-
1
-
-
38049079362
-
Protein-protein interaction networks and biology - what's the connection?
-
Hakes L, Pinney JW, Robertson DL, Lvell SC, (2008) Protein-protein interaction networks and biology - what's the connection? Nat Biotechnol 26: 69-72.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 69-72
-
-
Hakes, L.1
Pinney, J.W.2
Robertson, D.L.3
Lvell, S.C.4
-
2
-
-
0034846334
-
Shifting paradigms in gene-mapping methodology for complex traits
-
Sham P, (2001) Shifting paradigms in gene-mapping methodology for complex traits. Pharmacogenomics 2: 195-202.
-
(2001)
Pharmacogenomics
, vol.2
, pp. 195-202
-
-
Sham, P.1
-
3
-
-
59849125136
-
Dynamic modularity in protein interaction networks predicts breast cancer outcome
-
Taylor IW, Linding R, Warde-Farley D, Liu Y, Pesquita C, et al. (2009) Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol 27: 199-204.
-
(2009)
Nat Biotechnol
, vol.27
, pp. 199-204
-
-
Taylor, I.W.1
Linding, R.2
Warde-Farley, D.3
Liu, Y.4
Pesquita, C.5
-
5
-
-
0037932865
-
Identification of genotype-selective antitumor agents using synthetic lethal chemical screening in engineered human tumor cells
-
Dolma S, Lessnick SL, Hahn WC, Stockwell BR, (2003) Identification of genotype-selective antitumor agents using synthetic lethal chemical screening in engineered human tumor cells. Cancer Cell 3: 285-296.
-
(2003)
Cancer Cell
, vol.3
, pp. 285-296
-
-
Dolma, S.1
Lessnick, S.L.2
Hahn, W.C.3
Stockwell, B.R.4
-
6
-
-
5044229321
-
The impact of systems approaches on biological problems in drug discovery
-
Hood L, Perlmutter RM, (2004) The impact of systems approaches on biological problems in drug discovery. Nat Biotechnol 22: 1215-1217.
-
(2004)
Nat Biotechnol
, vol.22
, pp. 1215-1217
-
-
Hood, L.1
Perlmutter, R.M.2
-
7
-
-
35148824614
-
Network pharmacology
-
Hopkins AL, (2007) Network pharmacology. Nat Biotechnol 25: 1110-1111.
-
(2007)
Nat Biotechnol
, vol.25
, pp. 1110-1111
-
-
Hopkins, A.L.1
-
8
-
-
35148838537
-
Drug-target network
-
Yildirim MA, Goh KI, Cusick ME, Barabási AL, Vidal M, (2007) Drug-target network. Nat Biotechnol 25: 1119-1126.
-
(2007)
Nat Biotechnol
, vol.25
, pp. 1119-1126
-
-
Yildirim, M.A.1
Goh, K.I.2
Cusick, M.E.3
Barabási, A.L.4
Vidal, M.5
-
9
-
-
0035212065
-
Is there a bias in proteome research?
-
Mrowka R, Patzak A, Herzel H, (2001) Is there a bias in proteome research? Genome Res 11: 1971-1973.
-
(2001)
Genome Res
, vol.11
, pp. 1971-1973
-
-
Mrowka, R.1
Patzak, A.2
Herzel, H.3
-
10
-
-
0037161731
-
Comparative assessment of large-scale data sets of proteinprotein interactions
-
von Mering C, Krause R, Snel B, Cornell M, Oliver SG, et al. (2002) Comparative assessment of large-scale data sets of proteinprotein 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
-
11
-
-
53349117774
-
High Quality Binary Protein Interaction Map of the Yeast Interactome Network
-
Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, et al. (2008) High Quality Binary Protein Interaction Map of the Yeast Interactome Network. Science 322: 104-110.
-
(2008)
Science
, vol.322
, pp. 104-110
-
-
Yu, H.1
Braun, P.2
Yildirim, M.A.3
Lemmens, I.4
Venkatesan, K.5
-
12
-
-
59549083190
-
Precision and recall estimates for two-hybrid screens
-
Huang H, Bader JS, (2009) Precision and recall estimates for two-hybrid screens. Bioinformatics, 25: 372-378.
-
(2009)
Bioinformatics,
, vol.25
, pp. 372-378
-
-
Huang, H.1
Bader, J.S.2
-
13
-
-
31144432293
-
Literature mining for the biologist: from information retrieval to biological discovery
-
Jensen LJ, Saric J, Bork P, (2006) Literature mining for the biologist: from information retrieval to biological discovery. Nat Rev Genet 7: 119-129.
-
(2006)
Nat Rev Genet
, vol.7
, pp. 119-129
-
-
Jensen, L.J.1
Saric, J.2
Bork, P.3
-
14
-
-
12344282809
-
Discovering patterns to extract protein-protein interactions from full texts
-
Huang M, Zhu X, Hao Y, Payan DG, Qu K, et al. (2004) Discovering patterns to extract protein-protein interactions from full texts. Bioinformatics 20: 3604-3612.
-
(2004)
Bioinformatics
, vol.20
, pp. 3604-3612
-
-
Huang, M.1
Zhu, X.2
Hao, Y.3
Payan, D.G.4
Qu, K.5
-
15
-
-
33645104154
-
Extraction of regulatory gene/protein networks from Medline
-
Saric J, Jensen LJ, Ouzounova R, Rojas I, Bork P, (2006) Extraction of regulatory gene/protein networks from Medline. Bioinformatics 22: 645-650.
-
(2006)
Bioinformatics
, vol.22
, pp. 645-650
-
-
Saric, J.1
Jensen, L.J.2
Ouzounova, R.3
Rojas, I.4
Bork, P.5
-
16
-
-
48449105927
-
PIE: an online prediction system for protein-protein interactions from text
-
Kim S, Shin S-Y, Lee I-H, Kim S-J, Sriram R, et al. (2008) PIE: an online prediction system for protein-protein interactions from text. Nucleic Acids Res 36: W411-W415.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Kim, S.1
Shin, S.-Y.2
Lee, I.-H.3
Kim, S.-J.4
Sriram, R.5
-
17
-
-
33748656691
-
Combination of text-mining algorithms increases the performance
-
Malik R, Franke L, Siebes A, (2006) Combination of text-mining algorithms increases the performance. Bioinformatics 22: 2151-2157.
-
(2006)
Bioinformatics
, vol.22
, pp. 2151-2157
-
-
Malik, R.1
Franke, L.2
Siebes, A.3
-
18
-
-
66349121774
-
Bayesian inference of protein-protein interactions from biological literature
-
Chowdhary R, Zhang J, Liu JS, (2009) Bayesian inference of protein-protein interactions from biological literature. Bioinformatics 25: 1536-1542.
-
(2009)
Bioinformatics
, vol.25
, pp. 1536-1542
-
-
Chowdhary, R.1
Zhang, J.2
Liu, J.S.3
-
19
-
-
12144290243
-
Structure-based assembly of protein complexes in yeast
-
Aloy P, Böttcher B, Ceulemans H, Leutwein C, Mellwig C, et al. (2004) Structure-based assembly of protein complexes in yeast. Science 302: 2026-2029.
-
(2004)
Science
, vol.302
, pp. 2026-2029
-
-
Aloy, P.1
Böttcher, B.2
Ceulemans, H.3
Leutwein, C.4
Mellwig, C.5
-
20
-
-
0033523989
-
Protein interaction maps for complete genomes based on gene fusion events
-
Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA, (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature 402: 86-90.
-
(1999)
Nature
, vol.402
, pp. 86-90
-
-
Enright, A.J.1
Iliopoulos, I.2
Kyrpides, N.C.3
Ouzounis, C.A.4
-
21
-
-
0036435908
-
Co-evolutionary analysis reveals insights into protein-protein interactions
-
Goh CS, Cohen FE, (2002) Co-evolutionary analysis reveals insights into protein-protein interactions. J Mol Biol 324: 177-179.
-
(2002)
J Mol Biol
, vol.324
, pp. 177-179
-
-
Goh, C.S.1
Cohen, F.E.2
-
22
-
-
0142052944
-
A Bayesian networks approach for predicting protein-protein interactions from genomic data
-
Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, et al. (2003) A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302: 449-53.
-
(2003)
Science
, vol.302
, pp. 449-453
-
-
Jansen, R.1
Yu, H.2
Greenbaum, D.3
Kluger, Y.4
Krogan, N.J.5
-
23
-
-
0038817799
-
Multimeric threading-based prediction of protein-protein interactions on a genomic scale: Application to the Saccharomyces cerevisiae proteome
-
Lu L, Arakaki AK, Lu H, Skolnick J, (2003) Multimeric threading-based prediction of protein-protein interactions on a genomic scale: Application to the Saccharomyces cerevisiae proteome. Genome Res 13: 1146-1154.
-
(2003)
Genome Res
, vol.13
, pp. 1146-1154
-
-
Lu, L.1
Arakaki, A.K.2
Lu, H.3
Skolnick, J.4
-
25
-
-
0035177259
-
Similarity of phylogenetic trees as indicator of protein-protein interaction
-
Pazos F, Valencia A, (2001) Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng 14: 609-614.
-
(2001)
Protein Eng
, vol.14
, pp. 609-614
-
-
Pazos, F.1
Valencia, A.2
-
26
-
-
0037436412
-
Exploiting the coevolution of interacting proteins to discover interaction specificity
-
Ramani AK, Marcotte EM, (2003) Exploiting the coevolution of interacting proteins to discover interaction specificity. J Mol Biol 327: 273-284.
-
(2003)
J Mol Biol
, vol.327
, pp. 273-284
-
-
Ramani, A.K.1
Marcotte, E.M.2
-
27
-
-
0033780375
-
Prediction of protein interactions: Metabolic enzymes are frequently involved in gene fusion
-
Tsoka S, Ouzounis CA, (2000) Prediction of protein interactions: Metabolic enzymes are frequently involved in gene fusion. Nature Genetics 26: 141-142.
-
(2000)
Nature Genetics
, vol.26
, pp. 141-142
-
-
Tsoka, S.1
Ouzounis, C.A.2
-
28
-
-
2942544498
-
Protein interaction networks from yeast to human
-
Bork P, Jensen LJ, von Mering C, Ramani AK, Lee I, et al. (2004) Protein interaction networks from yeast to human. Curr Opin Struct Biol 14: 292-299.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 292-299
-
-
Bork, P.1
Jensen, L.J.2
von Mering, C.3
Ramani, A.K.4
Lee, I.5
-
29
-
-
34247586171
-
Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners
-
Shoemaker BA, Panchenko AR, (2007) Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners. PLoS Comput Biol 3: e43.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Shoemaker, B.A.1
Panchenko, A.R.2
-
30
-
-
0036601150
-
Computational methods for the prediction of protein interactions
-
Valencia A, Pazos F, (2002) Computational methods for the prediction of protein interactions. Curr Opin Struct Biol 12: 368-373.
-
(2002)
Curr Opin Struct Biol
, vol.12
, pp. 368-373
-
-
Valencia, A.1
Pazos, F.2
-
31
-
-
13244265581
-
Information assessment on predicting protein protein interactions
-
Lin N, Wu B, Jansen R, Gerstein M, Zhao H, (2004) Information assessment on predicting protein protein interactions. BMC Bioinformatics 5: 154.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 154
-
-
Lin, N.1
Wu, B.2
Jansen, R.3
Gerstein, M.4
Zhao, H.5
-
32
-
-
2942541277
-
Predicting co-complexed protein pairs using genomic and proteomic data integration
-
Zhang LV, Wong SL, King OD, Roth FP, (2004) Predicting co-complexed protein pairs using genomic and proteomic data integration. BMC Bioinformatics 5: 38.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 38
-
-
Zhang, L.V.1
Wong, S.L.2
King, O.D.3
Roth, F.P.4
-
33
-
-
42149163727
-
A mixture of feature experts approach for protein-protein interaction prediction
-
Qi Y, Klein-Seetharaman J, Bar-Joseph Z, (2007) A mixture of feature experts approach for protein-protein interaction prediction. BMC Bioinformatics 8: S6.
-
(2007)
BMC Bioinformatics
, vol.8
-
-
Qi, Y.1
Klein-Seetharaman, J.2
Bar-Joseph, Z.3
-
34
-
-
0034602774
-
Knowledge-based analysis of microarray gene expression data by using support vector machines
-
Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, et al. (2000) Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci U S A 97: 262-7.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 262-267
-
-
Brown, M.P.1
Grundy, W.N.2
Lin, D.3
Cristianini, N.4
Sugnet, C.W.5
-
35
-
-
33645510456
-
Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale
-
Date SV, Stoeckert CJ Jr, (2006) Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale. Genome Res 16: 542-549.
-
(2006)
Genome Res
, vol.16
, pp. 542-549
-
-
Date, S.V.1
Stoeckert Jr., C.J.2
-
36
-
-
9444239213
-
A probabilistic functional network of yeast genes
-
Lee I, Date SV, Adai AT, Marcotte EM, (2004) A probabilistic functional network of yeast genes. Science 306: 1555-1558.
-
(2004)
Science
, vol.306
, pp. 1555-1558
-
-
Lee, I.1
Date, S.V.2
Adai, A.T.3
Marcotte, E.M.4
-
37
-
-
22244447463
-
Assessing the limits of genomic data integration for predicting protein networks
-
Lu LJ, Xia Y, Paccanaro A, Yu H, Gerstein M, (2005) Assessing the limits of genomic data integration for predicting protein networks. Genome Res 15: 945-953.
-
(2005)
Genome Res
, vol.15
, pp. 945-953
-
-
Lu, L.J.1
Xia, Y.2
Paccanaro, A.3
Yu, H.4
Gerstein, M.5
-
38
-
-
23444452564
-
Probabilistic model of the human protein-protein interaction network
-
Rhodes DR, Tomlins SA, Varambally S, Mahavisno V, Barrette T, et al. (2005) Probabilistic model of the human protein-protein interaction network. Nat Biotechnol 23: 951-959.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 951-959
-
-
Rhodes, D.R.1
Tomlins, S.A.2
Varambally, S.3
Mahavisno, V.4
Barrette, T.5
-
39
-
-
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
-
40
-
-
34547693013
-
Probabilistic prediction and ranking of human protein-protein interactions
-
Scott MS, Barton GJ, (2007) Probabilistic prediction and ranking of human protein-protein interactions. BMC Bioinformatics 8: 239.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 239
-
-
Scott, M.S.1
Barton, G.J.2
-
41
-
-
0038492417
-
A Bayesian framework for combining heterogeneous data sources for gene function predition (in S. cerevisiae)
-
Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D, (2003) A Bayesian framework for combining heterogeneous data sources for gene function predition (in S. cerevisiae). Proc Natl Acad Sci USA 100: 8348-8353.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 8348-8353
-
-
Troyanskaya, O.G.1
Dolinski, K.2
Owen, A.B.3
Altman, R.B.4
Botstein, D.5
-
42
-
-
13444249988
-
STRING: known and predicted protein-protein associations, integrated and transferred across organisms
-
von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, et al. (2005) STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res 33: D433-D437.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
von Mering, C.1
Jensen, L.J.2
Snel, B.3
Hooper, S.D.4
Krupp, M.5
-
43
-
-
77549085334
-
A knowledge-driven probabilistic framework for the prediction of protein-protein interaction networks
-
Browne F, Wang H, Zheng H, Azuaje F, (2010) A knowledge-driven probabilistic framework for the prediction of protein-protein interaction networks. Comput Biol Med 40: 306-317.
-
(2010)
Comput Biol Med
, vol.40
, pp. 306-317
-
-
Browne, F.1
Wang, H.2
Zheng, H.3
Azuaje, F.4
-
44
-
-
70449562098
-
Accounting for redundancy when integrating gene interaction databases
-
Elefsinioti A, Ackermann M, Beyer A, (2009) Accounting for redundancy when integrating gene interaction databases. PLoS One 4: e7492.
-
(2009)
PLoS One
, vol.4
-
-
Elefsinioti, A.1
Ackermann, M.2
Beyer, A.3
-
45
-
-
77951953607
-
Prediction of human functional genetic networks from heterogeneous data using RVM-based ensemble learning
-
Wu CC, Asgharzadeh S, Triche TJ, D'Argenio DZ, (2010) Prediction of human functional genetic networks from heterogeneous data using RVM-based ensemble learning. Bioinformatics 26: 807-13.
-
(2010)
Bioinformatics
, vol.26
, pp. 807-813
-
-
Wu, C.C.1
Asgharzadeh, S.2
Triche, T.J.3
D'Argenio, D.Z.4
-
46
-
-
0347473809
-
Gaining confidence in high-throughput protein interaction networks
-
Bader JS, Chaudhuri A, Rothberg JM, Chant J, (2004) Gaining confidence in high-throughput protein interaction networks. Nat Biotechnol 22: 78-85.
-
(2004)
Nat Biotechnol
, vol.22
, pp. 78-85
-
-
Bader, J.S.1
Chaudhuri, A.2
Rothberg, J.M.3
Chant, J.4
-
47
-
-
38949215411
-
InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes
-
Sun J, Sun Y, Ding G, Liu Q, Wang C, et al. (2007) InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes. BMC Bioinformatics 8: 414.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 414
-
-
Sun, J.1
Sun, Y.2
Ding, G.3
Liu, Q.4
Wang, C.5
-
48
-
-
33646018046
-
Evaluation of Different Biological Data and Computational Classification Methods for Use in Protein Interaction Prediction
-
Qi Y, Bar-Joseph Z, Klein-Seetharaman J, (2006) Evaluation of Different Biological Data and Computational Classification Methods for Use in Protein Interaction Prediction. Proteins 63: 490-500.
-
(2006)
Proteins
, vol.63
, pp. 490-500
-
-
Qi, Y.1
Bar-Joseph, Z.2
Klein-Seetharaman, J.3
-
49
-
-
20144387067
-
The MIPS mammalian protein-protein interaction database
-
Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, et al. (2005) The MIPS mammalian protein-protein interaction database. Bioinformatics 21: 832-834.
-
(2005)
Bioinformatics
, vol.21
, pp. 832-834
-
-
Pagel, P.1
Kovac, S.2
Oesterheld, M.3
Brauner, B.4
Dunger-Kaltenbach, I.5
-
50
-
-
33947312507
-
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms
-
Persico M, Ceol A, Gavrila C, Hoffmann R, Florio A, et al. (2005) HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinformatics 6 (Suppl 4): S21.
-
(2005)
BMC Bioinformatics
, vol.6
, Issue.SUPPL. 4
-
-
Persico, M.1
Ceol, A.2
Gavrila, C.3
Hoffmann, R.4
Florio, A.5
-
51
-
-
57249098833
-
Bayesian nonparametric inference on stochastic ordering
-
Dunson DB, Peddada SD, (2008) Bayesian nonparametric inference on stochastic ordering. Biometrika 95: 859-874.
-
(2008)
Biometrika
, vol.95
, pp. 859-874
-
-
Dunson, D.B.1
Peddada, S.D.2
-
52
-
-
1842816362
-
Gibbs sampling methods for stick-breaking priors
-
Ishwaran H, James LF, (2001) Gibbs sampling methods for stick-breaking priors. J Am Statist Assoc 96: 16173.
-
(2001)
J Am Statist Assoc
, vol.96
, pp. 16173
-
-
Ishwaran, H.1
James, L.F.2
|