-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, Basic local alignment search tool, J Mol Biol 215:403-410, 1990.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
2
-
-
81955163188
-
Predicting protein functions from protein interaction networks
-
Chua NH, Sung WK, Wong L, Predicting protein functions from protein interaction networks, in Biological Data Mining in Protein Interaction Networks, IGI Global, Hershey, pp. 203-222, 2009.
-
(2009)
Biological Data Mining in Protein Interaction Networks, IGI Global, Hershey
, pp. 203-222
-
-
Chua, N.H.1
Sung, W.K.2
Wong, L.3
-
3
-
-
0033669189
-
A network of interacting proteins in yeast
-
Schwikowski B, Uetz P, Fields S, A network of interacting proteins in yeast, Nat Biotechnol 18:1257-1261, 2000.
-
(2000)
Nat Biotechnol
, vol.18
, pp. 1257-1261
-
-
Schwikowski, B.1
Uetz, P.2
Fields, S.3
-
4
-
-
23744481400
-
What do we learn from high-throughput protein interaction data
-
Titz B, Schlesner M, Uetz P, What do we learn from high-throughput protein interaction data, Expert Rev Proteomics 1:111-121, 2004.
-
(2004)
Expert Rev Proteomics
, vol.1
, pp. 111-121
-
-
Titz, B.1
Schlesner, M.2
Uetz, P.3
-
5
-
-
33745619564
-
Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
-
Chua HN, Sung WK, Wong L, Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions, Bioinformatics 22(13):1623-1630, 2006.
-
(2006)
Bioinformatics
, vol.22
, Issue.13
, pp. 1623-1630
-
-
Chua, H.N.1
Sung, W.K.2
Wong, L.3
-
6
-
-
85044707001
-
Network based protein function prediction
-
Sharan R, Ulitsky I, Shamir R, Network based protein function prediction, Mol Syst Biol 3:88, 2006.
-
(2006)
Mol Syst Biol
, vol.3
, pp. 88
-
-
Sharan, R.1
Ulitsky, I.2
Shamir, R.3
-
7
-
-
0035044077
-
Assessment of prediction accuracy of protein function from protein-protein interaction data
-
Hishigaki H, Nakai K, Ono T, Tanigami A, Takagi T, Assessment of prediction accuracy of protein function from protein-protein interaction data, Yeast 18:523-531, 2001.
-
(2001)
Yeast
, vol.18
, pp. 523-531
-
-
Hishigaki, H.1
Nakai, K.2
Ono, T.3
Tanigami, A.4
Takagi, T.5
-
8
-
-
0742304254
-
Prediction of protein function using protein-protein interaction data
-
Deng M, Zhang K, Mehta S, Chen T, Sun F, Prediction of protein function using protein-protein interaction data, J Comput Biol 10:947-960, 2003.
-
(2003)
J Comput Biol
, vol.10
, pp. 947-960
-
-
Deng, M.1
Zhang, K.2
Mehta, S.3
Chen, T.4
Sun, F.5
-
9
-
-
84901268258
-
Collective prediction of protein functions from protein-protein interaction networks
-
Wu QY, Ye YM, Michael KNg, Ho S-S, Shi R, Collective prediction of protein functions from protein-protein interaction networks, BMC Bioinformatics 15(2):S9, 2014.
-
(2014)
BMC Bioinformatics
, vol.15
, Issue.2
, pp. S9
-
-
Wu, Q.Y.1
Ye, Y.M.2
Michael, K.N.G.3
Ho, S.-S.4
Shi, R.5
-
10
-
-
84906936748
-
Active learning for protein function prediction in protein-protein interaction networks
-
Xiong W, Xie L, Zhou SG, Guan JH, Active learning for protein function prediction in protein-protein interaction networks, Neurocomputing 145:0925-2312, 2014.
-
(2014)
Neurocomputing
, vol.145
, pp. 0925-2312
-
-
Xiong, W.1
Xie, L.2
Zhou, S.G.3
Guan, J.H.4
-
11
-
-
0038699587
-
Global protein function prediction from protein-protein interaction networks
-
Vazquez A, Flammini A, Maritan A, Vespignani A, Global protein function prediction from protein-protein interaction networks, Nat Biotechnol 21:697-700, 2003.
-
(2003)
Nat Biotechnol
, vol.21
, pp. 697-700
-
-
Vazquez, A.1
Flammini, A.2
Maritan, A.3
Vespignani, A.4
-
12
-
-
1542327694
-
Whole-genome annotation by using evidence integration in functional-linkage networks
-
Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, Cantor CR, Kasif S, Whole-genome annotation by using evidence integration in functional-linkage networks, Proc Natl Acad Sci 101:2888-2893, 2004.
-
(2004)
Proc Natl Acad Sci
, vol.101
, pp. 2888-2893
-
-
Karaoz, U.1
Murali, T.M.2
Letovsky, S.3
Zheng, Y.4
Ding, C.5
Cantor, C.R.6
Kasif, S.7
-
13
-
-
29144442904
-
Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
-
Nabieva E, Jim K, Agarwal A, Chazelle B, Singh M, Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps, Bioinformatics 21(1): i302-i310, 2005.
-
(2005)
Bioinformatics
, vol.21
, Issue.1
, pp. i302-i310
-
-
Nabieva, E.1
Jim, K.2
Agarwal, A.3
Chazelle, B.4
Singh, M.5
-
14
-
-
80755159399
-
An iterative approach of protein function prediction
-
Chi XX, Hou JY, An iterative approach of protein function prediction, BMC Bioinformatics 12:43, 2011.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 43
-
-
Chi, X.X.1
Hou, J.Y.2
-
15
-
-
84947042904
-
Dynamically predicting protein functions from semantic associations of proteins
-
Hou J, Wei Z, Chen YP, Dynamically predicting protein functions from semantic associations of proteins, Netw Modeling Anal Health Inform Bioinf 2(4):175-183, 2013.
-
(2013)
Netw Modeling Anal Health Inform Bioinf
, vol.2
, Issue.4
, pp. 175-183
-
-
Hou, J.1
Wei, Z.2
Chen, Y.P.3
-
16
-
-
84899154353
-
Improving protein function prediction using domain and protein complexes in PPI networks
-
Wei P et al., Improving protein function prediction using domain and protein complexes in PPI networks, BMC Syst Biol 8:35, 2014.
-
(2014)
BMC Syst Biol
, vol.8
, pp. 35
-
-
Wei, P.1
-
17
-
-
84900834708
-
Algorithms and tools for protein-protein interaction networks clustering with a special focus on population-based stochastic methods
-
Pizzuti C, Rombo SE, Algorithms and tools for protein-protein interaction networks clustering, with a special focus on population-based stochastic methods, Bioinformatics 10:1343-1352, 2014.
-
(2014)
Bioinformatics
, vol.10
, pp. 1343-1352
-
-
Pizzuti, C.1
Rombo, S.E.2
-
18
-
-
2942552459
-
An automated method for ¯nding molecular complexes in large protein interaction networks
-
Bader GD, Hogue CW, An automated method for ¯nding molecular complexes in large protein interaction networks, BMC Bioinformatics 4:2, 2003.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 2
-
-
Bader, G.D.1
Hogue, C.W.2
-
19
-
-
33744805096
-
Development and implementation of an algorithm for detection of protein complexes in large interaction networks
-
Altaf-Ul-Amin M, Shinbo Y, Mihara K, Kurokawa K, Kanaya S, Development and implementation of an algorithm for detection of protein complexes in large interaction networks, BMC Bioinformatics 7:207, 2006.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 207
-
-
Altaf-Ul-Amin, M.1
Shinbo, Y.2
Mihara, K.3
Kurokawa, K.4
Kanaya, S.5
-
20
-
-
33645830948
-
CFinder: Locating cliques and overlapping modules in biological networks
-
Adamcsek B, Palla G, Farkas IJ, Derenyi I, Vicsek T, CFinder: Locating cliques and overlapping modules in biological networks, Bioinformatics 22:1021-1023, 2006.
-
(2006)
Bioinformatics
, vol.22
, pp. 1021-1023
-
-
Adamcsek, B.1
Palla, G.2
Farkas, I.J.3
Derenyi, I.4
Vicsek, T.5
-
21
-
-
10244264813
-
Protein complex prediction via cost-based clustering
-
King AD, Pržulj N, Jurisica I, Protein complex prediction via cost-based clustering, Bioinformatics 20:3013-3020, 2004.
-
(2004)
Bioinformatics
, vol.20
, pp. 3013-3020
-
-
King, A.D.1
Pržulj, N.2
Jurisica, I.3
-
22
-
-
84855178662
-
Multifunctional proteins revealed by overlapping clustering in protein interaction network
-
Becker E, Robisson B, Chapple CE, Guenoche A, Brun C, Multifunctional proteins revealed by overlapping clustering in protein interaction network, Bioinformatics 28:84-90, 2012.
-
(2012)
Bioinformatics
, vol.28
, pp. 84-90
-
-
Becker, E.1
Robisson, B.2
Chapple, C.E.3
Guenoche, A.4
Brun, C.5
-
23
-
-
0036529479
-
An e±cient algorithm for large-scale detection of protein families
-
Enright AJ, Dongen SV, Ouzounis CA, An e±cient algorithm for large-scale detection of protein families, Nucleic Acids Res 30:1575-1584, 2002.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 1575-1584
-
-
Enright, A.J.1
Dongen, S.V.2
Ouzounis, C.A.3
-
24
-
-
0346156102
-
Detection of functional modules from protein interaction networks
-
Pereira JB, Enright AJ, Ouzounis CA, Detection of functional modules from protein interaction networks, Proteins 54:49-57, 2004.
-
(2004)
Proteins
, vol.54
, pp. 49-57
-
-
Pereira, J.B.1
Enright, A.J.2
Ouzounis, C.A.3
-
25
-
-
77955518815
-
Link communities reveal multiscale complexity in networks
-
Ahn Y-Y, Bagrow JP, Lehmann S, Link communities reveal multiscale complexity in networks, Nature 466:761-764, 2010.
-
(2010)
Nature
, vol.466
, pp. 761-764
-
-
Ahn, Y.-Y.1
Bagrow, J.P.2
Lehmann, S.3
-
27
-
-
11244306358
-
Discovering statistically signi¯cant bi-clusters in gene expression data
-
Tanay A, Sharan R, Shamir R, Discovering statistically signi¯cant bi-clusters in gene expression data, Bioinformatics 18(1):S136-S144, 2002.
-
(2002)
Bioinformatics
, vol.18
, Issue.1
, pp. S136-S144
-
-
Tanay, A.1
Sharan, R.2
Shamir, R.3
-
28
-
-
84879477284
-
MS-kNN: Protein function prediction by integrating multiple data sources
-
Lan L, Djuric N, Guo Y, Vucetic S, MS-kNN: Protein function prediction by integrating multiple data sources, BMC Bioinformatics 14(3):S8, 2013.
-
(2013)
BMC Bioinformatics
, vol.14
, Issue.3
, pp. S8
-
-
Lan, L.1
Djuric, N.2
Guo, Y.3
Vucetic, S.4
-
29
-
-
84910122557
-
Joint clustering of protein interaction networks through Markov random walk
-
Yijie W, Xiaoning Q, Joint clustering of protein interaction networks through Markov random walk, BMC Syst Biol 8(1):S9, 2014.
-
(2014)
BMC Syst Biol
, vol.8
, Issue.1
, pp. S9
-
-
Yijie, W.1
Xiaoning, Q.2
-
30
-
-
36949038721
-
An e±cient strategy for extensive integration of diverse biological data for protein function prediction
-
Chua HN, Sung WK, Wong L, An e±cient strategy for extensive integration of diverse biological data for protein function prediction, Bioinformatics 23(24):3364-3373, 2007.
-
(2007)
Bioinformatics
, vol.23
, Issue.24
, pp. 3364-3373
-
-
Chua, H.N.1
Sung, W.K.2
Wong, L.3
-
31
-
-
0034069495
-
Gene ontology: Tool for the uni¯cation of biology
-
Ashburner et al., Gene ontology: Tool for the uni¯cation of biology, Nat Genet 25(1):25-29, 2000.
-
(2000)
Nat Genet
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner1
-
32
-
-
0033974688
-
Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins
-
Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, Nishizawa M, Yamamoto K, Kuhara S, Sakaki Y, Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins, Proc Natl Acad Sci 97:1143-1147, 2000.
-
(2000)
Proc Natl Acad Sci
, vol.97
, pp. 1143-1147
-
-
Ito, T.1
Tashiro, K.2
Muta, S.3
Ozawa, R.4
Chiba, T.5
Nishizawa, M.6
Yamamoto, K.7
Kuhara, S.8
Sakaki, Y.9
-
33
-
-
0035836765
-
A comprehensive two hybrid analysis to explore the yeast protein interactome
-
Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y, A comprehensive two hybrid analysis to explore the yeast protein interactome, Proc Natl Acad Sci 98:4569-4574, 2001.
-
(2001)
Proc Natl Acad Sci
, vol.98
, pp. 4569-4574
-
-
Ito, T.1
Chiba, T.2
Ozawa, R.3
Yoshida, M.4
Hattori, M.5
Sakaki, Y.6
-
34
-
-
0034069495
-
Gene ontology: Tool for the uni¯cation of biology
-
Ashburner M et al., Gene ontology: Tool for the uni¯cation of biology, Nat Genet 25(1):25-29, 2000.
-
(2000)
Nat Genet
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
-
35
-
-
78651280402
-
COXPRESdb: A database to compare gene coexpression in seven model animals
-
Obayashi T, Kinoshita K, COXPRESdb: A database to compare gene coexpression in seven model animals, Nucleic Acids Res 39:D1016-D1022, 2011.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D1016-D1022
-
-
Obayashi, T.1
Kinoshita, K.2
-
36
-
-
9144257282
-
The FunCat a functional annotation scheme for systematic classi¯cation of proteins from whole genomes
-
Ruepp A et al., The FunCat, a functional annotation scheme for systematic classi¯cation of proteins from whole genomes, Nucleic Acids Res 32(18):5539-5545, 2004.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.18
, pp. 5539-5545
-
-
Ruepp, A.1
|