-
1
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast proteinprotein interaction network
-
J. D. Han, N. Bertin, T. Hao, D. S. Goldberg, G. F. Berriz et al., " Evidence for dynamically organized modularity in the yeast proteinprotein interaction network," Nature, 430, pp. 88-93, 2004
-
(2004)
Nature
, vol.430
, pp. 88-93
-
-
Han, J.D.1
Bertin, N.2
Hao, T.3
Goldberg, D.S.4
Berriz, G.F.5
-
2
-
-
59849125136
-
Dynamic modularity in protein interaction networks predicts breast cancer outcome
-
I. W. Taylor, R. Linding, D. Warde-Farley, Y. Liu, C. Pesquita, et al., "Dynamic modularity in protein interaction networks predicts breast cancer outcome," Nature Biotechnology, 27, pp. 199-204, 2009
-
(2009)
Nature Biotechnology
, vol.27
, pp. 199-204
-
-
Taylor, I.W.1
Linding, R.2
Warde-Farley, D.3
Liu, Y.4
Pesquita, C.5
-
3
-
-
33845875196
-
Relating three-dimensional structures to protein networks provides evolutionary insights
-
P. M. Kim, L. J. Lu, Y. Xia, M. B. Gerstein, "Relating three-dimensional structures to protein networks provides evolutionary insights," Science,314, pp. 1938-1941, 2006
-
(2006)
Science
, vol.314
, pp. 1938-1941
-
-
Kim, P.M.1
Lu, L.J.2
Xia, Y.3
Gerstein, M.B.4
-
4
-
-
84877730113
-
Dynamic modular architecture of protein-protein interaction networks beyond the dichotomy of 'date' and 'party' hubs
-
Article number: 1691
-
X. Chang, T. Xu, Y. Li, and K. Wang, "Dynamic modular architecture of protein-protein interaction networks beyond the dichotomy of 'date' and 'party' hubs," Scientific Reports 3, Article number: 1691 doi:10. 1038/srep01691
-
Scientific Reports
, vol.3
-
-
Chang, X.1
Xu, T.2
Li, Y.3
Wang, K.4
-
5
-
-
84919657202
-
Organized modularity in the interactome: Evidence from the analysis of dynamic organization in the cell cycle
-
in press
-
H. Wang and H. Zheng, "Organized Modularity in the Interactome: Evidence from the Analysis of Dynamic Organization in the Cell Cycle," IEEE Transaction on Computational Biology and Bioinformatics, 2014, in press
-
(2014)
IEEE Transaction on Computational Biology and Bioinformatics
-
-
Wang, H.1
Zheng, H.2
-
6
-
-
33750238153
-
Stratus not altocumulus: A new view of the yeast protein interaction network
-
N. N. Batada, T. Reguly, A. Breitkretz, L. Boucher, B. J. Breitkreutz, et al., " Stratus not altocumulus: A new view of the yeast protein interaction network," PLoS Biol. 4(10): e317, 2006
-
(2006)
PLoS Biol.
, vol.4
, Issue.10
, pp. e317
-
-
Batada, N.N.1
Reguly, T.2
Breitkretz, A.3
Boucher, L.4
Breitkreutz, B.J.5
-
7
-
-
34250361148
-
Still stratus not altocumulus: Further evidence against the date/party hub distinction
-
N. N. Batada, T. Reguly, A. Breitkreutz, L. Boucher, B. J. Breitkreutz, L. D. Hurst, et al., "Still stratus not altocumulus: further evidence against the date/party hub distinction," PLoS Biol., 5:e154, 2007
-
(2007)
PLoS Biol.
, vol.5
, pp. e154
-
-
Batada, N.N.1
Reguly, T.2
Breitkreutz, A.3
Boucher, L.4
Breitkreutz, B.J.5
Hurst, L.D.6
-
8
-
-
77955480278
-
Revisiting date and party hubs: Novel approaches to role assignment in protein interaction networks
-
S. Agarwal, C. M. Deane, M. A. Porter, N. S. Jones, "Revisiting date and party hubs: novel approaches to role assignment in protein interaction networks," PLoS Comput. Biol., 6: e1000817, 2010
-
(2010)
PLoS Comput. Biol.
, vol.6
, pp. e1000817
-
-
Agarwal, S.1
Deane, C.M.2
Porter, M.A.3
Jones, N.S.4
-
9
-
-
84894266778
-
Controllability in Cancer Metabolic Networks According to Drug Targets as Driver Nodes
-
Y. Asgari, A. Salehzadeh-Yazdi, F. Schreiber, A. Masoudi-Nejad, "Controllability in Cancer Metabolic Networks According to Drug Targets as Driver Nodes," PLoS ONE 8(11): e79397. doi:10. 1371/journal. pone. 0079397.
-
PLoS ONE
, vol.8
, Issue.11
, pp. e79397
-
-
Asgari, Y.1
Salehzadeh-Yazdi, A.2
Schreiber, F.3
Masoudi-Nejad, A.4
-
10
-
-
84900503465
-
Controllability in protein interaction networks
-
S. Wuchty, "Controllability in protein interaction networks," Proc Natl Acad Sci U S A, 2014,111(19), pp. 7156-7160.
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, Issue.19
, pp. 7156-7160
-
-
Wuchty, S.1
-
11
-
-
84900803927
-
Detection of driver metabolites in the human liver metabolic network using structural controllability analysis
-
X. Liu and L. Pan, "Detection of driver metabolites in the human liver metabolic network using structural controllability analysis," BMC Systems Biology 2014, 8:51.
-
(2014)
BMC Systems Biology
, vol.8
, pp. 51
-
-
Liu, X.1
Pan, L.2
-
12
-
-
34247508686
-
Cell cycle regulation in the postmitotic neuron: Oxymoron or new biology
-
K. Herrup and Y. Yang, "Cell cycle regulation in the postmitotic neuron: oxymoron or new biology" Nature Reviews Neuroscience 8, 368-378, 2007
-
(2007)
Nature Reviews Neuroscience
, vol.8
, pp. 368-378
-
-
Herrup, K.1
Yang, Y.2
-
13
-
-
0034887884
-
Cell cycle-mediated drug resistance: An emerging concept in cancer therapy
-
M. Shah and G. Schwartz, "Cell cycle-mediated drug resistance: an emerging concept in cancer therapy," Clin Cancer Res, 7(8): 2168-2181, 2001.
-
(2001)
Clin Cancer Res
, vol.7
, Issue.8
, pp. 2168-2181
-
-
Shah, M.1
Schwartz, G.2
-
14
-
-
79954486228
-
Connectedness of PPI network neighborhoods identifies regulatory hub proteins
-
A. D. Fox1, B. J. Hescott, A. C. Blumer, D. K. Slonim, "Connectedness of PPI network neighborhoods identifies regulatory hub proteins," Bioinformatics, 2011, 27 (8), pp. 1135-1142.
-
(2011)
Bioinformatics
, vol.27
, Issue.8
, pp. 1135-1142
-
-
Fox, A.D.1
Hescott, B.J.2
Blumer, A.C.3
Slonim, D.K.4
-
15
-
-
0001173632
-
An automatic method of solving discrete programming problems
-
A. H. Land and A. G. Doig, "An automatic method of solving discrete programming problems," Econometrica, 1960, 28(3), pp. 497-520.
-
(1960)
Econometrica
, vol.28
, Issue.3
, pp. 497-520
-
-
Land, A.H.1
Doig, A.G.2
-
16
-
-
0242490780
-
Cytoscape: A software environment for integrated models of bio-molecular interaction networks
-
P. Shannon, A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, et al., "Cytoscape: a software environment for integrated models of bio-molecular interaction networks," Genome Res. 13, pp. 2498-2504, 2013
-
(2013)
Genome Res
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
-
17
-
-
13244284551
-
Dynamic complex formation during the yeast cell cycle
-
U. de Lichtenberg, L. Jensen, S. Brunak, and P. Bork, "Dynamic complex formation during the yeast cell cycle," Science, 307, pp. 724-727, 2005
-
(2005)
Science
, vol.307
, pp. 724-727
-
-
De Lichtenberg, U.1
Jensen, L.2
Brunak, S.3
Bork, P.4
-
18
-
-
58149197597
-
DEG 5. 0, a database of essential genes in both prokaryotes and eukaryotes
-
R. Zhang and Y. Lin Y, "DEG 5. 0, a database of essential genes in both prokaryotes and eukaryotes," Nucleic Acids Research, 37, pp. D455-D458, 2009
-
(2009)
Nucleic Acids Research
, vol.37
, pp. D455-D458
-
-
Zhang, R.1
Lin Y, Y.2
-
19
-
-
41149119083
-
The role of disorder in interaction networks: A structural analysis
-
P. M. Kim, A. Sboner, Y. Xia, and M. Gerstein, "The role of disorder in interaction networks: a structural analysis," Mol Syst Biol, vol. 4, pp. 179, 2008
-
(2008)
Mol Syst Biol
, vol.4
, pp. 179
-
-
Kim, P.M.1
Sboner, A.2
Xia, Y.3
Gerstein, M.4
-
20
-
-
0034887203
-
Creating the gene ontology resource: Design and implementation
-
The Gene Ontology Consortium
-
The Gene Ontology Consortium, "Creating the gene ontology resource: Design and implementation," Genome Research, 2001, vol. 11, pp. 1425-1433, 2001.
-
(2001)
Genome Research
, vol.11
, pp. 1425-1433
-
-
-
22
-
-
0037480738
-
Investigating semantic similarity measures across the Gene Ontology: The relationship between sequence and annotation
-
P. Lord, R. Stevens, A. Brass, and C. Goble, "Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation," Bioinformatics, vol. 19, pp. 1275-1283, 2003
-
(2003)
Bioinformatics
, vol.19
, pp. 1275-1283
-
-
Lord, P.1
Stevens, R.2
Brass, A.3
Goble, C.4
-
23
-
-
17044421977
-
Gene expression correlation and gene ontology-based similarity: An assessment of quantitative relationships
-
La Jolla, CA, USA
-
H. Wang, F. Azuaje, O. Bodenreider, and J. Dopazo, "Gene expression correlation and gene ontology-based similarity: an assessment of quantitative relationships", Proc. of IEEE 2004 Symposium on Computational Intelligence in Bioinformatics and Computational Biology, La Jolla, CA, USA, 2004, pp. 25-31
-
(2004)
Proc. of IEEE 2004 Symposium on Computational Intelligence in Bioinformatics and Computational Biology
, pp. 25-31
-
-
Wang, H.1
Azuaje, F.2
Bodenreider, O.3
Dopazo, J.4
-
24
-
-
38349164409
-
Computing topological parameters of biological networks
-
Y. Assenov, F. Ramírez, S. E. Schelhorn, T. Lengauer, M. Albrecht, "Computing topological parameters of biological networks," Bioinformatics, 24(2):282-284, 2008.
-
(2008)
Bioinformatics
, vol.24
, Issue.2
, pp. 282-284
-
-
Assenov, Y.1
Ramírez, F.2
Schelhorn, S.E.3
Lengauer, T.4
Albrecht, M.5
-
25
-
-
84891782659
-
The Pfam protein families database
-
M. Punta, P. C. Coggill, R. Y. Eberhardt, J. Mistry, J. Tate, C. Boursnell, N. Pang, K. Forslund, G. Ceric, J. Clements, A. Heger, L. Holm, E. L. L. Sonnhammer, S. R. Eddy, A. Bateman, R. D. Finn, "The Pfam protein families database," Nucleic Acids Research (2014) Database Issue 42:D222-D230
-
(2014)
Nucleic Acids Research
, Issue.DATABASE ISSUE 42
, pp. D222-D230
-
-
Punta, M.1
Coggill, P.C.2
Eberhardt, R.Y.3
Mistry, J.4
Tate, J.5
Boursnell, C.6
Pang, N.7
Forslund, K.8
Ceric, G.9
Clements, J.10
Heger, A.11
Holm, L.12
Sonnhammer, E.L.L.13
Eddy, S.R.14
Bateman, A.15
Finn, R.D.16
-
26
-
-
75549089771
-
Cyclebase. Org: Version 2. 0, an updated comprehensive, multispecies repository of cell cycle experiments and derived analysis results
-
N. P. Gauthier, L. J. Jensen, R. Wernersson, S. Brunak, and T. S. Jensen, "Cyclebase. org: version 2. 0, an updated comprehensive, multispecies repository of cell cycle experiments and derived analysis results," Nucleic Acids Research, 38(Database issue), pp. D699-D702, 2009
-
(2009)
Nucleic Acids Research
, vol.38
, Issue.DATABASE ISSUE
, pp. D699-D702
-
-
Gauthier, N.P.1
Jensen, L.J.2
Wernersson, R.3
Brunak, S.4
Jensen, T.S.5
-
27
-
-
84856918212
-
HIPPIE: Integrating protein interaction networks with experiment based quality scores
-
[link]
-
M. H. Schaefer, J-F. Fontaine, A. Vinayagam, P. Porras, EE. Wanker EE, et al., "HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores. " PLoS ONE, 2012, 7(2): e31826. doi:10. 1371/journal. pone. 0031826 [link]
-
(2012)
PLoS ONE
, vol.7
, Issue.2
, pp. e31826
-
-
Schaefer, M.H.1
Fontaine, J.-F.2
Vinayagam, A.3
Porras, P.4
Wanker, E.E.5
-
28
-
-
84873512768
-
Adding protein context to the human protein-protein interaction network to reveal meaningful interactions
-
M. H. Schaefer, TJS Lopes, N. Mah, J. E. Shoemaker, Y. Matsuoka, et al., "Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions. " PLoS Comput Biol., 2013, 9(1): e1002860. doi:10. 1371/journal. pcbi. 1002860
-
(2013)
PLoS Comput Biol.
, vol.9
, Issue.1
, pp. e1002860
-
-
Schaefer, M.H.1
Lopes, T.2
Mah, N.3
Shoemaker, J.E.4
Matsuoka, Y.5
-
29
-
-
84922774376
-
Analysis of critical and redundant nodes in controlling directed and undirected complex networks using dominating sets
-
J. C. Nacher and T. Akutsu, "Analysis of critical and redundant nodes in controlling directed and undirected complex networks using dominating sets," Journal of Complex Networks, 2014, doi:10. 1093/comnet/cnu029.
-
(2014)
Journal of Complex Networks
-
-
Nacher, J.C.1
Akutsu, T.2
-
30
-
-
53349117774
-
High quality binary protein interaction map of the yeast interactome network
-
H. Yu, P. Braun, M. A. Yildirim, I. Lemmens, K. Venkatesan, J. Sahalie, et al., "High quality binary protein interaction map of the yeast interactome network," Science, 322,pp. 104-110, 2008
-
(2008)
Science
, vol.322
, pp. 104-110
-
-
Yu, H.1
Braun, P.2
Yildirim, M.A.3
Lemmens, I.4
Venkatesan, K.5
Sahalie, J.6
|