-
1
-
-
84896452294
-
Identifying protein complexes and functional modules - From static PPI networks to dynamic PPI networks
-
Chen B., Fan W., Liu J., Wu F. X., Identifying protein complexes and functional modules-from static PPI networks to dynamic PPI networks. Briefings in Bioinformatics 2014 15 2 177 179 10.1093/bib/bbt039
-
(2014)
Briefings in Bioinformatics
, vol.15
, Issue.2
, pp. 177-179
-
-
Chen, B.1
Fan, W.2
Liu, J.3
Wu, F.X.4
-
2
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
2-s2.0-33644555054
-
Gavin A.-C., Aloy P., Grandi P., Krause R., Boesche M., Marzioch M., Rau C., Jensen L. J., Bastuck S., Dümpelfeld B., Edelmann A., Heurtier M.-A., Hoffman V., Hoefert C., Klein K., Hudak M., Michon A.-M., Schelder M., Schirle M., Remor M., Rudi T., Hooper S., Bauer A., Bouwmeester T., Casari G., Drewes G., Neubauer G., Rick J. M., Kuster B., Bork P., Russell R. B., Superti-Furga G., Proteome survey reveals modularity of the yeast cell machinery. Nature 2006 440 7084 631 636 10.1038/nature04532 2-s2.0-33644555054
-
(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
Dümpelfeld, B.10
Edelmann, A.11
Heurtier, M.-A.12
Hoffman, V.13
Hoefert, C.14
Klein, K.15
Hudak, M.16
Michon, A.-M.17
Schelder, M.18
Schirle, M.19
Remor, M.20
Rudi, T.21
Hooper, S.22
Bauer, A.23
Bouwmeester, T.24
Casari, G.25
Drewes, G.26
Neubauer, G.27
Rick, J.M.28
Kuster, B.29
Bork, P.30
Russell, R.B.31
Superti-Furga, G.32
more..
-
4
-
-
84891785632
-
Survey: Functional module detection from protein-protein interaction networks
-
Ji J. Z., Zhang A. D., Liu C. N., Quan X. M., Liu Z. J., Survey: functional module detection from protein-protein interaction networks. IEEE Transactions on Knowledge and Data Engineering 2014 26 2 261 277
-
(2014)
IEEE Transactions on Knowledge and Data Engineering
, vol.26
, Issue.2
, pp. 261-277
-
-
Ji, J.Z.1
Zhang, A.D.2
Liu, C.N.3
Quan, X.M.4
Liu, Z.J.5
-
5
-
-
78649679994
-
Recent advances in clustering methods for protein interaction networks
-
2-s2.0-78649679994
-
Wang J., Li M., Deng Y., Pan Y., Recent advances in clustering methods for protein interaction networks. BMC Genomics 2010 11 3, article S10 10.1186/1471-2164-11-S3-S10 2-s2.0-78649679994
-
(2010)
BMC Genomics
, vol.11
, Issue.3 ARTICLE S10
-
-
Wang, J.1
Li, M.2
Deng, Y.3
Pan, Y.4
-
6
-
-
76749150479
-
Computational approaches for detecting protein complexes from protein interaction networks: A survey
-
supplement 1, article S3 2-s2.0-76749150479
-
Li X., Wu M., Kwoh C.-K., Ng S.-K., Computational approaches for detecting protein complexes from protein interaction networks: A survey. BMC Genomics 2010 11 supplement 1, article S3 10.1186/1471-2164-11-S1-S3 2-s2.0-76749150479
-
(2010)
BMC Genomics
, vol.11
-
-
Li, X.1
Wu, M.2
Kwoh, C.-K.3
Ng, S.-K.4
-
7
-
-
33645761859
-
Fast and accurate method for identifying high-quality protein-interaction modules by clique merging and its application to yeast
-
2-s2.0-33645761859
-
Zhang C., Liu S., Zhou Y., Fast and accurate method for identifying high-quality protein-interaction modules by clique merging and its application to yeast. Journal of Proteome Research 2006 5 4 801 807 10.1021/pr050366g 2-s2.0-33645761859
-
(2006)
Journal of Proteome Research
, vol.5
, Issue.4
, pp. 801-807
-
-
Zhang, C.1
Liu, S.2
Zhou, Y.3
-
8
-
-
78149344632
-
Identifying protein complexes from interaction networks based on clique percolation and distance restriction
-
2-s2.0-78149344632
-
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 2, article S10 10.1186/1471-2164-11-S2-S10 2-s2.0-78149344632
-
(2010)
BMC Genomics
, vol.11
, Issue.2 ARTICLE S10
-
-
Wang, J.1
Liu, B.2
Li, M.3
Pan, Y.4
-
9
-
-
84872678695
-
Identifying protein complexes in protein-protein interaction networks by using clique seeds and graph entropy
-
2-s2.0-84872678695
-
Chen B., Shi J., Zhang S., Wu F.-X., 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 2-s2.0-84872678695
-
(2013)
Proteomics
, vol.13
, Issue.2
, pp. 269-277
-
-
Chen, B.1
Shi, J.2
Zhang, S.3
Wu, F.-X.4
-
10
-
-
33645830948
-
CFinder: Locating cliques and overlapping modules in biological networks
-
2-s2.0-33645830948
-
Adamcsek B., Palla G., Farkas I. J., Derényi I., Vicsek T., CFinder: Locating cliques and overlapping modules in biological networks. Bioinformatics 2006 22 8 1021 1023 10.1093/bioinformatics/btl039 2-s2.0-33645830948
-
(2006)
Bioinformatics
, vol.22
, Issue.8
, pp. 1021-1023
-
-
Adamcsek, B.1
Palla, G.2
Farkas, I.J.3
Derényi, I.4
Vicsek, T.5
-
11
-
-
20444504323
-
Uncovering the overlapping community structure of complex networks in nature and society
-
2-s2.0-20444504323
-
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 2-s2.0-20444504323
-
(2005)
Nature
, vol.435
, Issue.7043
, pp. 814-818
-
-
Palla, G.1
Derényi, I.2
Farkas, I.3
Vicsek, T.4
-
12
-
-
84855178662
-
Multifunctional proteins revealed by overlapping clustering in protein interaction network
-
btr621 2-s2.0-84855178662
-
Becker E., Robisson B., Chapple C. E., Guénoche A., Brun C., Multifunctional proteins revealed by overlapping clustering in protein interaction network. Bioinformatics 2012 28 1 84 90 btr621 10.1093/bioinformatics/btr621 2-s2.0-84855178662
-
(2012)
Bioinformatics
, vol.28
, Issue.1
, pp. 84-90
-
-
Becker, E.1
Robisson, B.2
Chapple, C.E.3
Guénoche, A.4
Brun, C.5
-
13
-
-
2942552459
-
An automated method for finding molecular complexes in large protein interaction networks
-
2-s2.0-0037566556
-
Bader G. D., Hogue C. W., An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003 4 1, article 2 10.1186/1471-2105-4-2 2-s2.0-0037566556
-
(2003)
BMC Bioinformatics
, vol.4
, Issue.1 ARTICLE 2
-
-
Bader, G.D.1
Hogue, C.W.2
-
14
-
-
84860361165
-
Detecting overlapping protein complexes in protein-protein interaction networks
-
2-s2.0-84860361165
-
Nepusz T., Yu H., Paccanaro A., Detecting overlapping protein complexes in protein-protein interaction networks. Nature Methods 2012 9 5 471 472 10.1038/nmeth.1938 2-s2.0-84860361165
-
(2012)
Nature Methods
, vol.9
, Issue.5
, pp. 471-472
-
-
Nepusz, T.1
Yu, H.2
Paccanaro, A.3
-
15
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
2-s2.0-0036529479
-
Enright A. J., Van Dongen S., Ouzounis C. A., An efficient algorithm for large-scale detection of protein families. Nucleic Acids Research 2002 30 7 1575 1584 10.1093/nar/30.7.1575 2-s2.0-0036529479
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.7
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
16
-
-
84891348523
-
Functional module identification in protein interaction networks by interaction patterns
-
Wang Y. J., Qian X. N., Functional module identification in protein interaction networks by interaction patterns. Bioinformatics 2014 30 1 81 93 10.1093/bioinformatics/btt569
-
(2014)
Bioinformatics
, vol.30
, Issue.1
, pp. 81-93
-
-
Wang, Y.J.1
Qian, X.N.2
-
17
-
-
49649104565
-
A structural approach for finding functional modules from large biological networks
-
2-s2.0-49649104565
-
Mete M., Tang F., Xu X., Yuruk N., A structural approach for finding functional modules from large biological networks. BMC Bioinformatics 2008 9 9, article S19 10.1186/1471-2105-9-S9-S19 2-s2.0-49649104565
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.9 ARTICLE S19
-
-
Mete, M.1
Tang, F.2
Xu, X.3
Yuruk, N.4
-
19
-
-
79959532395
-
Graph regularized nonnegative matrix factorization for data representation
-
2-s2.0-79959532395
-
Cai D., He X., Han J., Huang T. S., Graph regularized nonnegative matrix factorization for data representation. IEEE Transactions on Pattern Analysis and Machine Intelligence 2011 33 8 1548 1560 10.1109/TPAMI.2010.231 2-s2.0-79959532395
-
(2011)
IEEE Transactions on Pattern Analysis and Machine Intelligence
, vol.33
, Issue.8
, pp. 1548-1560
-
-
Cai, D.1
He, X.2
Han, J.3
Huang, T.S.4
-
21
-
-
84859170942
-
Protein complexes discovery based on protein-protein interaction data via a regularized sparse generative network model
-
2-s2.0-84859170942
-
Zhang X.-F., Dai D.-Q., Li X.-X., Protein complexes discovery based on protein-protein interaction data via a regularized sparse generative network model. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2012 9 3 857 870 10.1109/TCBB.2012.20 2-s2.0-84859170942
-
(2012)
IEEE/ACM Transactions on Computational Biology and Bioinformatics
, vol.9
, Issue.3
, pp. 857-870
-
-
Zhang, X.-F.1
Dai, D.-Q.2
Li, X.-X.3
-
22
-
-
41349117788
-
Finding community structure in very large networks
-
066111 2-s2.0-41349117788
-
Clauset A., Newman M., Moore C., Finding community structure in very large networks. Physical Review E 2004 70 6 066111 10.1103/PhysRevE.70.066111 2-s2.0-41349117788
-
(2004)
Physical Review e
, vol.70
, Issue.6
-
-
Clauset, A.1
Newman, M.2
Moore, C.3
-
23
-
-
33645453254
-
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
-
2-s2.0-33645453254
-
Krogan N. J., Cagney G., Yu H., Zhong G., Guo X., Ignatchenko A., Li J., Pu S., Datta N., Tikuisis A. P., Punna T., Peregrín-Alvarez J. M., Shales M., Zhang X., Davey M., Robinson M. D., Paccanaro A., Bray J. E., Sheung A., Beattie B., Richards D. P., Canadien V., Lalev A., Mena F., Wong P., Starostine A., Canete M. M., Vlasblom J., Wu S., Orsi C., Collins S. R., Chandran S., Haw R., Rilstone J. J., Gandi K., Thompson N. J., Musso G., St Onge P., Ghanny S., Lam M. H. Y., Butland G., Altaf-Ul A. M., Kanaya S., Shilatifard A., O'Shea E., Weissman J. S., Ingles C. J., Hughes T. R., Parkinson J., Gerstein M., Wodak S. J., Emili A., Greenblatt J. F., Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 2006 440 7084 637 643 10.1038/nature04670 2-s2.0-33645453254
-
(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
Punna, T.11
Peregrín-Alvarez, J.M.12
Shales, M.13
Zhang, X.14
Davey, M.15
Robinson, M.D.16
Paccanaro, A.17
Bray, J.E.18
Sheung, A.19
Beattie, B.20
Richards, D.P.21
Canadien, V.22
Lalev, A.23
Mena, F.24
Wong, P.25
Starostine, A.26
Canete, M.M.27
Vlasblom, J.28
Wu, S.29
Orsi, C.30
Collins, S.R.31
Chandran, S.32
Haw, R.33
Rilstone, J.J.34
Gandi, K.35
Thompson, N.J.36
Musso, G.37
St Onge, P.38
Ghanny, S.39
Lam, M.H.Y.40
Butland, G.41
Altaf-Ul, A.M.42
Kanaya, S.43
Shilatifard, A.44
O'Shea, E.45
Weissman, J.S.46
Ingles, C.J.47
Hughes, T.R.48
Parkinson, J.49
Gerstein, M.50
Wodak, S.J.51
Emili, A.52
Greenblatt, J.F.53
more..
-
24
-
-
34147121646
-
Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae
-
2-s2.0-34147121646
-
Collins S. R., Kemmeren P., Zhao X.-C., Greenblatt J. F., Spencer F., Hoolstege F. C. P., Weissman J. S., Krogan N. J., Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Molecular and Cellular Proteomics 2007 6 3 439 450 10.1074/mcp.M600381-MCP200 2-s2.0-34147121646
-
(2007)
Molecular and Cellular 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
Hoolstege, F.C.P.6
Weissman, J.S.7
Krogan, N.J.8
-
25
-
-
33644873184
-
BioGRID: A general repository for interaction datasets
-
supplement 1 2-s2.0-33644873184
-
Stark C., Breitkreutz B.-J., Reguly T., Boucher L., Breitkreutz A., Tyers M., BioGRID: a general repository for interaction datasets. Nucleic Acids Research 2006 34 supplement 1 D535 D539 10.1093/nar/gkj109 2-s2.0-33644873184
-
(2006)
Nucleic Acids Research
, vol.34
, pp. D535-D539
-
-
Stark, C.1
Breitkreutz, B.-J.2
Reguly, T.3
Boucher, L.4
Breitkreutz, A.5
Tyers, M.6
-
26
-
-
63349085550
-
Up-to-date catalogues of yeast protein complexes
-
2-s2.0-63349085550
-
Pu S., Wong J., Turner B., Cho E., Wodak S. J., Up-to-date catalogues of yeast protein complexes. Nucleic Acids Research 2009 37 3 825 831 10.1093/nar/gkn1005 2-s2.0-63349085550
-
(2009)
Nucleic Acids Research
, vol.37
, Issue.3
, pp. 825-831
-
-
Pu, S.1
Wong, J.2
Turner, B.3
Cho, E.4
Wodak, S.J.5
-
27
-
-
12344269924
-
GO:: TermFinder - Open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
-
2-s2.0-12344269924
-
Boyle E. I., Weng S., Gollub J., Jin H., Botstein D., Cherry J. M., 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 2-s2.0-12344269924
-
(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
-
28
-
-
38549123363
-
Gene Ontology annotations at SGD: New data sources and annotation methods
-
2-s2.0-38549123363
-
Hong E. L., Balakrishnan R., Dong Q., Christie K. R., Park J., Binkley G., Costanzo M. C., Dwight S. S., Engel S. R., Fisk D. G., Hirschman J. E., Hitz B. C., Krieger C. J., Livstone M. S., Miyasato S. R., Nash R. S., Oughtred R., Skrzypek M. S., Weng S., Wong E. D., Zhu K. K., Dolinski K., Botstein D., Cherry J. M., Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Research 2008 36 1 D577 D581 10.1093/nar/gkm909 2-s2.0-38549123363
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.1
, pp. D577-D581
-
-
Hong, E.L.1
Balakrishnan, R.2
Dong, Q.3
Christie, K.R.4
Park, J.5
Binkley, G.6
Costanzo, M.C.7
Dwight, S.S.8
Engel, S.R.9
Fisk, D.G.10
Hirschman, J.E.11
Hitz, B.C.12
Krieger, C.J.13
Livstone, M.S.14
Miyasato, S.R.15
Nash, R.S.16
Oughtred, R.17
Skrzypek, M.S.18
Weng, S.19
Wong, E.D.20
Zhu, K.K.21
Dolinski, K.22
Botstein, D.23
Cherry, J.M.24
more..
-
29
-
-
84885704334
-
Identifying protein complexes from heterogeneous biological data
-
Wu M., Xie Z. P., Li X. L., Kwoh C. K., Zheng J., Identifying protein complexes from heterogeneous biological data. Proteins-Structure Function and Bioinformatics 2013 81 11 2023 2033
-
(2013)
Proteins-Structure Function and Bioinformatics
, vol.81
, Issue.11
, pp. 2023-2033
-
-
Wu, M.1
Xie, Z.P.2
Li, X.L.3
Kwoh, C.K.4
Zheng, J.5
-
30
-
-
84896760571
-
Dynamic protein interaction network construction and applications
-
Wang J., Peng X., Peng W., Wu F. X., Dynamic protein interaction network construction and applications. Proteomics 2014 14 4-5 338 352 10.1002/pmic.201300257
-
(2014)
Proteomics
, vol.14
, Issue.4-5
, pp. 338-352
-
-
Wang, J.1
Peng, X.2
Peng, W.3
Wu, F.X.4
-
31
-
-
84874240374
-
Hierarchical classification of protein folds using a novel ensemble classifier
-
e56499 2-s2.0-84874240374
-
Lin C., Zou Y., Qin J., Liu X., Jiang Y., Ke C., Zou Q., Hierarchical classification of protein folds using a novel ensemble classifier. PLoS ONE 2013 8 2 e56499 10.1371/journal.pone.0056499 2-s2.0-84874240374
-
(2013)
PLoS ONE
, vol.8
, Issue.2
-
-
Lin, C.1
Zou, Y.2
Qin, J.3
Liu, X.4
Jiang, Y.5
Ke, C.6
Zou, Q.7
-
32
-
-
84911123541
-
Structure-based protein-protein interaction networks and drug design
-
Naveed H., Han J. J., Structure-based protein-protein interaction networks and drug design. Quantitative Biology 2013 1 3 183 191
-
(2013)
Quantitative Biology
, vol.1
, Issue.3
, pp. 183-191
-
-
Naveed, H.1
Han, J.J.2
-
33
-
-
84879259855
-
Prediction and analysis of post-translational pyruvoyl residue modification sites from internal serines in proteins
-
e66678 2-s2.0-84879259855
-
Jiang Y., Li B. Q., Zhang Y., Feng Y. M., Gao Y. F., Zhang N., Cai Y. D., Prediction and analysis of post-translational pyruvoyl residue modification sites from internal serines in proteins. PLoS ONE 2013 8 6 e66678 10.1371/journal.pone.0066678 2-s2.0-84879259855
-
(2013)
PLoS ONE
, vol.8
, Issue.6
-
-
Jiang, Y.1
Li, B.Q.2
Zhang, Y.3
Feng, Y.M.4
Gao, Y.F.5
Zhang, N.6
Cai, Y.D.7
|