-
1
-
-
84874663959
-
A large-scale evaluation of computational protein function prediction
-
P. Radivojac, W. T. Clark, T. R. Oron, A. M. Schnoes, T. Wittkop, A. Sokolov, K. Graim, C. Funk, K. Verspoor, A. Ben-Hur, G. Pandey, J. M. Yunes, A. S. Talwalkar, S. Repo, M. L. Souza, D. Piovesan, R. Casadio, Z. Wang, J. Cheng, H. Fang, J. Gough, P. Koskinen, P. Toronen, J. Nokso-Koivisto, L. Holm, D. Cozzetto, D. W. A. Buchan, K. Bryson, D. T. Jones, B. Limaye, H. Inamdar, A. Datta, S. K. Manjari, R. Joshi, M. Chitale, D. Kihara, A. M. Lisewski, S. Erdin, E. Venner, O. Lichtarge, R. Rentzsch, H. Yang, A. E. Romero, P. Bhat, A. Paccanaro, T. Hamp, R. Kaszner, S. Seemayer, E. Vicedo, C. Schaefer, D. Achten, F. Auer, A. Boehm, T. Braun, M. Hecht, M. Heron, P. Honigschmid, T. A. Hopf, S. Kaufmann, M. Kiening, D. Krompass, C. Landerer, Y. Mahlich, M. Roos, J. Bjorne, T. Salakoski, A. Wong, H. Shatkay, F. Gatzmann, I. Sommer, M. N. Wass, M. J. E. Sternberg, N. Skunca, F. Supek, M. Bosnjak, P. Panov, S. Dzeroski, T. Smuc, Y. A. I. Kourmpetis, A. D. J. van Dijk, C. J. F. t. Braak, Y. Zhou, Q. Gong, X. Dong,W. Tian, M. Falda, P. Fontana, E. Lavezzo, B. Di Camillo, S. Toppo, L. Lan, N. Djuric, Y. Guo, S. Vucetic, A. Bairoch, M. Linial, P. C. Babbitt, S. E. Brenner, C. Orengo, B. Rost, S. D. Mooney, and I. Friedberg, "A large-scale evaluation of computational protein function prediction," Nat. Method, vol. 10, no. 3, pp. 221-227, 2013.
-
(2013)
Nat. Method
, vol.10
, Issue.3
, pp. 221-227
-
-
Radivojac, P.1
Clark, W.T.2
Oron, T.R.3
Schnoes, A.M.4
Wittkop, T.5
Sokolov, A.6
Graim, K.7
Funk, C.8
Verspoor, K.9
Ben-Hur, A.10
Pandey, G.11
Yunes, J.M.12
Talwalkar, A.S.13
Repo, S.14
Souza, M.L.15
Piovesan, D.16
Casadio, R.17
Wang, Z.18
Cheng, J.19
Fang, H.20
Gough, J.21
Koskinen, P.22
Toronen, P.23
Nokso-Koivisto, J.24
Holm, L.25
Cozzetto, D.26
Buchan, D.W.A.27
Bryson, K.28
Jones, D.T.29
Limaye, B.30
Inamdar, H.31
Datta, A.32
Manjari, S.K.33
Joshi, R.34
Chitale, M.35
Kihara, D.36
Lisewski, A.M.37
Erdin, S.38
Venner, E.39
Lichtarge, O.40
Rentzsch, R.41
Yang, H.42
Romero, A.E.43
Bhat, P.44
Paccanaro, A.45
Hamp, T.46
Kaszner, R.47
Seemayer, S.48
Vicedo, E.49
Schaefer, C.50
Achten, D.51
Auer, F.52
Boehm, A.53
Braun, T.54
Hecht, M.55
Heron, M.56
Honigschmid, P.57
Hopf, T.A.58
Kaufmann, S.59
Kiening, M.60
Krompass, D.61
Landerer, C.62
Mahlich, Y.63
Roos, M.64
Bjorne, J.65
Salakoski, T.66
Wong, A.67
Shatkay, H.68
Gatzmann, F.69
Sommer, I.70
Wass, M.N.71
Sternberg, M.J.E.72
Skunca, N.73
Supek, F.74
Bosnjak, M.75
Panov, P.76
Dzeroski, S.77
Smuc, T.78
Kourmpetis, Y.A.I.79
Van Dijk, A.D.J.80
Braak, C.J.F.T.81
Zhou, Y.82
Gong, Q.83
Dong, X.84
Tian, W.85
Falda, M.86
Fontana, P.87
Lavezzo, E.88
Di Camillo, B.89
Toppo, S.90
Lan, L.91
Djuric, N.92
Guo, Y.93
Vucetic, S.94
Bairoch, A.95
Linial, M.96
Babbitt, P.C.97
Brenner, S.E.98
Orengo, C.99
more..
-
2
-
-
0043123211
-
Eva: Evaluation of protein structure prediction servers
-
I. Koh, V. Eyrich, M. Marti-Renom, D. Przybylski, and M. Madhusudhan, "Eva: Evaluation of protein structure prediction servers," Nucl. Acids Res., vol. 31, pp. 3311-3315, 2003.
-
(2003)
Nucl. Acids Res.
, vol.31
, pp. 3311-3315
-
-
Koh, I.1
Eyrich, V.2
Marti-Renom, M.3
Przybylski, D.4
Madhusudhan, M.5
-
3
-
-
84899154353
-
Improving protein function prediction using domain and protein complexes in ppi networks
-
W. Peng, J. Wang, J. Cai, L. Chen, M. Li, and F.-X. Wu, "Improving protein function prediction using domain and protein complexes in ppi networks," BMC Syst. Biol., vol. 8, no. 1, p. 35, 2014.
-
(2014)
BMC Syst. Biol.
, vol.8
, Issue.1
, pp. 35
-
-
Peng, W.1
Wang, J.2
Cai, J.3
Chen, L.4
Li, M.5
Wu, F.-X.6
-
4
-
-
84864460609
-
Cofactor: An accurate comparative algorithm for structure-based protein function annotation
-
A. Roy, J. Yang, and Y. Zhang, "Cofactor: An accurate comparative algorithm for structure-based protein function annotation," Nucl. Acids Res., p. gks372, 2012.
-
(2012)
Nucl. Acids Res.
, pp. gks372
-
-
Roy, A.1
Yang, J.2
Zhang, Y.3
-
5
-
-
23844447959
-
Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data
-
R. Sharan, T. Ideker, B. Kelley, R. Shamir, and R. M. Karp, "Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data," J. Comput. Biol., vol. 12, no. 6, pp. 835-846, 2005.
-
(2005)
J. Comput. Biol.
, vol.12
, Issue.6
, pp. 835-846
-
-
Sharan, R.1
Ideker, T.2
Kelley, B.3
Shamir, R.4
Karp, R.M.5
-
6
-
-
84884262140
-
A review of protein function prediction under machine learning perspective
-
J. S. Bernardes, "A review of protein function prediction under machine learning perspective," Recent Patents Biotechnol., vol. 7, no. 2, pp. 122-141, 2013.
-
(2013)
Recent Patents Biotechnol.
, vol.7
, Issue.2
, pp. 122-141
-
-
Bernardes, J.S.1
-
7
-
-
84870863673
-
Identification of hierarchical and overlapping functional modules in ppi networks
-
Aug.
-
J. Wang, J. Ren, M. Li, and F.-x. Wu, "Identification of hierarchical and overlapping functional modules in ppi networks," IEEE Trans. NanoBiosci., vol. 11, no. 4, pp. 386-393, Aug. 2012.
-
(2012)
IEEE Trans. NanoBiosci.
, vol.11
, Issue.4
, pp. 386-393
-
-
Wang, J.1
Ren, J.2
Li, M.3
Wu, F.-X.4
-
8
-
-
77951288682
-
Identification of hierarchical and overlapping functional modules in ppi networksidentifying the overlapping complexes in protein interaction networks
-
M. Li, J. Wang, J. Chen, Z. Cai, and G. Chen, "Identification of hierarchical and overlapping functional modules in ppi networksidentifying the overlapping complexes in protein interaction networks," Int. J. DataMing Bioinf., vol. 4, no. 1, pp. 91-108, 2010.
-
(2010)
Int. J. DataMing Bioinf.
, vol.4
, Issue.1
, pp. 91-108
-
-
Li, M.1
Wang, J.2
Chen, J.3
Cai, Z.4
Chen, G.5
-
9
-
-
84893171062
-
Clustering based on multiple biological information: Approach for predicting protein complexes
-
X. Tang, Q. Feng, J. Wang, Y. He, and Y. Pan, "Clustering based on multiple biological information: approach for predicting protein complexes," IET Syst. Biol., vol. 7, no. 5, pp. 223-230, 2013.
-
(2013)
IET Syst. Biol.
, vol.7
, Issue.5
, pp. 223-230
-
-
Tang, X.1
Feng, Q.2
Wang, J.3
He, Y.4
Pan, Y.5
-
10
-
-
84876269415
-
Mining protein complexes from ppi networks using the minimum vertex cut
-
X. Ding, W. Wang, X. Peng, and J. Wang, "Mining protein complexes from ppi networks using the minimum vertex cut," Tsinghua Sci. Technol., vol. 17, no. 6, pp. 674-681, 2012.
-
(2012)
Tsinghua Sci. Technol.
, vol.17
, Issue.6
, pp. 674-681
-
-
Ding, X.1
Wang, W.2
Peng, X.3
Wang, J.4
-
11
-
-
84870926113
-
Identifying protein complexes from interactome based on essential proteins and local fitness method
-
Jun.
-
J. Wang, G. Chen, B. Liu, M. Li, and Y. Pan, "Identifying protein complexes from interactome based on essential proteins and local fitness method," IEEE Trans. NanoBiosci., vol. 11, no. 4, pp. 324-335, Jun. 2012.
-
(2012)
IEEE Trans. NanoBiosci.
, vol.11
, Issue.4
, pp. 324-335
-
-
Wang, J.1
Chen, G.2
Liu, B.3
Li, M.4
Pan, Y.5
-
12
-
-
78149344632
-
Identifying protein complexes from interaction networks based on clique percolation and distance restraction
-
J. Wang, B. Liu, M. Li, and Y. Pan, "Identifying protein complexes from interaction networks based on clique percolation and distance restraction," BMC Genomics, vol. 11, no. 2, p. S10, 2010.
-
(2010)
BMC Genomics
, vol.11
, Issue.2
, pp. S10
-
-
Wang, J.1
Liu, B.2
Li, M.3
Pan, Y.4
-
13
-
-
84939136773
-
Clusterviz: A cytoscape app for clustering analysis of biological network
-
preprint, 03 Oct.
-
J. Wang, J. Zhong, G. Chen, M. Li, F.-x. Wu, and Y. Pan, "Clusterviz: A cytoscape app for clustering analysis of biological network," IEEE/ACM Trans. Comput. Biol. Bioinf., preprint, 03 Oct. 2014, doi: 10.1109/TCBB.2014.2361348.
-
(2014)
IEEE/ACM Trans. Comput. Biol. Bioinf.
-
-
Wang, J.1
Zhong, J.2
Chen, G.3
Li, M.4
Wu, F.-X.5
Pan, Y.6
-
14
-
-
84927617846
-
A topology potentialbased method for identifying essential proteins from ppi networks
-
preprint, 03 Oct.
-
M. Li, Y. Lu, J. Wang, F.-X. Wu, and Y. Pan, "A topology potentialbased method for identifying essential proteins from ppi networks," IEEE/ACM Trans. Comput. Biol. Bioinf., preprint, 03 Oct. 2014, doi: 10.1109/TCBB.2014.2361350.
-
(2014)
IEEE/ACM Trans. Comput. Biol. Bioinf.
-
-
Li, M.1
Lu, Y.2
Wang, J.3
Wu, F.-X.4
Pan, Y.5
-
15
-
-
33947252154
-
Network-based prediction of protein function
-
R. Sharan, I. Ulitsky, and R. Shamir, "Network-based prediction of protein function," Molecular Syst. Biol., vol. 3, no. 1, 2007.
-
(2007)
Molecular Syst. Biol.
, vol.3
, Issue.1
-
-
Sharan, R.1
Ulitsky, I.2
Shamir, R.3
-
16
-
-
0033669189
-
A network of protein-protein interactions in yeast
-
B. Schwikowski, P. Uetz, and S. Fields, "A network of protein-protein interactions in yeast," Nature Biotechnol., vol. 18, no. 12, pp. 1257-1261, 2000.
-
(2000)
Nature Biotechnol.
, vol.18
, Issue.12
, pp. 1257-1261
-
-
Schwikowski, B.1
Uetz, P.2
Fields, S.3
-
17
-
-
0035044077
-
Assessment of prediction accuracy of protein function from protein-protein interaction data
-
H. Hishigaki, K. Nakai, T. Ono, A. Tanigami, and T. Takagi, "Assessment of prediction accuracy of protein function from protein-protein interaction data," Yeast, vol. 18, no. 6, pp. 523-531, 2001.
-
(2001)
Yeast
, vol.18
, Issue.6
, pp. 523-531
-
-
Hishigaki, H.1
Nakai, K.2
Ono, T.3
Tanigami, A.4
Takagi, T.5
-
18
-
-
33745619564
-
Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
-
H. N. Chua, W.-K. Sung, and L. Wong, "Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions," Bioinf., vol. 22, no. 13, pp. 1623-1630, 2006.
-
(2006)
Bioinf.
, vol.22
, Issue.13
, pp. 1623-1630
-
-
Chua, H.N.1
Sung, W.-K.2
Wong, L.3
-
19
-
-
29144442904
-
Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
-
E. Nabieva, K. Jim, A. Agarwal, B. Chazelle, and M. Singh, "Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps," Bioinf., vol. 21, no. suppl 1, pp. i302-i310, 2005.
-
(2005)
Bioinf.
, vol.21
, pp. i302-i310
-
-
Nabieva, E.1
Jim, K.2
Agarwal, A.3
Chazelle, B.4
Singh, M.5
-
20
-
-
80755159399
-
An iterative approach of protein function prediction
-
X. Chi and J. Hou, "An iterative approach of protein function prediction," BMC Bioinf., vol. 12, no. 1, p. 437, 2011.
-
(2011)
BMC Bioinf.
, vol.12
, Issue.1
, pp. 437
-
-
Chi, X.1
Hou, J.2
-
21
-
-
3142622851
-
An integrated probabilistic model for functional prediction of proteins
-
M. Deng, T. Chen, and F. Sun, "An integrated probabilistic model for functional prediction of proteins," J. Comput. Biol., vol. 11, no. 2-3, pp. 463-475, 2004.
-
(2004)
J. Comput. Biol.
, vol.11
, Issue.2-3
, pp. 463-475
-
-
Deng, M.1
Chen, T.2
Sun, F.3
-
22
-
-
75149153011
-
Predicting protein functions by relaxation labelling protein interaction network
-
P. Hu, H. Jiang, and A. Emili, "Predicting protein functions by relaxation labelling protein interaction network," BMC Bioinf., vol. 11, no. Suppl 1, p. S64, 2010.
-
(2010)
BMC Bioinf.
, vol.11
, pp. S64
-
-
Hu, P.1
Jiang, H.2
Emili, A.3
-
23
-
-
36949038721
-
An efficient strategy for extensive integration of diverse biological data for protein function prediction
-
H. N. Chua, W.-K. Sung, and L. Wong, "An efficient strategy for extensive integration of diverse biological data for protein function prediction," Bioinf., vol. 23, no. 24, pp. 3364-3373, 2007.
-
(2007)
Bioinf.
, vol.23
, Issue.24
, pp. 3364-3373
-
-
Chua, H.N.1
Sung, W.-K.2
Wong, L.3
-
24
-
-
80052879984
-
Protein annotation from protein interaction networks and gene ontology
-
C. D. Nguyen, K. J. Gardiner, and K. J. Cios, "Protein annotation from protein interaction networks and gene ontology," J. Biomed. Inform., vol. 44, no. 5, pp. 824-829, 2011.
-
(2011)
J. Biomed. Inform.
, vol.44
, Issue.5
, pp. 824-829
-
-
Nguyen, C.D.1
Gardiner, K.J.2
Cios, K.J.3
-
25
-
-
47549104748
-
Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function
-
W. Tian, L. V. Zhang, M. Tasan, F. D. Gibbons, O. D. King, J. Park, Z. Wunderlich, J. M. Cherry, and F. P. Roth, "Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function," Genome Biol, vol. 9, no. Suppl 1, p. S7, 2008.
-
(2008)
Genome Biol
, vol.9
, pp. S7
-
-
Tian, W.1
Zhang, L.V.2
Tasan, M.3
Gibbons, F.D.4
King, O.D.5
Park, J.6
Wunderlich, Z.7
Cherry, J.M.8
Roth, F.P.9
-
26
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
M. Ashburner, C. A. Ball, J. A. Blake, D. Botstein, H. Butler, J. M. Cherry, A. P. Davis, K. Dolinski, S. S. Dwight, J. T. Eppig, M. A. Harris, D. P. Hill DP, L.Issel-Tarver, A. Kasarskis, S. Lewis, J. C. Matese, J. E. Richardson, M. Ringwald, G.M. Rubin, G. Sherlock, "Gene ontology: Tool for the unification of biology," Nat. Genetics, vol. 25, no. 1, pp. 25-29, 2000.
-
(2000)
Nat. Genetics
, 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
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
27
-
-
0005180705
-
An information-theoretic definition of similarity
-
D. Lin, "An information-theoretic definition of similarity." in Proc. Int. Conf. Mach. Learning, vol. 98, 1998, pp. 296-304.
-
(1998)
Proc. Int. Conf. Mach. Learning
, vol.98
, pp. 296-304
-
-
Lin, D.1
-
28
-
-
34447294237
-
A new method to measure the semantic similarity of go terms
-
J. Z. Wang, Z. Du, R. Payattakool, S. Y. Philip, and C.-F. Chen, "A new method to measure the semantic similarity of go terms," Bioinf., vol. 23, no. 10, pp. 1274-1281, 2007.
-
(2007)
Bioinf.
, vol.23
, Issue.10
, pp. 1274-1281
-
-
Wang, J.Z.1
Du, Z.2
Payattakool, R.3
Philip, S.Y.4
Chen, C.-F.5
-
29
-
-
84859205429
-
A framework for incorporating functional interrelationships into protein function prediction algorithms
-
May
-
X.-F. Zhang and D.-Q. Dai, "A framework for incorporating functional interrelationships into protein function prediction algorithms," IEEE/ACM Trans. Comput. Biol. Bioinf., vol. 9, no. 3, pp. 740-753, May 2012.
-
(2012)
IEEE/ACM Trans. Comput. Biol. Bioinf.
, vol.9
, Issue.3
, pp. 740-753
-
-
Zhang, X.-F.1
Dai, D.-Q.2
-
30
-
-
84906919789
-
Predicting protein functions by using unbalanced bi-random walk algorithm on protein-protein interaction network and functional interrelationship network
-
W. Peng, J. Wang, L. Chen, J. Zhong, Z. Zhang, and Y. Pan, "Predicting protein functions by using unbalanced bi-random walk algorithm on protein-protein interaction network and functional interrelationship network," Current Protein Peptide Sci., vol. 15, no. 6, pp. 529-539, 2014.
-
(2014)
Current Protein Peptide Sci.
, vol.15
, Issue.6
, pp. 529-539
-
-
Peng, W.1
Wang, J.2
Chen, L.3
Zhong, J.4
Zhang, Z.5
Pan, Y.6
-
31
-
-
84864123907
-
Reconstructing disease phenome-genome association by bi-random walk
-
M. Xie, T. Hwang, and R. Kuang, "Reconstructing disease phenome-genome association by bi-random walk," Bioinf., p. bts067, 2012.
-
(2012)
Bioinf.
, pp. bts067
-
-
Xie, M.1
Hwang, T.2
Kuang, R.3
-
32
-
-
84879310012
-
Three-level prediction of protein function by combining profile-sequence search, profile-profile search, and domain co-occurrence networks
-
Z. Wang, R. Cao, and J. Cheng, "Three-level prediction of protein function by combining profile-sequence search, profile-profile search, and domain co-occurrence networks," BMC Bioinf., vol. 14, no. Suppl 3, p. S3, 2013.
-
(2013)
BMC Bioinf.
, vol.14
, pp. S3
-
-
Wang, Z.1
Cao, R.2
Cheng, J.3
-
33
-
-
72549092050
-
Inferring protein function by domain context similarities in protein-protein interaction networks
-
S. Zhang, H. Chen, K. Liu, and Z. Sun, "Inferring protein function by domain context similarities in protein-protein interaction networks," BMC Bioinf., vol. 10, no. 1, p. 395, 2009.
-
(2009)
BMC Bioinf.
, vol.10
, Issue.1
, pp. 395
-
-
Zhang, S.1
Chen, H.2
Liu, K.3
Sun, Z.4
-
34
-
-
3142622851
-
An integrated probabilistic model for functional prediction of proteins
-
T. C. Minghua Deng and F. Sun, "An integrated probabilistic model for functional prediction of proteins," J. Comput. Biol., vol. 11, no. 2-3, pp. 463-475, 2004.
-
(2004)
J. Comput. Biol.
, vol.11
, Issue.2-3
, pp. 463-475
-
-
Minghua Deng, T.C.1
Sun, F.2
-
35
-
-
0033971642
-
Dip: The database of interacting proteins
-
I. Xenarios, D. W. Rice, L. Salwinski, M. K. Baron, E. M. Marcotte, and D. Eisenberg, "Dip: The database of interacting proteins," Nucl. Acids Res., vol. 28, no. 1, pp. 289-291, 2000.
-
(2000)
Nucl. Acids Res.
, vol.28
, Issue.1
, pp. 289-291
-
-
Xenarios, I.1
Rice, D.W.2
Salwinski, L.3
Baron, M.K.4
Marcotte, E.M.5
Eisenberg, D.6
-
36
-
-
75849153303
-
The universal protein resource (uniprot) in 2010
-
U. Consortium, "The universal protein resource (uniprot) in 2010," Nucleic Acids Res., vol. 38, no. suppl 1, pp. D142-D148, 2010.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. D142-D148
-
-
Consortium, U.1
-
37
-
-
9144257886
-
The pfam protein families database
-
A. Bateman, L. Coin, R. Durbin, R. D. Finn, V. Hollich, S. Griffiths-Jones, A. Khanna, M. Marshall, S. Moxon, E. L. Sonnhammer, D. J. Studholme, C. Yeats, S. R. Eddy, "The pfam protein families database," Nucl. Acids Res., vol. 32, no. suppl 1, pp. D138-D141, 2004.
-
(2004)
Nucl. Acids Res.
, vol.32
, pp. D138-D141
-
-
Bateman, A.1
Coin, L.2
Durbin, R.3
Finn, R.D.4
Hollich, V.5
Griffiths-Jones, S.6
Khanna, A.7
Marshall, M.8
Moxon, S.9
Sonnhammer, E.L.10
Studholme, D.J.11
Yeats, C.12
Eddy, S.R.13
-
38
-
-
70450171827
-
Go semantic similarity-based false positive reduction of protein-protein interactions
-
J. Wang, L. Dai, and M. Li, "Go semantic similarity-based false positive reduction of protein-protein interactions," in Proc. IEEE Bioinf., Syst. Biol. Intell. Comput. Int. Joint Conf., 2009, pp. 211-214.
-
(2009)
Proc. IEEE Bioinf., Syst. Biol. Intell. Comput. Int. Joint Conf.
, pp. 211-214
-
-
Wang, J.1
Dai, L.2
Li, M.3
-
39
-
-
84872679737
-
Hf-measure: A new measurement for evaluating clusters in protein-protein interaction networks
-
M. Li, X. Wu, Y. Pan, and J. Wang, "hf-measure: A new measurement for evaluating clusters in protein-protein interaction networks," Proteomics, vol. 13, no. 1, pp. 291-300, 2013.
-
(2013)
Proteomics
, vol.13
, Issue.1
, pp. 291-300
-
-
Li, M.1
Wu, X.2
Pan, Y.3
Wang, J.4
-
40
-
-
84861492539
-
Identification of essential proteins based on edge clustering coefficient
-
Jul./Aug.
-
J. Wang, M. Li, H. Wang, and Y. Pan, "Identification of essential proteins based on edge clustering coefficient," IEEE/ACM Trans. Comput. Biol. Bioinf., vol. 9, no. 4, pp. 1070-1080, Jul./Aug. 2012.
-
(2012)
IEEE/ACM Trans. Comput. Biol. Bioinf.
, vol.9
, Issue.4
, pp. 1070-1080
-
-
Wang, J.1
Li, M.2
Wang, H.3
Pan, Y.4
-
41
-
-
79952841798
-
A fast hierarchical clustering algorithm for functional modules discovery in protein interaction networks
-
May
-
J. Wang, M. Li, J. Chen, and Y. Pan, "A fast hierarchical clustering algorithm for functional modules discovery in protein interaction networks," IEEE/ACM Trans. Comput. Biol. Bioinf., vol. 8, no. 3, pp. 607-620, May 2011.
-
(2011)
IEEE/ACM Trans. Comput. Biol. Bioinf.
, vol.8
, Issue.3
, pp. 607-620
-
-
Wang, J.1
Li, M.2
Chen, J.3
Pan, Y.4
-
42
-
-
84899149219
-
Detecting protein complexes based on uncertain graph model
-
Jun.
-
B. Zhao, J. Wang, M. Li, F. Wu, and Y. Pan, "Detecting protein complexes based on uncertain graph model," IEEE/ACM Trans. Comput. Biol. Bioinf., vol. 11, no. 3, pp. 486-497, Jun. 2014.
-
(2014)
IEEE/ACM Trans. Comput. Biol. Bioinf.
, vol.11
, Issue.3
, pp. 486-497
-
-
Zhao, B.1
Wang, J.2
Li, M.3
Wu, F.4
Pan, Y.5
-
43
-
-
84923167599
-
Identification of protein complexes using weighted pagerank-nibble algorithm and coreattachment structure
-
preprint, 04 Jul.
-
W. Peng, J. Wang, B. Zhao, and L. Wang, "Identification of protein complexes using weighted pagerank-nibble algorithm and coreattachment structure," IEEE/ACM Trans. Comput. Biol. Bioinf., preprint, 04 Jul. 2014, doi: 10.1109/TCBB.2014.2343954.
-
(2014)
IEEE/ACM Trans. Comput. Biol. Bioinf.
-
-
Peng, W.1
Wang, J.2
Zhao, B.3
Wang, L.4
-
44
-
-
84867613437
-
Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks
-
W. Peng, J. Wang, W. Wang, Q. Liu, F.-X. Wu, and Y. Pan, "Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks," BMC Syst. Biol., vol. 6, no. 1, p. 87, 2012.
-
(2012)
BMC Syst. Biol.
, vol.6
, Issue.1
, pp. 87
-
-
Peng, W.1
Wang, J.2
Wang, W.3
Liu, Q.4
Wu, F.-X.5
Pan, Y.6
-
45
-
-
84900017400
-
Predicting essential proteins based on weighted degree centrality
-
May
-
X. Tang, J. Wang, J. Zhong, and Y. Pan, "Predicting essential proteins based on weighted degree centrality," IEEE/ACM Trans. Comput. Biol. Bioinf., vol. 11, no. 2, pp. 407-418, May 2014.
-
(2014)
IEEE/ACM Trans. Comput. Biol. Bioinf.
, vol.11
, Issue.2
, pp. 407-418
-
-
Tang, X.1
Wang, J.2
Zhong, J.3
Pan, Y.4
-
46
-
-
84901397951
-
Effective identification of essential proteins based on priori knowledge, network topology and gene expressions
-
M. Li, R. Zheng, H. Zhang, J. Wang, and Y. Pan, "Effective identification of essential proteins based on priori knowledge, network topology and gene expressions," Methods, vol. 67, no. 3, pp. 325-33, 2014.
-
(2014)
Methods
, vol.67
, Issue.3
, pp. 325-333
-
-
Li, M.1
Zheng, R.2
Zhang, H.3
Wang, J.4
Pan, Y.5
-
47
-
-
84862787765
-
A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data
-
M. Li, H. Zhang, J. Wang, and Y. Pan, "A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data," BMC Syst. Biol., vol. 6, no. 1, p. 15, 2012.
-
(2012)
BMC Syst. Biol.
, vol.6
, Issue.1
, pp. 15
-
-
Li, M.1
Zhang, H.2
Wang, J.3
Pan, Y.4
-
48
-
-
84894571460
-
Udonc: An algorithm for identifying essential proteins based on protein domains and protein-protein interaction networks
-
preprint, 04 Jul.
-
W. Peng, J. Wang, Y. Cheng, Y. Lu, F.-x. Wu, and Y. Pan, "Udonc: An algorithm for identifying essential proteins based on protein domains and protein-protein interaction networks," IEEE/ACM Trans. Comput. Biol. Bioinf., preprint, 04 Jul. 2014, doi: 10.1109/ TCBB.2014.2338317.
-
(2014)
IEEE/ACM Trans. Comput. Biol. Bioinf.
-
-
Peng, W.1
Wang, J.2
Cheng, Y.3
Lu, Y.4
Wu, F.-X.5
Pan, Y.6
-
49
-
-
84994524242
-
Cytonca: A cytoscape plugin for centrality analysis and evaluation of protein interaction networks
-
Y. Tang, M. Li, J. Wang, Y. Pan, and F.-X. Wu, "Cytonca: A cytoscape plugin for centrality analysis and evaluation of protein interaction networks," Biosystems, 2014.
-
(2014)
Biosystems
-
-
Tang, Y.1
Li, M.2
Wang, J.3
Pan, Y.4
Wu, F.-X.5
-
50
-
-
54349096842
-
Modifying the dpclus algorithm for identifying protein complexes based on new topological structures
-
M. Li, J. Chen, J. Wang, B. Hu, and G. Chen, "Modifying the dpclus algorithm for identifying protein complexes based on new topological structures," BMC Bioinf., vol. 9, no. 1, p. 398, 2008.
-
(2008)
BMC Bioinf.
, vol.9
, Issue.1
, pp. 398
-
-
Li, M.1
Chen, J.2
Wang, J.3
Hu, B.4
Chen, G.5
-
51
-
-
0242268461
-
Predicting protein functions from redundancies in large-scale protein interaction networks
-
M. P. Samanta and S. Liang, "Predicting protein functions from redundancies in large-scale protein interaction networks," in Proc. Nat. Academy Sci., vol. 100, no. 22, pp. 12579-12583, 2003.
-
(2003)
Proc. Nat. Academy Sci.
, vol.100
, Issue.22
, pp. 12579-12583
-
-
Samanta, M.P.1
Liang, S.2
-
52
-
-
84861331860
-
Towards the identification of protein complexes and functional modules by integrating ppi network and gene expression data
-
M. Li, X. Wu, J. Wang, and Y. Pan, "Towards the identification of protein complexes and functional modules by integrating ppi network and gene expression data," BMC Bioinf., vol. 13, no. 1, p. 109, 2012.
-
(2012)
BMC Bioinf.
, vol.13
, Issue.1
, pp. 109
-
-
Li, M.1
Wu, X.2
Wang, J.3
Pan, Y.4
-
53
-
-
84902170916
-
Identifying dynamic protein complexes based on gene expression profiles and ppi networks
-
M. Li, W. Chen, J. Wang, F.-X. Wu, and Y. Pan, "Identifying dynamic protein complexes based on gene expression profiles and ppi networks," Biomed Res. Int., vol. 2014, p. 5, 2014.
-
(2014)
Biomed Res. Int.
, vol.2014
, pp. 5
-
-
Li, M.1
Chen, W.2
Wang, J.3
Wu, F.-X.4
Pan, Y.5
|