-
1
-
-
0034628508
-
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
-
Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627.
-
(2000)
Nature
, vol.403
, pp. 623-627
-
-
Uetz, P.1
Giot, L.2
Cagney, G.3
Mansfield, T.A.4
Judson, R.S.5
-
2
-
-
0035836765
-
A comprehensive two-hybrid analysis to explore the yeast protein interactome
-
Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 98: 4569-74.
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, pp. 4569-4574
-
-
Ito, T.1
Chiba, T.2
Ozawa, R.3
Yoshida, M.4
Hattori, M.5
-
3
-
-
0037050004
-
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
-
Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183.
-
(2002)
Nature
, vol.415
, pp. 180-183
-
-
Ho, Y.1
Gruhler, A.2
Heilbut, A.3
Bader, G.D.4
Moore, L.5
-
4
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, 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
Aloy, P.2
Grandi, P.3
Krause, R.4
Boesche, M.5
-
5
-
-
33645453254
-
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
-
Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, 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
Cagney, G.2
Yu, H.3
Zhong, G.4
Guo, X.5
-
6
-
-
53349117774
-
High-quality binary protein interaction map of the yeast interactome network
-
Yu H, Braun P, Yildirim MA, et al. (2008) High-quality binary protein interaction map of the yeast interactome network. Science 322: 104-110.
-
(2008)
Science
, vol.322
, pp. 104-110
-
-
Yu, H.1
Braun, P.2
Yildirim, M.A.3
-
7
-
-
0345600247
-
A protein interaction map of Drosophila melanogaster
-
Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, et al. (2003) A protein interaction map of Drosophila melanogaster. Science 302: 1727-1736.
-
(2003)
Science
, vol.302
, pp. 1727-1736
-
-
Giot, L.1
Bader, J.S.2
Brouwer, C.3
Chaudhuri, A.4
Kuang, B.5
-
8
-
-
80155171417
-
A protein complex network of Drosophila melanogaster
-
Guruharsha KG, Rual JF, Zhai B, Mintseris J, Vaidya P, et al. (2011) A protein complex network of Drosophila melanogaster. Cell 147: 690-703.
-
(2011)
Cell
, vol.147
, pp. 690-703
-
-
Guruharsha, K.G.1
Rual, J.F.2
Zhai, B.3
Mintseris, J.4
Vaidya, P.5
-
9
-
-
84857780876
-
Evidence for Network Evolution in an Arabidopsis Interactome Map
-
Arabidopsis Interactome Mapping Consortium
-
Arabidopsis Interactome Mapping Consortium (2011) Evidence for Network Evolution in an Arabidopsis Interactome Map. Science 333: 601-607.
-
(2011)
Science
, vol.333
, pp. 601-607
-
-
-
10
-
-
27144530248
-
Towards a proteome-scale map of the human protein-protein interaction network
-
Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178.
-
(2005)
Nature
, vol.437
, pp. 1173-1178
-
-
Rual, J.F.1
Venkatesan, K.2
Hao, T.3
Hirozane-Kishikawa, T.4
Dricot, A.5
-
11
-
-
25144498379
-
A human protein-protein interaction network: a resource for annotating the proteome
-
Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, et al. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell 122: 957-968.
-
(2005)
Cell
, vol.122
, pp. 957-968
-
-
Stelzl, U.1
Worm, U.2
Lalowski, M.3
Haenig, C.4
Brembeck, F.H.5
-
12
-
-
33947219266
-
Large-scale mapping of human protein-protein interactions by mass spectrometry
-
Ewing RM, Chu P, Elisma F, Li H, Taylor P, et al. (2007) Large-scale mapping of human protein-protein interactions by mass spectrometry. Molecular Systems Biology 3: 89.
-
(2007)
Molecular Systems Biology
, vol.3
, pp. 89
-
-
Ewing, R.M.1
Chu, P.2
Elisma, F.3
Li, H.4
Taylor, P.5
-
13
-
-
0742305866
-
Network biology: understanding the cell's functional organization
-
Barabási AL, Oltvai ZN, (2004) Network biology: understanding the cell's functional organization. Nature reviews Genetics 5: 101-13.
-
(2004)
Nature Reviews Genetics
, vol.5
, pp. 101-113
-
-
Barabási, A.L.1
Oltvai, Z.N.2
-
14
-
-
34247623628
-
Getting connected: analysis and principles of biological networks
-
Zhu X, Gerstein M, Snyder M, (2007) Getting connected: analysis and principles of biological networks. Genes and Development 21: 1010-1024.
-
(2007)
Genes and Development
, vol.21
, pp. 1010-1024
-
-
Zhu, X.1
Gerstein, M.2
Snyder, M.3
-
17
-
-
34248396293
-
Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations
-
Zotenko E, Guimaraes K, Jothi R, Przytycka T, (2006) Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations. Algorithms for Molecular Biology 1: 7.
-
(2006)
Algorithms for Molecular Biology
, vol.1
, pp. 7
-
-
Zotenko, E.1
Guimaraes, K.2
Jothi, R.3
Przytycka, T.4
-
18
-
-
34548742517
-
Identification of functional modules using network topology and high-throughput data
-
Ulitsky I, Shamir R, (2007) Identification of functional modules using network topology and high-throughput data. BMC Systems Biology 1: 8.
-
(2007)
BMC Systems Biology
, vol.1
, pp. 8
-
-
Ulitsky, I.1
Shamir, R.2
-
19
-
-
75949120438
-
How and when should interactome-derived clusters be used to predict functional modules and protein function?
-
Song J, Singh M, (2009) How and when should interactome-derived clusters be used to predict functional modules and protein function? Bioinformatics 25: 3143-3150.
-
(2009)
Bioinformatics
, vol.25
, pp. 3143-3150
-
-
Song, J.1
Singh, M.2
-
20
-
-
84855947669
-
Modular analysis of biological networks
-
In: Goryanin II, Goryachev AB, editors, Springer New York, of Advances in Experimental Medicine and Biology
-
Kaltenbach HM, Stelling J (2012) Modular analysis of biological networks. In: Goryanin II, Goryachev AB, editors, Advances in Systems Biology, Springer New York, volume 736 of Advances in Experimental Medicine and Biology. pp. 3-17.
-
(2012)
Advances in Systems Biology
, vol.736
, pp. 3-17
-
-
Kaltenbach, H.M.1
Stelling, J.2
-
21
-
-
0035799707
-
Lethality and centrality in protein networks
-
Jeong H, Mason SP, Barabási AL, Oltvai ZN, (2001) Lethality and centrality in protein networks. Nature 411: 41-42.
-
(2001)
Nature
, vol.411
, pp. 41-42
-
-
Jeong, H.1
Mason, S.P.2
Barabási, A.L.3
Oltvai, Z.N.4
-
22
-
-
50949092459
-
Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality
-
Zotenko E, Mestre J, O'Leary DP, Przytycka TM, (2008) Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLoS Computational Biology 4: e1000140.
-
(2008)
PLoS Computational Biology
, vol.4
-
-
Zotenko, E.1
Mestre, J.2
O'Leary, D.P.3
Przytycka, T.M.4
-
23
-
-
84874772501
-
From hub proteins to hub modules: The relationship between essentiality and centrality in the yeast interactome at different scales of organization
-
Song J, Singh M, (2013) From hub proteins to hub modules: The relationship between essentiality and centrality in the yeast interactome at different scales of organization. PLoS Computational Biology 9: e1002910.
-
(2013)
PLoS Computational Biology
, vol.9
-
-
Song, J.1
Singh, M.2
-
24
-
-
33745686603
-
What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?
-
Ekman D, Light S, Björklund A, Elofsson A, (2006) What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? Genome biology 7: R45.
-
(2006)
Genome Biology
, vol.7
-
-
Ekman, D.1
Light, S.2
Björklund, A.3
Elofsson, A.4
-
25
-
-
0037177560
-
Evolutionary rate in the protein interaction network
-
Fraser HB, (2002) Evolutionary rate in the protein interaction network. Science 296: 750-752.
-
(2002)
Science
, vol.296
, pp. 750-752
-
-
Fraser, H.B.1
-
26
-
-
28444448000
-
Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues
-
Wachi S, Yoneda K, Wu R, (2005) Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues. Bioinformatics 21: 4205-4208.
-
(2005)
Bioinformatics
, vol.21
, pp. 4205-4208
-
-
Wachi, S.1
Yoneda, K.2
Wu, R.3
-
27
-
-
84872187316
-
Disentangling function from topology to infer the network properties of disease genes
-
Ghersi D, Singh M, (2013) Disentangling function from topology to infer the network properties of disease genes. BMC Systems Biology 7: 5.
-
(2013)
BMC Systems Biology
, vol.7
, pp. 5
-
-
Ghersi, D.1
Singh, M.2
-
28
-
-
79954486228
-
Connectedness of ppi network neighborhoods identifies regulatory hub proteins
-
Fox A, Hescott B, Blumer A, Slonim D, (2011) Connectedness of ppi network neighborhoods identifies regulatory hub proteins. Bioinformatics 27: 1135-1142.
-
(2011)
Bioinformatics
, vol.27
, pp. 1135-1142
-
-
Fox, A.1
Hescott, B.2
Blumer, A.3
Slonim, D.4
-
29
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
-
Han JJ, Bertin N, Hao T, et al. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430: 88-93.
-
(2004)
Nature
, vol.430
, pp. 88-93
-
-
Han, J.J.1
Bertin, N.2
Hao, T.3
-
30
-
-
16844363315
-
Modularity and evolutionary constraint on proteins
-
Fraser HB, (2005) Modularity and evolutionary constraint on proteins. Nature genetics 37: 351-2.
-
(2005)
Nature Genetics
, vol.37
, pp. 351-352
-
-
Fraser, H.B.1
-
31
-
-
34250345292
-
Confirmation of organized modularity in the yeast interactome
-
Bertin N, Simonis N, Dupuy D, et al. (2007) Confirmation of organized modularity in the yeast interactome. PLoS Biology 5: e153.
-
(2007)
PLoS Biology
, vol.5
-
-
Bertin, N.1
Simonis, N.2
Dupuy, D.3
-
32
-
-
34247464637
-
Revealing static and dynamic modular architecture of the eukaryotic protein interaction network
-
Komurov K, White M, (2007) Revealing static and dynamic modular architecture of the eukaryotic protein interaction network. Molecular Systems Biology 3: 110.
-
(2007)
Molecular Systems Biology
, vol.3
, pp. 110
-
-
Komurov, K.1
White, M.2
-
33
-
-
59849125136
-
Dynamic modularity in protein interaction networks predicts breast cancer outcome
-
Taylor IW, Linding R, Wardey-Farley D, et al. (2009) Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nature Biotechnology 27: 199-204.
-
(2009)
Nature Biotechnology
, vol.27
, pp. 199-204
-
-
Taylor, I.W.1
Linding, R.2
Wardey-Farley, D.3
-
34
-
-
79952689290
-
SnapShot: Protein-Protein Interaction Networks
-
Seebacher J, Gavin AC, (2011) SnapShot: Protein-Protein Interaction Networks. Cell 144: 1000.
-
(2011)
Cell
, vol.144
, pp. 1000
-
-
Seebacher, J.1
Gavin, A.C.2
-
35
-
-
33750238153
-
Stratus not altocumulus: A new view of the yeast protein interaction network
-
Batada N, Reguly T, Breitkreutz A, et al. (2006) Stratus not altocumulus: A new view of the yeast protein interaction network. PLoS Biology 4: e317.
-
(2006)
PLoS Biology
, vol.4
-
-
Batada, N.1
Reguly, T.2
Breitkreutz, A.3
-
36
-
-
34250361148
-
Still stratus not altocumulus: Further evidence against the date/party hub distinction
-
Batada N, Reguly T, Breitkreutz A, et al. (2007) Still stratus not altocumulus: Further evidence against the date/party hub distinction. PLoS Biology 5: e154.
-
(2007)
PLoS Biology
, vol.5
-
-
Batada, N.1
Reguly, T.2
Breitkreutz, A.3
-
37
-
-
77955480278
-
Revisiting date and party hubs: Novel approches to role assignment in protein interaction networks
-
Agarwal S, Deane CM, Porter M, et al. (2010) Revisiting date and party hubs: Novel approches to role assignment in protein interaction networks. PLoS Computational Biology 6: e1000817.
-
(2010)
PLoS Computational Biology
, vol.6
-
-
Agarwal, S.1
Deane, C.M.2
Porter, M.3
-
38
-
-
78651339534
-
NCBI GEO: archive for functional genomics data sets-10 years on
-
Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, et al. (2011) NCBI GEO: archive for functional genomics data sets-10 years on. Nucleic Acids Research 39: D1005-D1010.
-
(2011)
Nucleic Acids Research
, vol.39
-
-
Barrett, T.1
Troup, D.B.2
Wilhite, S.E.3
Ledoux, P.4
Evangelista, C.5
-
39
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics 25: 25-29.
-
(2000)
Nature Genetics
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
-
42
-
-
84864117363
-
Genome-scale analysis of interaction dynamics reveals organization of biological networks
-
Das J, Mohammed J, Yu H, (2012) Genome-scale analysis of interaction dynamics reveals organization of biological networks. Bioinformatics 28: 1873-1878.
-
(2012)
Bioinformatics
, vol.28
, pp. 1873-1878
-
-
Das, J.1
Mohammed, J.2
Yu, H.3
-
43
-
-
40749088394
-
The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists
-
Heinicke S, Livstone MS, Lu C, Oughtred R, Kang F, et al. (2007) The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists. PLoS ONE 2: e766.
-
(2007)
PLoS ONE
, vol.2
-
-
Heinicke, S.1
Livstone, M.S.2
Lu, C.3
Oughtred, R.4
Kang, F.5
-
44
-
-
0000801240
-
Discovering regulatory and signalling circuits in molecular interaction networks
-
Ideker T, Ozier O, Schwikowski B, Siegel A, (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18 Suppl 1: S233-S240.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL.
-
-
Ideker, T.1
Ozier, O.2
Schwikowski, B.3
Siegel, A.4
-
45
-
-
20844450402
-
Differential network expression during drug and stress response
-
Cabusora L, Sutton E, Fulmer A, Forst C, (2005) Differential network expression during drug and stress response. Bioinformatics 21: 2898-2905.
-
(2005)
Bioinformatics
, vol.21
, pp. 2898-2905
-
-
Cabusora, L.1
Sutton, E.2
Fulmer, A.3
Forst, C.4
-
46
-
-
84863525909
-
How networks change with time
-
Park Y, Bader J, (2012) How networks change with time. Bioinformatics 28: i40-i48.
-
(2012)
Bioinformatics
, vol.28
-
-
Park, Y.1
Bader, J.2
-
48
-
-
16344381521
-
Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks
-
Hahn MW, Kern AD, (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Molecular Biology and Evolution 22: 803-806.
-
(2005)
Molecular Biology and Evolution
, vol.22
, pp. 803-806
-
-
Hahn, M.W.1
Kern, A.D.2
-
49
-
-
33644617753
-
Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets
-
Gandhi TKB, Zhong J, Mathivanan S, Karthick L, Chandrika KN, et al. (2006) Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genetics 38: 285-293.
-
(2006)
Nature Genetics
, vol.38
, pp. 285-293
-
-
Gandhi, T.K.B.1
Zhong, J.2
Mathivanan, S.3
Karthick, L.4
Chandrika, K.N.5
-
50
-
-
13844314048
-
Conserved patterns of protein interaction in multiple species
-
Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, et al. (2005) Conserved patterns of protein interaction in multiple species. Proceedings of the National Academy of Sciences of the United States of America 102: 1974-9.
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, pp. 1974-1979
-
-
Sharan, R.1
Suthram, S.2
Kelley, R.M.3
Kuhn, T.4
McCuine, S.5
-
51
-
-
33645732240
-
Modeling cellular machinery through biological network comparison
-
Sharan R, Ideker T, (2006) Modeling cellular machinery through biological network comparison. Nature biotechnology 24: 427-33.
-
(2006)
Nature Biotechnology
, vol.24
, pp. 427-433
-
-
Sharan, R.1
Ideker, T.2
-
52
-
-
79551578034
-
Improving evolutionary models of protein interaction networks
-
Gibson T, Goldberg D, (2011) Improving evolutionary models of protein interaction networks. Bioinformatics 27: 376-382.
-
(2011)
Bioinformatics
, vol.27
, pp. 376-382
-
-
Gibson, T.1
Goldberg, D.2
-
53
-
-
0037174670
-
Network motifs: Simple building blocks of complex networks
-
Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, et al. (2002) Network motifs: Simple building blocks of complex networks. Science 298: 824-827.
-
(2002)
Science
, vol.298
, pp. 824-827
-
-
Milo, R.1
Shen-Orr, S.2
Itzkovitz, S.3
Kashtan, N.4
Chklovskii, D.5
-
55
-
-
74049124545
-
Exploring biological network structure with clustered random networks
-
Bansal S, Khandelwal S, Meyers L, (2009) Exploring biological network structure with clustered random networks. BMC Bioinformatics 10: 405.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 405
-
-
Bansal, S.1
Khandelwal, S.2
Meyers, L.3
-
57
-
-
84887272391
-
Choosing appropriate models for protein-protein interaction networks: a comparison study
-
doi:10.1093/bib/bbt014
-
Shao M, Yang Y, Guan J, Zhou S, (2013) Choosing appropriate models for protein-protein interaction networks: a comparison study. Brief Bioinform doi:10.1093/bib/bbt014.
-
(2013)
Brief Bioinform
-
-
Shao, M.1
Yang, Y.2
Guan, J.3
Zhou, S.4
-
58
-
-
84864376672
-
HINT: High-quality protein interactomes and their applications in understanding human disease
-
Das J, Yu H, (2012) HINT: High-quality protein interactomes and their applications in understanding human disease. BMC Systems Biology 6: 92.
-
(2012)
BMC Systems Biology
, vol.6
, pp. 92
-
-
Das, J.1
Yu, H.2
-
59
-
-
64349094767
-
Tissue specificity and the human protein interaction network
-
Bossi A, Lehner B, (2009) Tissue specificity and the human protein interaction network. Molecular systems biology 5: 260.
-
(2009)
Molecular Systems Biology
, vol.5
, pp. 260
-
-
Bossi, A.1
Lehner, B.2
-
60
-
-
78651343711
-
DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila
-
Murali T, Pacifico S, Yu J, Guest S, Roberts GG, et al. (2011) DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. Nucleic Acids Research 39: D736-D743.
-
(2011)
Nucleic Acids Research
, vol.39
-
-
Murali, T.1
Pacifico, S.2
Yu, J.3
Guest, S.4
Roberts, G.G.5
-
61
-
-
75549087047
-
The IntAct molecular interaction database in 2010
-
Aranda B, Achuthan P, Alam-Faruque Y, et al. (2010) The IntAct molecular interaction database in 2010. Nucleic Acids Research 38 (suppl. 1) (): D525-D531.
-
(2010)
Nucleic Acids Research
, vol.38
, Issue.SUPPL. 1
-
-
Aranda, B.1
Achuthan, P.2
Alam-Faruque, Y.3
-
62
-
-
79959846617
-
PSICQUIC and PSISCORE: accessing and scoring molecular interactions
-
Aranda B, Blankenburg H, Kerrien S, Brinkman FSL, Ceol A, et al. (2011) PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nature Methods 8: 528-529.
-
(2011)
Nature Methods
, vol.8
, pp. 528-529
-
-
Aranda, B.1
Blankenburg, H.2
Kerrien, S.3
Brinkman, F.S.L.4
Ceol, A.5
-
63
-
-
14644396645
-
Functional cartography of complex metabolic networks
-
Guimerá R, Amaral LAN, (2005) Functional cartography of complex metabolic networks. Nature 433: 895-900.
-
(2005)
Nature
, vol.433
, pp. 895-900
-
-
Guimerá, R.1
Amaral, L.A.N.2
-
64
-
-
77951967208
-
SPICi: a fast clustering algorithm for large biological networks
-
Jiang P, 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
|