-
1
-
-
33645830948
-
CFinder: Locating cliques and overlapping modules in biological networks
-
Adamcsek B, Palla G, Farkas IJ, Derenyi I, Vicsek T (2006) CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics 22: 1021-1023
-
(2006)
Bioinformatics
, vol.22
, pp. 1021-1023
-
-
Adamcsek, B.1
Palla, G.2
Farkas, I.J.3
Derenyi, I.4
Vicsek, T.5
-
2
-
-
0037435030
-
Mass spectrometry-based proteomics
-
Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422: 198-207
-
(2003)
Nature
, vol.422
, pp. 198-207
-
-
Aebersold, R.1
Mann, M.2
-
3
-
-
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 (2006) Development and implementation of an algorithm for detection of protein complexes in large interaction networks. BMC Bioinformatics 7: 207
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 207
-
-
Altaf-Ul-Amin, M.1
Shinbo, Y.2
Mihara, K.3
Kurokawa, K.4
Kanaya, S.5
-
4
-
-
13844264514
-
Iterative cluster analysis of protein interaction data
-
Arnau V, Mars S, Marin I (2005) Iterative cluster analysis of protein interaction data. Bioinformatics 21: 364-378
-
(2005)
Bioinformatics
, vol.21
, pp. 364-378
-
-
Arnau, V.1
Mars, S.2
Marin, I.3
-
5
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29
-
(2000)
Nat Genet
, vol.25
, 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..
-
6
-
-
3042523388
-
Predicting protein complex membership using probabilistic network reliability
-
Asthana S, King OD, Gibbons FD, Roth FP (2004) Predicting protein complex membership using probabilistic network reliability. Genome Res 14: 1170-1175
-
(2004)
Genome Res
, vol.14
, pp. 1170-1175
-
-
Asthana, S.1
King, O.D.2
Gibbons, F.D.3
Roth, F.P.4
-
7
-
-
2942552459
-
An automated method for finding molecular complexes in large protein interaction networks
-
Bader GD, Hogue CW (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4: 2
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 2
-
-
Bader, G.D.1
Hogue, C.W.2
-
8
-
-
0142241336
-
Greedily building protein networks with confidence
-
Bader JS (2003) Greedily building protein networks with confidence. Bioinformatics 19: 1869-1874
-
(2003)
Bioinformatics
, vol.19
, pp. 1869-1874
-
-
Bader, J.S.1
-
9
-
-
20344379457
-
Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli
-
Balazsi G, Barabasi AL, Oltvai ZN (2005) Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc Natl Acad Sci USA 102: 7841-7846
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 7841-7846
-
-
Balazsi, G.1
Barabasi, A.L.2
Oltvai, Z.N.3
-
10
-
-
32144442519
-
PRODISTIN Web Site: A tool for the functional classification of proteins from interaction networks
-
Baudot A, Martin D, Mouren P, Chevenet F, Guenoche A, Jacq B, Brun C (2006) PRODISTIN Web Site: a tool for the functional classification of proteins from interaction networks. Bioinformatics 22: 248-250
-
(2006)
Bioinformatics
, vol.22
, pp. 248-250
-
-
Baudot, A.1
Martin, D.2
Mouren, P.3
Chevenet, F.4
Guenoche, A.5
Jacq, B.6
Brun, C.7
-
11
-
-
0000913755
-
Spatial interaction and the statistical analysis of lattice systems
-
Besag J (1974) Spatial interaction and the statistical analysis of lattice systems. J R Stat Soc Ser B 36: 192-236
-
(1974)
J R Stat Soc Ser B
, vol.36
, pp. 192-236
-
-
Besag, J.1
-
12
-
-
0000521616
-
Superparamagnetic clustering of data
-
Blatt M, Wiseman S, Domany E (1996) Superparamagnetic clustering of data. Phys Rev Lett 76: 3251-3254
-
(1996)
Phys Rev Lett
, vol.76
, pp. 3251-3254
-
-
Blatt, M.1
Wiseman, S.2
Domany, E.3
-
13
-
-
33751255087
-
Evaluation of clustering algorithms for protein-protein interaction networks
-
Brohee S, 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
-
14
-
-
33745454509
-
Global analysis of gene function in yeast by quantitative phenotypic profiling
-
Brown JA, Sherlock G, Myers CL, Burrows NM, Deng C, Wu HI, McCann KE, Troyanskaya OG, Brown JM (2006) Global analysis of gene function in yeast by quantitative phenotypic profiling. Mol Syst Biol 2: 1
-
(2006)
Mol Syst Biol
, vol.2
, pp. 1
-
-
Brown, J.A.1
Sherlock, G.2
Myers, C.L.3
Burrows, N.M.4
Deng, C.5
Wu, H.I.6
McCann, K.E.7
Troyanskaya, O.G.8
Brown, J.M.9
-
15
-
-
1442329655
-
Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network
-
Brun C, Chevenet F, Martin D, Wojcik J, Guenoche A, Jacq B (2003) Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network. Genome Biol 5: R6
-
(2003)
Genome Biol
, vol.5
-
-
Brun, C.1
Chevenet, F.2
Martin, D.3
Wojcik, J.4
Guenoche, A.5
Jacq, B.6
-
16
-
-
0038074373
-
Topological structure analysis of the protein-protein interaction network in budding yeast
-
Bu D, Zhao Y, Cai L, Xue H, Zhu X, Lu H, Zhang J, Sun S, Ling L, Zhang N, Li G, Chen R (2003) Topological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Res 31: 2443-2450
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 2443-2450
-
-
Bu, D.1
Zhao, Y.2
Cai, L.3
Xue, H.4
Zhu, X.5
Lu, H.6
Zhang, J.7
Sun, S.8
Ling, L.9
Zhang, N.10
Li, G.11
Chen, R.12
-
17
-
-
20844450402
-
Differential network expression during drug and stress response
-
Cabusora L, Sutton E, Fulmer A, Forst CV (2005) Differential network expression during drug and stress response. Bioinformatics 21: 2898-2905
-
(2005)
Bioinformatics
, vol.21
, pp. 2898-2905
-
-
Cabusora, L.1
Sutton, E.2
Fulmer, A.3
Forst, C.V.4
-
18
-
-
33644644466
-
Identification and analysis of evolutionarily cohesive functional modules in protein networks
-
Campillos M, von Mering C, Jensen LJ, Bork P (2006) Identification and analysis of evolutionarily cohesive functional modules in protein networks. Genome Res 16: 374-382
-
(2006)
Genome Res
, vol.16
, pp. 374-382
-
-
Campillos, M.1
von Mering, C.2
Jensen, L.J.3
Bork, P.4
-
19
-
-
33745619564
-
Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
-
Chua HN, Sung WK, Wong L (2006) Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics 22: 1623-1630
-
(2006)
Bioinformatics
, vol.22
, pp. 1623-1630
-
-
Chua, H.N.1
Sung, W.K.2
Wong, L.3
-
20
-
-
0004116989
-
-
Cambridge, MA, New York: MIT Press, McGraw-Hill
-
Cormen TH, Leiserson CE, Rivest RL (1990) Introduction to Algorithms. Cambridge, MA, New York: MIT Press, McGraw-Hill
-
(1990)
Introduction to Algorithms
-
-
Cormen, T.H.1
Leiserson, C.E.2
Rivest, R.L.3
-
21
-
-
33947218088
-
-
CPLEX
-
CPLEX. http://www.ilog.com/products/cplex/
-
-
-
-
22
-
-
0028484228
-
The complexity of multiterminal cuts
-
Dahlhaus E, Johnson DS, Papadimitriou CH, Seymour PD, Yannakakis M(1994) The complexity of multiterminal cuts. SIAM J Comput 23: 864-894
-
(1994)
SIAM J Comput
, vol.23
, pp. 864-894
-
-
Dahlhaus, E.1
Johnson, D.S.2
Papadimitriou, C.H.3
Seymour, P.D.4
Yannakakis, M.5
-
24
-
-
2342435295
-
Mapping Gene Ontology to proteins based on protein-protein interaction data
-
Deng M, Tu Z, Sun F, Chen T (2004) Mapping Gene Ontology to proteins based on protein-protein interaction data. Bioinformatics 20: 895-902
-
(2004)
Bioinformatics
, vol.20
, pp. 895-902
-
-
Deng, M.1
Tu, Z.2
Sun, F.3
Chen, T.4
-
25
-
-
0742304254
-
Prediction of protein function using protein-protein interaction data
-
Deng M, Zhang K, Mehta S, Chen T, Sun F (2003) Prediction of protein function using protein-protein interaction data. J Comput Biol 10: 947-960
-
(2003)
J Comput Biol
, vol.10
, pp. 947-960
-
-
Deng, M.1
Zhang, K.2
Mehta, S.3
Chen, T.4
Sun, F.5
-
26
-
-
25444490121
-
The use of edge-betweenness clustering to investigate biological function in protein interaction networks
-
Dunn R, Dudbridge F, Sanderson CM (2005) The use of edge-betweenness clustering to investigate biological function in protein interaction networks. BMC Bioinformatics 6: 39
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 39
-
-
Dunn, R.1
Dudbridge, F.2
Sanderson, C.M.3
-
27
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
Enright AJ, Van Dongen S, Ouzounis CA (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30: 1575-1584
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
28
-
-
27644576841
-
High-throughput two-hybrid analysis. The promise and the peril
-
Fields S (2005) High-throughput two-hybrid analysis. The promise and the peril. FEBS J 272: 5391-5399
-
(2005)
FEBS J
, vol.272
, pp. 5391-5399
-
-
Fields, S.1
-
29
-
-
33748257786
-
Graemlin: General and robust alignment of multiple large interaction networks
-
Flannick J, Novak A, Srinivasan BS, McAdams HH, Batzoglou S (2006) Graemlin: general and robust alignment of multiple large interaction networks. Genome Res 16: 1169-1181
-
(2006)
Genome Res
, vol.16
, pp. 1169-1181
-
-
Flannick, J.1
Novak, A.2
Srinivasan, B.S.3
McAdams, H.H.4
Batzoglou, S.5
-
30
-
-
33644617753
-
Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets
-
Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nagaraju S, Periaswamy B, Mishra G, Nandakumar K, Shen B, Deshpande N, Nayak R, Sarker M, Boeke JD, Parmigiani G, Schultz J, Bader JS, Pandey A (2006) Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet 38: 285-293
-
(2006)
Nat Genet
, vol.38
, pp. 285-293
-
-
Gandhi, T.K.1
Zhong, J.2
Mathivanan, S.3
Karthick, L.4
Chandrika, K.N.5
Mohan, S.S.6
Sharma, S.7
Pinkert, S.8
Nagaraju, S.9
Periaswamy, B.10
Mishra, G.11
Nandakumar, K.12
Shen, B.13
Deshpande, N.14
Nayak, R.15
Sarker, M.16
Boeke, J.D.17
Parmigiani, G.18
Schultz, J.19
Bader, J.S.20
Pandey, A.21
more..
-
31
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631-636
-
(2006)
Nature
, vol.440
, pp. 631-636
-
-
Gavin, A.C.1
Aloy, P.2
Grandi, P.3
Krause, R.4
Boesche, M.5
Marzioch, M.6
-
32
-
-
0035733690
-
Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae
-
Ge H, Liu Z, Church GM, Vidal M (2001) Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet 29: 482-486
-
(2001)
Nat Genet
, vol.29
, pp. 482-486
-
-
Ge, H.1
Liu, Z.2
Church, G.M.3
Vidal, M.4
-
33
-
-
0037062448
-
Community structure in social and biological networks
-
Girvan M, Newman ME (2002) Community structure in social and biological networks. Proc Natl Acad Sci USA 99: 7821-7826
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 7821-7826
-
-
Girvan, M.1
Newman, M.E.2
-
34
-
-
0037447257
-
Assessing experimentally derived interactions in a small world
-
Goldberg DS, Roth FP (2003) Assessing experimentally derived interactions in a small world. Proc Natl Acad Sci USA 100: 4372-4376
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 4372-4376
-
-
Goldberg, D.S.1
Roth, F.P.2
-
36
-
-
0038014879
-
Co-clustering of biological networks and gene expression data
-
Hanisch D, Zien A, Zimmer R, Lengauer T (2002) Co-clustering of biological networks and gene expression data. Bioinformatics 18 (Suppl 1): S145-S154
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Hanisch, D.1
Zien, A.2
Zimmer, R.3
Lengauer, T.4
-
37
-
-
33847744247
-
How complete are current yeast and human protein-interaction networks?
-
Hart GT, Ramani AK, Marcotte EM (2006) How complete are current yeast and human protein-interaction networks? Genome Biol 7: 120
-
(2006)
Genome Biol
, vol.7
, pp. 120
-
-
Hart, G.T.1
Ramani, A.K.2
Marcotte, E.M.3
-
39
-
-
0034515528
-
A clustering algorithm based on graph connectivity
-
Hartuv E, Shamir R (2000) A clustering algorithm based on graph connectivity. Inform Process Lett 76: 175-181
-
(2000)
Inform Process Lett
, vol.76
, pp. 175-181
-
-
Hartuv, E.1
Shamir, R.2
-
41
-
-
18944372150
-
Integrating phenotypic and expression profiles to map arsenic-response networks
-
Haugen AC, Kelley R, Collins JB, Tucker CJ, Deng C, Afshari CA, Brown JM, Ideker T, Van Houten B (2004) Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biol 5: R95
-
(2004)
Genome Biol
, vol.5
-
-
Haugen, A.C.1
Kelley, R.2
Collins, J.B.3
Tucker, C.J.4
Deng, C.5
Afshari, C.A.6
Brown, J.M.7
Ideker, T.8
Van Houten, B.9
-
42
-
-
0035044077
-
Assessment of prediction accuracy of protein function from protein-protein interaction data
-
Hishigaki H, Nakai K, Ono T, Tanigami A, Takagi T (2001) Assessment of prediction accuracy of protein function from protein-protein interaction data. Yeast 18: 523-531
-
(2001)
Yeast
, vol.18
, pp. 523-531
-
-
Hishigaki, H.1
Nakai, K.2
Ono, T.3
Tanigami, A.4
Takagi, T.5
-
43
-
-
20044372938
-
Identification and characterization of protein subcomplexes in yeast
-
Hollunder J, Beyer A, Wilhelm T (2005) Identification and characterization of protein subcomplexes in yeast. Proteomics 5: 2082-2089
-
(2005)
Proteomics
, vol.5
, pp. 2082-2089
-
-
Hollunder, J.1
Beyer, A.2
Wilhelm, T.3
-
44
-
-
0142184341
-
Global analysis of protein localization in budding yeast
-
Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK (2003) Global analysis of protein localization in budding yeast. Nature 425: 686-691
-
(2003)
Nature
, vol.425
, pp. 686-691
-
-
Huh, W.K.1
Falvo, J.V.2
Gerke, L.C.3
Carroll, A.S.4
Howson, R.W.5
Weissman, J.S.6
O'Shea, E.K.7
-
45
-
-
0000801240
-
Discovering regulatory and signalling circuits in molecular interaction networks
-
Ideker T, Ozier O, Schwikowski B, Siegel AF (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18 (Suppl 1): S233-S240
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Ideker, T.1
Ozier, O.2
Schwikowski, B.3
Siegel, A.F.4
-
46
-
-
0036699526
-
Revealing modular organization in the yeast transcriptional network
-
Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y, Barkai N (2002) Revealing modular organization in the yeast transcriptional network. Nat Genet 31: 370-377
-
(2002)
Nat Genet
, vol.31
, pp. 370-377
-
-
Ihmels, J.1
Friedlander, G.2
Bergmann, S.3
Sarig, O.4
Ziv, Y.5
Barkai, N.6
-
47
-
-
0036141992
-
Relating whole-genome expression data with protein-protein interactions
-
Jansen R, Greenbaum D, Gerstein M (2002) Relating whole-genome expression data with protein-protein interactions. Genome Res 12: 37-46
-
(2002)
Genome Res
, vol.12
, pp. 37-46
-
-
Jansen, R.1
Greenbaum, D.2
Gerstein, M.3
-
48
-
-
13844271482
-
Genome-scale gene function prediction using multiple sources of high-throughput data in yeast Saccharomyces cerevisiae
-
Joshi T, Chen Y, Becker JM, Alexandrov N, Xu D (2004) Genome-scale gene function prediction using multiple sources of high-throughput data in yeast Saccharomyces cerevisiae. Omics 8: 322-333
-
(2004)
Omics
, vol.8
, pp. 322-333
-
-
Joshi, T.1
Chen, Y.2
Becker, J.M.3
Alexandrov, N.4
Xu, D.5
-
49
-
-
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 (2004) Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci USA 101: 2888-2893
-
(2004)
Proc Natl Acad Sci USA
, 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
-
50
-
-
0141593601
-
Conserved pathways within bacteria and yeast as revealed by global protein network alignment
-
Kelley BP, Sharan R, Karp RM, Sittler T, Root DE, Stockwell BR, Ideker T (2003) Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci USA 100: 11394-11399
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 11394-11399
-
-
Kelley, B.P.1
Sharan, R.2
Karp, R.M.3
Sittler, T.4
Root, D.E.5
Stockwell, B.R.6
Ideker, T.7
-
51
-
-
22844450110
-
Systematic interpretation of genetic interactions using protein networks
-
Kelley R, Ideker T (2005) Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol 23: 561-566
-
(2005)
Nat Biotechnol
, vol.23
, pp. 561-566
-
-
Kelley, R.1
Ideker, T.2
-
52
-
-
10244264813
-
Protein complex prediction via cost-based clustering
-
King AD, Przulj N, Jurisica I (2004) Protein complex prediction via cost-based clustering. Bioinformatics 20: 3013-3020
-
(2004)
Bioinformatics
, vol.20
, pp. 3013-3020
-
-
King, A.D.1
Przulj, N.2
Jurisica, I.3
-
53
-
-
33645993265
-
Global survey of organ and organelle protein expression in mouse: Combined proteomic and transcriptomic profiling
-
Kislinger T, Cox B, Kannan A, Chung C, Hu P, Ignatchenko A, Scott MS, Gramolini AO, Morris Q, Hallett MT, Rossant J, Hughes TR, Frey B, Emili A (2006) Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell 125: 173-186
-
(2006)
Cell
, vol.125
, pp. 173-186
-
-
Kislinger, T.1
Cox, B.2
Kannan, A.3
Chung, C.4
Hu, P.5
Ignatchenko, A.6
Scott, M.S.7
Gramolini, A.O.8
Morris, Q.9
Hallett, M.T.10
Rossant, J.11
Hughes, T.R.12
Frey, B.13
Emili, A.14
-
54
-
-
0142148210
-
A comprehensive set of protein complexes in yeast: Mining large scale protein-protein interaction screens
-
Krause R, von Mering C, Bork P (2003) A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens. Bioinformatics 19: 1901-1908
-
(2003)
Bioinformatics
, vol.19
, pp. 1901-1908
-
-
Krause, R.1
von Mering, C.2
Bork, P.3
-
55
-
-
33645453254
-
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
-
Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-643
-
(2006)
Nature
, vol.440
, pp. 637-643
-
-
Krogan, N.J.1
Cagney, G.2
Yu, H.3
Zhong, G.4
Guo, X.5
Ignatchenko, A.6
-
56
-
-
30344475200
-
Progress over the first decade of CASP experiments
-
Kryshtafovych A, Venclovas C, Fidelis K, Moult J (2005) Progress over the first decade of CASP experiments. Proteins 61 (Suppl 7): 225-236
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 225-236
-
-
Kryshtafovych, A.1
Venclovas, C.2
Fidelis, K.3
Moult, J.4
-
57
-
-
27644484749
-
A protein interaction network of the malaria parasite Plasmodium falciparum
-
LaCount DJ, Vignali M, Chettier R, Phansalkar A, Bell R, Hesselberth JR, Schoenfeld LW, Ota I, Sahasrabudhe S, Kurschner C, Fields S, Hughes RE (2005) A protein interaction network of the malaria parasite Plasmodium falciparum. Nature 438: 103-107
-
(2005)
Nature
, vol.438
, pp. 103-107
-
-
LaCount, D.J.1
Vignali, M.2
Chettier, R.3
Phansalkar, A.4
Bell, R.5
Hesselberth, J.R.6
Schoenfeld, L.W.7
Ota, I.8
Sahasrabudhe, S.9
Kurschner, C.10
Fields, S.11
Hughes, R.E.12
-
58
-
-
8844263749
-
A statistical framework for genomic data fusion
-
Lanckriet GR, De Bie T, Cristianini N, Jordan MI, Noble WS (2004) A statistical framework for genomic data fusion. Bioinformatics 20: 2626-2635
-
(2004)
Bioinformatics
, vol.20
, pp. 2626-2635
-
-
Lanckriet, G.R.1
De Bie, T.2
Cristianini, N.3
Jordan, M.I.4
Noble, W.S.5
-
59
-
-
33645901213
-
Diffusion kernel-based logistic regression models for protein function prediction
-
Lee H, Tu Z, Deng M, Sun F, Chen T (2006) Diffusion kernel-based logistic regression models for protein function prediction. Omics 10: 40-55
-
(2006)
Omics
, vol.10
, pp. 40-55
-
-
Lee, H.1
Tu, Z.2
Deng, M.3
Sun, F.4
Chen, T.5
-
60
-
-
3042514191
-
Coexpression analysis of human genes across many microarray data sets
-
Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P (2004) Coexpression analysis of human genes across many microarray data sets. Genome Res 14: 1085-1094
-
(2004)
Genome Res
, vol.14
, pp. 1085-1094
-
-
Lee, H.K.1
Hsu, A.K.2
Sajdak, J.3
Qin, J.4
Pavlidis, P.5
-
61
-
-
1542271409
-
Predicting protein function from protein/ protein interaction data: A probabilistic approach
-
Letovsky S, Kasif S (2003) Predicting protein function from protein/ protein interaction data: a probabilistic approach. Bioinformatics 19 (Suppl 1): i197-i204
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 1
-
-
Letovsky, S.1
Kasif, S.2
-
62
-
-
0037480738
-
Investigating semantic similarity measures across the Gene Ontology: The relationship between sequence and annotation
-
Lord PW, Stevens RD, Brass A, Goble CA (2003) Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 19: 1275-1283
-
(2003)
Bioinformatics
, vol.19
, pp. 1275-1283
-
-
Lord, P.W.1
Stevens, R.D.2
Brass, A.3
Goble, C.A.4
-
63
-
-
4644326931
-
Genomic analysis of regulatory network dynamics reveals large topological changes
-
Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431: 308-312
-
(2004)
Nature
, vol.431
, pp. 308-312
-
-
Luscombe, N.M.1
Babu, M.M.2
Yu, H.3
Snyder, M.4
Teichmann, S.A.5
Gerstein, M.6
-
64
-
-
33645832853
-
Systems-level analyses identify extensive coupling among gene expression machines
-
Maciag K, Altschuler SJ, Slack MD, Krogan NJ, Emili A, Greenblatt JF, Maniatis T, Wu LF (2006) Systems-level analyses identify extensive coupling among gene expression machines. Mol Syst Biol 2: 3
-
(2006)
Mol Syst Biol
, vol.2
, pp. 3
-
-
Maciag, K.1
Altschuler, S.J.2
Slack, M.D.3
Krogan, N.J.4
Emili, A.5
Greenblatt, J.F.6
Maniatis, T.7
Wu, L.F.8
-
65
-
-
0033523854
-
A combined algorithm for genome-wide prediction of protein function
-
Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D (1999) A combined algorithm for genome-wide prediction of protein function. Nature 402: 83-86
-
(1999)
Nature
, vol.402
, pp. 83-86
-
-
Marcotte, E.M.1
Pellegrini, M.2
Thompson, M.J.3
Yeates, T.O.4
Eisenberg, D.5
-
66
-
-
0036081347
-
MIPS: A database for genomes and protein sequences
-
MewesHW, Frishman D, Guldener U, Mannhaupt G, Mayer K, Mokrejs M, Morgenstern B, Munsterkotter M, Rudd S, Weil B (2002) MIPS: a database for genomes and protein sequences. Nucleic Acids Res 30: 31-34
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 31-34
-
-
Mewes, H.W.1
Frishman, D.2
Guldener, U.3
Mannhaupt, G.4
Mayer, K.5
Mokrejs, M.6
Morgenstern, B.7
Munsterkotter, M.8
Rudd, S.9
Weil, B.10
-
68
-
-
29144442904
-
Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
-
Nabieva E, Jim K, Agarwal A, Chazelle B, Singh M (2005) Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics 21 (Suppl 1): i302-i310
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Nabieva, E.1
Jim, K.2
Agarwal, A.3
Chazelle, B.4
Singh, M.5
-
69
-
-
0034818556
-
Gene functional classification from heterogeneous data
-
Montreal, Quebec, Canada: ACM Press
-
Pavlidis P, Weston J, Cai J, Grundy WN (2001) Gene functional classification from heterogeneous data. Proceedings of the Fifth Annual International Conference on Computational Biology. Montreal, Quebec, Canada: ACM Press
-
(2001)
Proceedings of the Fifth Annual International Conference on Computational Biology
-
-
Pavlidis, P.1
Weston, J.2
Cai, J.3
Grundy, W.N.4
-
70
-
-
0346156102
-
Detection of functional modules from protein interaction networks
-
Pereira-Leal JB, Enright AJ, Ouzounis CA (2004) Detection of functional modules from protein interaction networks. Proteins 54: 49-57
-
(2004)
Proteins
, vol.54
, pp. 49-57
-
-
Pereira-Leal, J.B.1
Enright, A.J.2
Ouzounis, C.A.3
-
71
-
-
33646137384
-
A systematic comparison and evaluation of biclustering methods for gene expression data
-
Prelic A, Bleuler S, Zimmermann P, Wille A, Buhlmann P, Gruissem W, Hennig L, Thiele L, Zitzler E (2006) A systematic comparison and evaluation of biclustering methods for gene expression data. Bioinformatics 22: 1122-1129
-
(2006)
Bioinformatics
, vol.22
, pp. 1122-1129
-
-
Prelic, A.1
Bleuler, S.2
Zimmermann, P.3
Wille, A.4
Buhlmann, P.5
Gruissem, W.6
Hennig, L.7
Thiele, L.8
Zitzler, E.9
-
72
-
-
1342330546
-
Functional topology in a network of protein interactions
-
Przulj N, Wigle DA, Jurisica I (2004) Functional topology in a network of protein interactions. Bioinformatics 20: 340-348
-
(2004)
Bioinformatics
, vol.20
, pp. 340-348
-
-
Przulj, N.1
Wigle, D.A.2
Jurisica, I.3
-
73
-
-
0037417817
-
Modular organization of cellular networks
-
Rives AW, Galitski T (2003) Modular organization of cellular networks. Proc Natl Acad Sci USA 100: 1128-1133
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 1128-1133
-
-
Rives, A.W.1
Galitski, T.2
-
74
-
-
27144530248
-
Towards a proteome-scale map of the human protein-protein interaction network
-
Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178
-
(2005)
Nature
, vol.437
, pp. 1173-1178
-
-
Rual, J.F.1
Venkatesan, K.2
Hao, T.3
Hirozane-Kishikawa, T.4
Dricot, A.5
-
75
-
-
0242268461
-
Predicting protein functions from redundancies in large-scale protein interaction networks
-
Samanta MP, Liang S (2003) Predicting protein functions from redundancies in large-scale protein interaction networks. Proc Natl Acad Sci USA 100: 12579-12583
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 12579-12583
-
-
Samanta, M.P.1
Liang, S.2
-
76
-
-
0028806048
-
Quantitative monitoring of gene expression patterns with a complementary DNA microarray
-
Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470
-
(1995)
Science
, vol.270
, pp. 467-470
-
-
Schena, M.1
Shalon, D.2
Davis, R.W.3
Brown, P.O.4
-
77
-
-
24144486554
-
Local modeling of global interactome networks
-
Scholtens D, Vidal M, Gentleman R (2005) Local modeling of global interactome networks. Bioinformatics 21: 3548-3557
-
(2005)
Bioinformatics
, vol.21
, pp. 3548-3557
-
-
Scholtens, D.1
Vidal, M.2
Gentleman, R.3
-
78
-
-
0033669189
-
A network of protein-protein interactions in yeast
-
Schwikowski B, Uetz P, Fields S (2000) A network of protein-protein interactions in yeast. Nat Biotechnol 18: 1257-1261
-
(2000)
Nat Biotechnol
, vol.18
, pp. 1257-1261
-
-
Schwikowski, B.1
Uetz, P.2
Fields, S.3
-
79
-
-
33645983211
-
Efficient algorithms for detecting signaling pathways in protein interaction networks
-
Scott J, Ideker T, Karp RM, Sharan R (2006) Efficient algorithms for detecting signaling pathways in protein interaction networks. J Comput Biol 13: 133-144
-
(2006)
J Comput Biol
, vol.13
, pp. 133-144
-
-
Scott, J.1
Ideker, T.2
Karp, R.M.3
Sharan, R.4
-
80
-
-
20044388557
-
From signatures to models: Understanding cancer using microarrays
-
Segal E, Friedman N, Kaminski N, Regev A, Koller D (2005) From signatures to models: understanding cancer using microarrays. Nat Genet 37 (Suppl): S38-S45
-
(2005)
Nat Genet
, vol.37
, Issue.SUPPL.
-
-
Segal, E.1
Friedman, N.2
Kaminski, N.3
Regev, A.4
Koller, D.5
-
81
-
-
0842309161
-
Discovering molecular pathways from protein interaction and gene expression data
-
Segal E, Wang H, Koller D (2003) Discovering molecular pathways from protein interaction and gene expression data. Bioinformatics 19 (Suppl 1): i264-i271
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 1
-
-
Segal, E.1
Wang, H.2
Koller, D.3
-
82
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504
-
(2003)
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
Schwikowski, B.8
Ideker, T.9
-
83
-
-
33645732240
-
Modeling cellular machinery through biological network comparison
-
Sharan R, Ideker T (2006) Modeling cellular machinery through biological network comparison. Nat Biotechnol 24: 427-433
-
(2006)
Nat Biotechnol
, vol.24
, pp. 427-433
-
-
Sharan, R.1
Ideker, T.2
-
84
-
-
23844447959
-
Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data
-
Sharan R, Ideker T, Kelley B, Shamir R, Karp RM (2005) Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. J Comput Biol 12: 835-846
-
(2005)
J Comput Biol
, vol.12
, pp. 835-846
-
-
Sharan, R.1
Ideker, T.2
Kelley, B.3
Shamir, R.4
Karp, R.M.5
-
86
-
-
0142059836
-
Protein complexes and functional modules in molecular networks
-
Spirin V, Mirny LA (2003) Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci USA 100: 12123-12128
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 12123-12128
-
-
Spirin, V.1
Mirny, L.A.2
-
87
-
-
33644873184
-
BioGRID: A general repository for interaction datasets
-
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res 34: D535-D539
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Stark, C.1
Breitkreutz, B.J.2
Reguly, T.3
Boucher, L.4
Breitkreutz, A.5
Tyers, M.6
-
88
-
-
0003009091
-
Automated modelling of signal transduction networks
-
Steffen M, Petti A, Aach J, D'Haeseleer P, Church G (2002) Automated modelling of signal transduction networks. BMC Bioinformatics 3: 34
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 34
-
-
Steffen, M.1
Petti, A.2
Aach, J.3
D'Haeseleer, P.4
Church, G.5
-
89
-
-
11244306358
-
Discovering statistically significant biclusters in gene expression data
-
Tanay A, Sharan R, Shamir R (2002) Discovering statistically significant biclusters in gene expression data. Bioinformatics 18 (Suppl 1): S136-S144
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Tanay, A.1
Sharan, R.2
Shamir, R.3
-
90
-
-
1542357674
-
Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data
-
Tanay A, Sharan R, Kupiec M, Shamir R (2004) Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proc Natl Acad Sci USA 101: 2981-2986
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 2981-2986
-
-
Tanay, A.1
Sharan, R.2
Kupiec, M.3
Shamir, R.4
-
91
-
-
33746903958
-
Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium
-
Tanay A, Steinfeld I, Kupiec M, Shamir R (2005) Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium. Mol Syst Biol 1: 2
-
(2005)
Mol Syst Biol
, vol.1
, pp. 2
-
-
Tanay, A.1
Steinfeld, I.2
Kupiec, M.3
Shamir, R.4
-
92
-
-
21144439147
-
Assessing computational tools for the discovery of transcription factor binding sites
-
Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol 23: 137-144
-
(2005)
Nat Biotechnol
, vol.23
, pp. 137-144
-
-
Tompa, M.1
Li, N.2
Bailey, T.L.3
Church, G.M.4
De Moor, B.5
Eskin, E.6
-
93
-
-
0345305369
-
Functional modules by relating protein interaction networks and gene expression
-
Tornow S, Mewes HW (2003) Functional modules by relating protein interaction networks and gene expression. Nucleic Acids Res 31: 6283-6289
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 6283-6289
-
-
Tornow, S.1
Mewes, H.W.2
-
94
-
-
27544435126
-
Fast protein classification with multiple networks
-
ii59-ii65
-
Tsuda K, Shin H, Scholkopf B (2005) Fast protein classification with multiple networks. Bioinformatics 21 (Suppl 2): ii59-ii65
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 2
-
-
Tsuda, K.1
Shin, H.2
Scholkopf, B.3
-
95
-
-
0038699587
-
Global protein function prediction from protein-protein interaction networks
-
Vazquez A, Flammini A, Maritan A, Vespignani A (2003) Global protein function prediction from protein-protein interaction networks. Nat Biotechnol 21: 697-700
-
(2003)
Nat Biotechnol
, vol.21
, pp. 697-700
-
-
Vazquez, A.1
Flammini, A.2
Maritan, A.3
Vespignani, A.4
-
96
-
-
0037161731
-
Comparative assessment of large-scale data sets of protein-protein interactions
-
von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399-403
-
(2002)
Nature
, vol.417
, pp. 399-403
-
-
von Mering, C.1
Krause, R.2
Snel, B.3
Cornell, M.4
Oliver, S.G.5
Fields, S.6
Bork, P.7
-
97
-
-
28444448000
-
Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues
-
Wachi S, Yoneda K, Wu R (2005) Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues. Bioinformatics 21: 4205-4208
-
(2005)
Bioinformatics
, vol.21
, pp. 4205-4208
-
-
Wachi, S.1
Yoneda, K.2
Wu, R.3
-
98
-
-
0032482432
-
Collective dynamics of 'small-world' networks
-
Watts DJ, Strogatz SH (1998) Collective dynamics of 'small-world' networks. Nature 393: 440-442
-
(1998)
Nature
, vol.393
, pp. 440-442
-
-
Watts, D.J.1
Strogatz, S.H.2
-
100
-
-
27744521520
-
Validation and refinement of gene-regulatory pathways on a network of physical interactions
-
Yeang CH, Mak HC, McCuine S, Workman C, Jaakkola T, Ideker T (2005) Validation and refinement of gene-regulatory pathways on a network of physical interactions. Genome Biol 6: R62
-
(2005)
Genome Biol
, vol.6
-
-
Yeang, C.H.1
Mak, H.C.2
McCuine, S.3
Workman, C.4
Jaakkola, T.5
Ideker, T.6
|