Armache, K.J.2
Baumli, S.3
Benkert, S.4
Brueckner, F.5
Buchen, C.6
Damsma, G.E.7
Dengl, S.8
Geiger, S.R.9
Jasiak, A.J.10
-
32
-
-
33645453254
-
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
-
10.1038/nature04670, 16554755
-
Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 2006, 440(7084):637-643. 10.1038/nature04670, 16554755.
-
(2006)
Nature
, vol.440
, Issue.7084
, pp. 637-643
-
-
Krogan, N.J.1
Cagney, G.2
Yu, H.3
Zhong, G.4
Guo, X.5
Ignatchenko, A.6
Li, J.7
Pu, S.8
Datta, N.9
Tikuisis, A.P.10
-
33
-
-
0036141992
-
Relating whole-genome expression data with protein-protein interactions
-
10.1101/gr.205602, 155252, 11779829
-
Jansen R, Greenbaum D, Gerstein M. Relating whole-genome expression data with protein-protein interactions. Genome Res 2002, 12(1):37-46. 10.1101/gr.205602, 155252, 11779829.
-
(2002)
Genome Res
, vol.12
, Issue.1
, pp. 37-46
-
-
Jansen, R.1
Greenbaum, D.2
Gerstein, M.3
-
34
-
-
0345305369
-
Functional modules by relating protein interaction networks and gene expression
-
10.1093/nar/gkg838, 275479, 14576317
-
Tornow S, Mewes HW. Functional modules by relating protein interaction networks and gene expression. Nucleic Acids Res 2003, 31(21):6283-6289. 10.1093/nar/gkg838, 275479, 14576317.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.21
, pp. 6283-6289
-
-
Tornow, S.1
Mewes, H.W.2
-
35
-
-
84888284137
-
MATISSE website
-
MATISSE website. , http://acgt.cs.tau.ac.il/matisse/
-
-
-
|