-
1
-
-
3042523388
-
Predicting protein complex membership using probabilistic network reliability
-
DOI 10.1101/gr.2203804
-
Asthana, S. et al. (2004) Predicting protein complex membership using probabilistic network reliability. Genome Res., 14, 1170-1175. (Pubitemid 38811553)
-
(2004)
Genome Research
, vol.14
, Issue.6
, pp. 1170-1175
-
-
Asthana, S.1
King, O.D.2
Gibbons, F.D.3
Roth, F.P.4
-
2
-
-
0036789265
-
Analyzing yeast protein-protein interaction data obtained from different sources
-
Bader, G. and Hogue, C. (2002) Analyzing yeast protein-protein interaction data obtained from different sources. Nat. Biotechnol., 20, 991-997.
-
(2002)
Nat. Biotechnol
, vol.20
, pp. 991-997
-
-
Bader, G.1
Hogue, C.2
-
3
-
-
33751255087
-
Evaluation of clustering algorithms for protein-protein interaction networks
-
Brohee, S. and van Helden, J. (2006) Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics, 7, 488.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 488
-
-
Brohee, S.1
Van Helden, J.2
-
4
-
-
77955287981
-
Microarray meta-analysis database (m2db): A uniformly pre-processed, quality controlled, and manually curated human clinical microarray database
-
Cheng, W.-C. et al. (2010) Microarray meta-analysis database (m2db): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database. BMC Bioinformatics, 11, 421.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 421
-
-
Cheng, W.-C.1
-
5
-
-
33745619564
-
Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
-
DOI 10.1093/bioinformatics/btl145
-
Chua, H.N. et al. (2006) Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics, 22, 1623-1630. (Pubitemid 43985296)
-
(2006)
Bioinformatics
, vol.22
, Issue.13
, pp. 1623-1630
-
-
Chua, H.N.1
Sung, W.-K.2
Wong, L.3
-
6
-
-
35348891430
-
Network-based classification of breast cancer metastasis
-
Chuang, H.Y. et al. (2007) Network-based classification of breast cancer metastasis. Mol. Syst. Biol., 3, 140-140.
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 140-140
-
-
Chuang, H.Y.1
-
7
-
-
6044249965
-
Saccharomyces genome database: Underlying principles and organisation
-
Dwight, S. et al. (2004) Saccharomyces genome database: underlying principles and organisation. Brief. Bioinform., 5, 9-22.
-
(2004)
Brief. Bioinform
, vol.5
, pp. 9-22
-
-
Dwight, S.1
-
8
-
-
79955787030
-
Global geometric affinity for revealing high fidelity protein interaction network
-
Fang, Y. et al. (2011) Global geometric affinity for revealing high fidelity protein interaction network. PLoS ONE, 6, e19349.
-
(2011)
PLoS ONE
, vol.6
-
-
Fang, Y.1
-
9
-
-
33847766633
-
Random-walk computation of similarities between nodes of a graph with application to collaborative recommendation
-
DOI 10.1109/TKDE.2007.46
-
Fouss, F. et al. (2007) Random-walk computation of similarities between nodes of a graph with application to collaborative recommendation. IEEE Trans. Knowl. Data Eng., 19, 355-369. (Pubitemid 46374533)
-
(2007)
IEEE Transactions on Knowledge and Data Engineering
, vol.19
, Issue.3
, pp. 355-369
-
-
Fouss, F.1
Pirotte, A.2
Renders, J.-M.3
Saerens, M.4
-
10
-
-
84945923591
-
A method for comparing two hierarchical clusterings
-
Fowlkes, E. and Mallows, C. (1983) A method for comparing two hierarchical clusterings. J. Am. Stat. Assoc., 78, 553-569.
-
(1983)
J. Am. Stat. Assoc
, vol.78
, pp. 553-569
-
-
Fowlkes, E.1
Mallows, C.2
-
11
-
-
70349212097
-
Bootstrapping the interactome: Unsupervised identification of protein complexes in yeast
-
Friedel, C. et al. (2009) Bootstrapping the interactome: unsupervised identification of protein complexes in yeast. J. Comput. Biol., 16, 1-17.
-
(2009)
J. Comput. Biol
, vol.16
, pp. 1-17
-
-
Friedel, C.1
-
12
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch, A. et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell, 11, 4241-4257.
-
(2000)
Mol. Biol. Cell
, vol.11
, pp. 4241-4257
-
-
Gasch, A.1
-
13
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
Gavin, A. 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.1
-
14
-
-
0038607954
-
Mnd2 and Swm1 are core subunits of the Saccharomyces cerevisiae anaphase-promoting complex
-
DOI 10.1074/jbc.M213109200
-
Hall, M.C. et al. (2003) Mnd2 and swm1 are core subunits of the saccharomyces cerevisiae anaphase-promoting complex. J. Biol. Chem., 278, 16698-16705. (Pubitemid 36799534)
-
(2003)
Journal of Biological Chemistry
, vol.278
, Issue.19
, pp. 16698-16705
-
-
Hall, M.C.1
Torres, M.P.2
Schroeder, G.K.3
Borchers, C.H.4
-
15
-
-
74249100674
-
Genome-wide association data reveal a global map of genetic interactions among protein complexes
-
Hannum, G. et al. (2009) Genome-wide association data reveal a global map of genetic interactions among protein complexes. PLoS Genet., 5, e1000782.
-
(2009)
PLoS Genet
, vol.5
-
-
Hannum, G.1
-
16
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
-
DOI 10.1038/nature02555
-
Han, J.-D. J. et al. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature, 430, 88-93. (Pubitemid 38915230)
-
(2004)
Nature
, vol.430
, Issue.6995
, pp. 88-93
-
-
Han, J.-D.J.1
Berlin, N.2
Hao, T.3
Goldberg, D.S.4
Berriz, G.F.5
Zhang, L.V.6
Dupuy, D.7
Walhout, A.J.M.8
Cusick, M.E.9
Roth, F.P.10
Vidal, M.11
-
17
-
-
66249129037
-
A dynamic network approach for the study of human phenotypes
-
Hidalgo, C. et al. (2009) A dynamic network approach for the study of human phenotypes. PLoS Comput. Biol., 5, e1000353.
-
(2009)
PLoS Comput. Biol
, vol.5
-
-
Hidalgo, C.1
-
18
-
-
36949000237
-
Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps
-
Huang, H. et al. (2007) Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps. PLoS Comput. Biol., 3, e214.
-
(2007)
PLoS Comput. Biol
, vol.3
-
-
Huang, H.1
-
19
-
-
41649119247
-
Protein networks in disease
-
DOI 10.1101/gr.071852.107
-
Ideker, T. and Sharan, R. (2008) Protein networks in disease. Genome Res., 18, 644-652. (Pubitemid 351482789)
-
(2008)
Genome Research
, vol.18
, Issue.4
, pp. 644-652
-
-
Ideker, T.1
Sharan, R.2
-
20
-
-
0035799707
-
Lethality and centrality in protein networks
-
DOI 10.1038/35075138
-
Jeong, H. et al. (2001) Lethality and centrality in protein networks. Nature, 411, 41-42. (Pubitemid 32428180)
-
(2001)
Nature
, vol.411
, Issue.6833
, pp. 41-42
-
-
Jeong, H.1
Mason, S.P.2
Barabasi, A.-L.3
Oltvai, Z.N.4
-
21
-
-
58149193222
-
Human protein reference database-2009 update
-
Keshava Prasad, T.S. et al. (2009) Human protein reference database-2009 update. Nucleic Acids Res., 37, D767-D772.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Keshava Prasad, T.S.1
-
22
-
-
79953645463
-
Identifying causal genes and dysregulated pathways in complex diseases
-
Kim, Y. et al. (2011) Identifying causal genes and dysregulated pathways in complex diseases. PLoS Comput. Biol., 7, e1001095.
-
(2011)
PLoS Comput. Biol
, vol.7
-
-
Kim, Y.1
-
23
-
-
10244264813
-
Protein complex prediction via cost-based clustering
-
DOI 10.1093/bioinformatics/bth351
-
King, A. et al. (2004) Protein complex prediction via cost-based clustering. Bioinformatics, 20, 3013-3020. (Pubitemid 39619193)
-
(2004)
Bioinformatics
, vol.20
, Issue.17
, pp. 3013-3020
-
-
King, A.D.1
Przulj, N.2
Jurisica, I.3
-
24
-
-
33645453254
-
Global landscape of protein complexes in the yeast saccharomyces cerevisiae
-
Krogan, N. 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.1
-
25
-
-
70049106408
-
Geometric de-noising of protein-protein interaction networks
-
Kuchaiev, O. et al. (2009) Geometric de-noising of protein-protein interaction networks. PLoS Comput. Biol., 5, e1000454.
-
(2009)
PLoS Comput. Biol
, vol.5
-
-
Kuchaiev, O.1
-
26
-
-
56649094590
-
Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species
-
Lee, K. et al. (2008) Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. Nucleic Acids Res., 36, e136.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Lee, K.1
-
27
-
-
33846705486
-
Network neighborhood analysis with the multi-node topological overlap measure
-
DOI 10.1093/bioinformatics/btl581
-
Li, A. and Horvath, S. (2007) Network neighborhood analysis with the multi-node topological overlap measure. Bioinformatics, 23, 222-231. (Pubitemid 46189613)
-
(2007)
Bioinformatics
, vol.23
, Issue.2
, pp. 222-231
-
-
Li, A.1
Horvath, S.2
-
29
-
-
78751613300
-
Link prediction in complex networks: A survey
-
Lü, L. and Zhou, T. (2011) Link prediction in complex networks: a survey. Physica A, 390, 1150-1170.
-
(2011)
Physica A
, vol.390
, pp. 1150-1170
-
-
Lü, L.1
Zhou, T.2
-
31
-
-
33644875537
-
MIPS: Analysis and annotation of proteins from whole genomes in 2005
-
Mewes, H. et al. (2006) MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res., 34, D169-D172.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Mewes, H.1
-
32
-
-
78651455332
-
Protein-protein interactions: Making sense of networks via graph-theoretic modeling
-
Przulj, N. (2011) Protein-protein interactions: making sense of networks via graph-theoretic modeling. Bioessays, 33, 115-123.
-
(2011)
Bioessays
, vol.33
, pp. 115-123
-
-
Przulj, N.1
-
33
-
-
1542357701
-
Defining and identifying communities in networks
-
DOI 10.1073/pnas.0400054101
-
Radicchi, F. et al. (2004) Defining and identifying communities in networks. Proc. Natl Acad. Sci. USA, 101, 2658-2663. (Pubitemid 38327665)
-
(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
Paris, D.5
-
34
-
-
33750719615
-
Identification and evaluation of weak community structures in networks
-
Proceedings of the 21st National Conference on Artificial Intelligence and the 18th Innovative Applications of Artificial Intelligence Conference, AAAI-06/IAAI-06
-
Ruan, J. and Zhang, W. (2006) Identification and evaluation of weak community structures in networks. In Proceedings National Conference on Artificial Intelligence (AAAI-06). Boston, MA, AAAI press, pp. 470-475. (Pubitemid 44705328)
-
(2006)
Proceedings of the National Conference on Artificial Intelligence
, vol.1
, pp. 470-475
-
-
Ruan, J.1
Zhang, W.2
-
35
-
-
38349191347
-
Identifying network community structures with a high resolution
-
Ruan, J. and Zhang, W. (2008) Identifying network community structures with a high resolution. Phys. Rev. E, 77, 016104.
-
(2008)
Phys. Rev. e
, vol.77
, pp. 016104
-
-
Ruan, J.1
Zhang, W.2
-
36
-
-
77951202722
-
A fully automated method for discovering community structures in high dimensional data
-
Miami, FL, IEEE
-
Ruan, J. (2009) A fully automated method for discovering community structures in high dimensional data. In Proceedings of IEEE International Conference on Data Mining (ICDM-09). Miami, FL, IEEE.
-
(2009)
Proceedings of IEEE International Conference on Data Mining (ICDM-09)
-
-
Ruan, J.1
-
37
-
-
33947252154
-
Network-based prediction of protein function
-
Sharan, R. et al. (2007) Network-based prediction of protein function. Mol. Syst. Biol., 3, 88.
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 88
-
-
Sharan, R.1
-
38
-
-
78651328883
-
The BioGRID interaction database: 2011 update
-
Stark, C. et al. (2011) The BioGRID interaction database: 2011 update. Nucleic Acids Res., 39, D698-D704.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Stark, C.1
-
39
-
-
45849110261
-
An in vivo map of the yeast protein interactome
-
DOI 10.1126/science.1153878
-
Tarassov, K. et al. (2008) An in vivo map of the yeast protein interactome. Science, 320, 1465-1470. (Pubitemid 351929421)
-
(2008)
Science
, vol.320
, Issue.5882
, pp. 1465-1470
-
-
Tarassov, K.1
Messier, V.2
Landry, C.R.3
Radinovic, S.4
Serna Molina, M.M.5
Shames, I.6
Malitskaya, Y.7
Vogel, J.8
Bussey, H.9
Michnick, S.W.10
-
40
-
-
34748827346
-
Fast random walk with restart and its applications
-
ICDM '06. Washington DC IEEE Computer Society
-
Tong, H. et al. (2006) Fast random walk with restart and its applications. In Proceedings of the Sixth International Conference on Data Mining, 2006, ICDM '06. Washington, DC, IEEE Computer Society, pp. 613-622.
-
(2006)
Proceedings of the Sixth International Conference on Data Mining 2006
, pp. 613-622
-
-
Tong, H.1
-
41
-
-
65449141657
-
Identifying functional modules using expression profiles and confidence-scored protein interactions
-
Ulitsky, I. and Shamir, R. (2009) Identifying functional modules using expression profiles and confidence-scored protein interactions. Bioinformatics, 25, 1158-1164.
-
(2009)
Bioinformatics
, vol.25
, pp. 1158-1164
-
-
Ulitsky, I.1
Shamir, R.2
-
42
-
-
65849100458
-
Markov clustering versus affinity propagation for the partitioning of protein interaction graphs
-
Vlasblom, J. and Wodak, S. (2009) Markov clustering versus affinity propagation for the partitioning of protein interaction graphs. BMC Bioinformatics, 10, 99.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 99
-
-
Vlasblom, J.1
Wodak, S.2
-
43
-
-
40449109730
-
Consistent dissection of the protein interaction network by combining global and local metrics
-
Wang, C. et al. (2007a) Consistent dissection of the protein interaction network by combining global and local metrics. Genome Biol., 8, R271.
-
(2007)
Genome Biol
, vol.8
-
-
Wang, C.1
-
44
-
-
34447294237
-
A new method to measure the semantic similarity of GO terms
-
DOI 10.1093/bioinformatics/btm087
-
Wang, J. et al. (2007b) A new method to measure the semantic similarity of go terms. Bioinformatics, 23, 1274-1281. (Pubitemid 47050544)
-
(2007)
Bioinformatics
, vol.23
, Issue.10
, pp. 1274-1281
-
-
Wang, J.Z.1
Du, Z.2
Payattakool, R.3
Yu, P.S.4
Chen, C.-F.5
-
45
-
-
78649679994
-
Recent advances in clustering methods for protein interaction networks
-
Wang, J. et al. (2010) Recent advances in clustering methods for protein interaction networks. BMC Genomics, 11 (Suppl. 3), S10.
-
(2010)
BMC Genomics
, vol.11
, Issue.SUPPL. 3
-
-
Wang, J.1
-
46
-
-
77950444122
-
Building and analyzing protein interactome networks by cross-species comparisons
-
Wiles, A. et al. (2010) Building and analyzing protein interactome networks by cross-species comparisons. BMC Syst. Biol., 4, 36.
-
(2010)
BMC Syst. Biol
, vol.4
, pp. 36
-
-
Wiles, A.1
-
47
-
-
77951942707
-
Gosemsim: An R package for measuring semantic similarity among go terms and gene products
-
Yu, G. et al. (2010) Gosemsim: an R package for measuring semantic similarity among go terms and gene products. Bioinformatics, 26, 976-978.
-
(2010)
Bioinformatics
, vol.26
, pp. 976-978
-
-
Yu, G.1
-
48
-
-
34247622363
-
The importance of bottlenecks in protein networks: Correlation with gene essentiality and expression dynamics
-
Yu, H. et al. (2007) The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput. Biol., 3, e59.
-
(2007)
PLoS Comput. Biol
, vol.3
-
-
Yu, H.1
-
49
-
-
53349117774
-
High-quality binary protein interaction map of the yeast interactome network
-
Yu, H. et al. (2008) High-quality binary protein interaction map of the yeast interactome network. Science, 322, 1158684-1158110.
-
(2008)
Science
, vol.322
, pp. 1158684-1158110
-
-
Yu, H.1
|