-
1
-
-
0033518234
-
From molecular to modular cell biology
-
10.1038/35011540, 10591225
-
Hartwell LH, Hopfield JJ, Leibler S, Murray AW. From molecular to modular cell biology. Nature 1999, 402:C47-52. 10.1038/35011540, 10591225.
-
(1999)
Nature
, vol.402
-
-
Hartwell, L.H.1
Hopfield, J.J.2
Leibler, S.3
Murray, A.W.4
-
2
-
-
0034660322
-
Protein function in the post-genomic era
-
10.1038/35015694, 10866208
-
Eisenberg D, Marcotte EM, Xenarios I, Yeates TO. Protein function in the post-genomic era. Nature 2000, 405:823-826. 10.1038/35015694, 10866208.
-
(2000)
Nature
, vol.405
, pp. 823-826
-
-
Eisenberg, D.1
Marcotte, E.M.2
Xenarios, I.3
Yeates, T.O.4
-
3
-
-
0742305866
-
Network biology: understanding the cell's functional organization
-
10.1038/nrg1272, 14735121
-
Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5:101-113. 10.1038/nrg1272, 14735121.
-
(2004)
Nat Rev Genet
, vol.5
, pp. 101-113
-
-
Barabasi, A.L.1
Oltvai, Z.N.2
-
4
-
-
41649119247
-
Protein networks in disease
-
10.1101/gr.071852.107, 18381899
-
Ideker T, Sharan R. Protein networks in disease. Genome Res 2008, 18:644-652. 10.1101/gr.071852.107, 18381899.
-
(2008)
Genome Res
, vol.18
, pp. 644-652
-
-
Ideker, T.1
Sharan, R.2
-
5
-
-
48249103483
-
Networking metabolites and diseases
-
10.1073/pnas.0805644105, 2481360, 18632571
-
Braun P, Rietman E, Vidal M. Networking metabolites and diseases. Proc Natl Acad Sci USA 2008, 105:9849-9850. 10.1073/pnas.0805644105, 2481360, 18632571.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 9849-9850
-
-
Braun, P.1
Rietman, E.2
Vidal, M.3
-
6
-
-
3943087720
-
Analyzing cellular biochemistry in terms of molecular networks
-
10.1146/annurev.biochem.73.011303.073950, 15189167
-
Xia Y, Yu H, Jansen R, Seringhaus M, Baxter S, Greenbaum D, Zhao H, Gerstein M. Analyzing cellular biochemistry in terms of molecular networks. Annu Rev Biochem 2004, 73:1051-1087. 10.1146/annurev.biochem.73.011303.073950, 15189167.
-
(2004)
Annu Rev Biochem
, vol.73
, pp. 1051-1087
-
-
Xia, Y.1
Yu, H.2
Jansen, R.3
Seringhaus, M.4
Baxter, S.5
Greenbaum, D.6
Zhao, H.7
Gerstein, M.8
-
7
-
-
0037050026
-
Functional organization of the yeast proteome by systematic analysis of protein complexes
-
10.1038/415141a, 11805826
-
Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415:141-147. 10.1038/415141a, 11805826.
-
(2002)
Nature
, vol.415
, pp. 141-147
-
-
Gavin, A.C.1
Bosche, M.2
Krause, R.3
Grandi, P.4
Marzioch, M.5
Bauer, A.6
Schultz, J.7
Rick, J.M.8
Michon, A.M.9
Cruciat, C.M.10
-
8
-
-
9144264169
-
A map of the interactome network of the metazoan C. elegans
-
10.1126/science.1091403, 1698949, 14704431
-
Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T, et al. A map of the interactome network of the metazoan C. elegans. Science 2004, 303:540-543. 10.1126/science.1091403, 1698949, 14704431.
-
(2004)
Science
, vol.303
, pp. 540-543
-
-
Li, S.1
Armstrong, C.M.2
Bertin, N.3
Ge, H.4
Milstein, S.5
Boxem, M.6
Vidalain, P.O.7
Han, J.D.8
Chesneau, A.9
Hao, T.10
-
9
-
-
0346463223
-
Essentiality and damage in metabolic networks
-
10.1093/bioinformatics/btg386, 14693817
-
Lemke N, Heredia F, Barcellos CK, Dos Reis AN, Mombach JC. Essentiality and damage in metabolic networks. Bioinformatics 2004, 20:115-119. 10.1093/bioinformatics/btg386, 14693817.
-
(2004)
Bioinformatics
, vol.20
, pp. 115-119
-
-
Lemke, N.1
Heredia, F.2
Barcellos, C.K.3
Dos Reis, A.N.4
Mombach, J.C.5
-
10
-
-
0042093610
-
The connectivity structure, giant strong component and centrality of metabolic networks
-
10.1093/bioinformatics/btg177, 12874056
-
Ma HW, Zeng AP. The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics 2003, 19:1423-1430. 10.1093/bioinformatics/btg177, 12874056.
-
(2003)
Bioinformatics
, vol.19
, pp. 1423-1430
-
-
Ma, H.W.1
Zeng, A.P.2
-
11
-
-
1242319556
-
The metabolic world of Escherichia coli is not small
-
10.1073/pnas.0306458101, 341771, 14757824
-
Arita M. The metabolic world of Escherichia coli is not small. Proc Natl Acad Sci USA 2004, 101:1543-1547. 10.1073/pnas.0306458101, 341771, 14757824.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 1543-1547
-
-
Arita, M.1
-
12
-
-
20344379457
-
Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli
-
10.1073/pnas.0500365102, 1142363, 15908506
-
Balazsi G, Barabasi AL, Oltvai ZN. Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc Natl Acad Sci USA 2005, 102:7841-7846. 10.1073/pnas.0500365102, 1142363, 15908506.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 7841-7846
-
-
Balazsi, G.1
Barabasi, A.L.2
Oltvai, Z.N.3
-
13
-
-
23644437498
-
Formation of regulatory patterns during signal propagation in a Mammalian cellular network
-
10.1126/science.1108876, 16099987
-
Ma'ayan A, Jenkins SL, Neves S, Hasseldine A, Grace E, Dubin-Thaler B, Eungdamrong NJ, Weng G, Ram PT, Rice JJ, et al. Formation of regulatory patterns during signal propagation in a Mammalian cellular network. Science 2005, 309:1078-1083. 10.1126/science.1108876, 16099987.
-
(2005)
Science
, vol.309
, pp. 1078-1083
-
-
Ma'ayan, A.1
Jenkins, S.L.2
Neves, S.3
Hasseldine, A.4
Grace, E.5
Dubin-Thaler, B.6
Eungdamrong, N.J.7
Weng, G.8
Ram, P.T.9
Rice, J.J.10
-
14
-
-
10744230485
-
Global mapping of the yeast genetic interaction network
-
10.1126/science.1091317, 14764870
-
Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, et al. Global mapping of the yeast genetic interaction network. Science 2004, 303:808-813. 10.1126/science.1091317, 14764870.
-
(2004)
Science
, vol.303
, pp. 808-813
-
-
Tong, A.H.1
Lesage, G.2
Bader, G.D.3
Ding, H.4
Xu, H.5
Xin, X.6
Young, J.7
Berriz, G.F.8
Brost, R.L.9
Chang, M.10
-
15
-
-
33947252154
-
Network-based prediction of protein function
-
10.1038/msb4100129, 1847944, 17353930
-
Sharan R, Ulitsky I, Shamir R. Network-based prediction of protein function. Mol Syst Biol 2007, 3:88. 10.1038/msb4100129, 1847944, 17353930.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 88
-
-
Sharan, R.1
Ulitsky, I.2
Shamir, R.3
-
16
-
-
27144530248
-
Towards a proteome-scale map of the human protein-protein interaction network
-
10.1038/nature04209, 16189514
-
Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005, 437:1173-1178. 10.1038/nature04209, 16189514.
-
(2005)
Nature
, vol.437
, pp. 1173-1178
-
-
Rual, J.F.1
Venkatesan, K.2
Hao, T.3
Hirozane-Kishikawa, T.4
Dricot, A.5
Li, N.6
Berriz, G.F.7
Gibbons, F.D.8
Dreze, M.9
Ayivi-Guedehoussou, N.10
-
17
-
-
33846660878
-
Dependence network modeling for biomarker identification
-
10.1093/bioinformatics/btl553, 17077095
-
Qiu P, Wang ZJ, Liu KJ, Hu ZZ, Wu CH. Dependence network modeling for biomarker identification. Bioinformatics 2007, 23:198-206. 10.1093/bioinformatics/btl553, 17077095.
-
(2007)
Bioinformatics
, vol.23
, pp. 198-206
-
-
Qiu, P.1
Wang, Z.J.2
Liu, K.J.3
Hu, Z.Z.4
Wu, C.H.5
-
18
-
-
35348891430
-
Network-based classification of breast cancer metastasis
-
10.1038/msb4100180, 2063581, 17940530
-
Chuang HY, Lee E, Liu YT, Lee D, Ideker T. Network-based classification of breast cancer metastasis. Mol Syst Biol 2007, 3:140. 10.1038/msb4100180, 2063581, 17940530.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 140
-
-
Chuang, H.Y.1
Lee, E.2
Liu, Y.T.3
Lee, D.4
Ideker, T.5
-
19
-
-
34047216368
-
Dynamic simulations on the arachidonic acid metabolic network
-
10.1371/journal.pcbi.0030055, 1829479,1829479, 17381237
-
Yang K, Ma W, Liang H, Ouyang Q, Tang C, Lai L. Dynamic simulations on the arachidonic acid metabolic network. PLoS Comput Biol 2007, 3:e55. 10.1371/journal.pcbi.0030055, 1829479,1829479, 17381237.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Yang, K.1
Ma, W.2
Liang, H.3
Ouyang, Q.4
Tang, C.5
Lai, L.6
-
20
-
-
54249155522
-
Network pharmacology: the next paradigm in drug discovery
-
10.1038/nchembio.118, 18936753
-
Hopkins AL. Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol 2008, 4:682-690. 10.1038/nchembio.118, 18936753.
-
(2008)
Nat Chem Biol
, vol.4
, pp. 682-690
-
-
Hopkins, A.L.1
-
21
-
-
43049156566
-
Human metabolic network reconstruction and its impact on drug discovery and development
-
10.1016/j.drudis.2008.02.002, 18468557
-
Ma H, Goryanin I. Human metabolic network reconstruction and its impact on drug discovery and development. Drug Discov Today 2008, 13:402-408. 10.1016/j.drudis.2008.02.002, 18468557.
-
(2008)
Drug Discov Today
, vol.13
, pp. 402-408
-
-
Ma, H.1
Goryanin, I.2
-
22
-
-
22844450110
-
Systematic interpretation of genetic interactions using protein networks
-
10.1038/nbt1096, 2814446, 15877074
-
Kelley R, Ideker T. Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol 2005, 23:561-566. 10.1038/nbt1096, 2814446, 15877074.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 561-566
-
-
Kelley, R.1
Ideker, T.2
-
23
-
-
0035799707
-
Lethality and centrality in protein networks
-
10.1038/35075138, 11333967
-
Jeong H, Mason SP, Barabasi AL, Oltvai ZN. Lethality and centrality in protein networks. Nature 2001, 411:41-42. 10.1038/35075138, 11333967.
-
(2001)
Nature
, vol.411
, pp. 41-42
-
-
Jeong, H.1
Mason, S.P.2
Barabasi, A.L.3
Oltvai, Z.N.4
-
24
-
-
0036578654
-
Topological and causal structure of the yeast transcriptional regulatory network
-
10.1038/ng873, 11967534
-
Guelzim N, Bottani S, Bourgine P, Kepes F. Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet 2002, 31:60-63. 10.1038/ng873, 11967534.
-
(2002)
Nat Genet
, vol.31
, pp. 60-63
-
-
Guelzim, N.1
Bottani, S.2
Bourgine, P.3
Kepes, F.4
-
25
-
-
53749085229
-
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
-
10.1038/nbt1492, 18846089
-
Herrgard MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Bluthgen N, Borger S, Costenoble R, Heinemann M, et al. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol 2008, 26:1155-1160. 10.1038/nbt1492, 18846089.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1155-1160
-
-
Herrgard, M.J.1
Swainston, N.2
Dobson, P.3
Dunn, W.B.4
Arga, K.Y.5
Arvas, M.6
Bluthgen, N.7
Borger, S.8
Costenoble, R.9
Heinemann, M.10
-
26
-
-
4644326931
-
Genomic analysis of regulatory network dynamics reveals large topological changes
-
10.1038/nature02782, 15372033
-
Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 2004, 431:308-312. 10.1038/nature02782, 15372033.
-
(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
-
27
-
-
27844551326
-
Dynamic properties of network motifs contribute to biological network organization
-
10.1371/journal.pbio.0030343, 1239925,1239925, 16187794
-
Prill RJ, Iglesias PA, Levchenko A. Dynamic properties of network motifs contribute to biological network organization. PLoS Biol 2005, 3:e343. 10.1371/journal.pbio.0030343, 1239925,1239925, 16187794.
-
(2005)
PLoS Biol
, vol.3
-
-
Prill, R.J.1
Iglesias, P.A.2
Levchenko, A.3
-
28
-
-
1542287343
-
Superfamilies of evolved and designed networks
-
10.1126/science.1089167, 15001784
-
Milo R, Itzkovitz S, Kashtan N, Levitt R, Shen-Orr S, Ayzenshtat I, Sheffer M, Alon U. Superfamilies of evolved and designed networks. Science 2004, 303:1538-1542. 10.1126/science.1089167, 15001784.
-
(2004)
Science
, vol.303
, pp. 1538-1542
-
-
Milo, R.1
Itzkovitz, S.2
Kashtan, N.3
Levitt, R.4
Shen-Orr, S.5
Ayzenshtat, I.6
Sheffer, M.7
Alon, U.8
-
29
-
-
2442537233
-
Gene regulatory network growth by duplication
-
10.1038/ng1340, 15107850
-
Teichmann SA, Babu MM. Gene regulatory network growth by duplication. Nat Genet 2004, 36:492-496. 10.1038/ng1340, 15107850.
-
(2004)
Nat Genet
, vol.36
, pp. 492-496
-
-
Teichmann, S.A.1
Babu, M.M.2
-
30
-
-
34247622363
-
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics
-
10.1371/journal.pcbi.0030059, 1853125,1853125, 17447836
-
Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M. The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol 2007, 3:e59. 10.1371/journal.pcbi.0030059, 1853125,1853125, 17447836.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Yu, H.1
Kim, P.M.2
Sprecher, E.3
Trifonov, V.4
Gerstein, M.5
-
31
-
-
33646948892
-
Dynamic changes in subgraph preference profiles of crucial transcription factors
-
10.1371/journal.pcbi.0020047, 1458966,1458966, 16699597
-
Zhang Z, Liu C, Skogerbo G, Zhu X, Lu H, Chen L, Shi B, Zhang Y, Wang J, Wu T, Chen R. Dynamic changes in subgraph preference profiles of crucial transcription factors. PLoS Comput Biol 2006, 2:e47. 10.1371/journal.pcbi.0020047, 1458966,1458966, 16699597.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Zhang, Z.1
Liu, C.2
Skogerbo, G.3
Zhu, X.4
Lu, H.5
Chen, L.6
Shi, B.7
Zhang, Y.8
Wang, J.9
Wu, T.10
Chen, R.11
-
32
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
-
10.1038/nature02555, 15190252
-
Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJ, Cusick ME, Roth FP, Vidal M. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 2004, 430:88-93. 10.1038/nature02555, 15190252.
-
(2004)
Nature
, vol.430
, pp. 88-93
-
-
Han, J.D.1
Bertin, N.2
Hao, T.3
Goldberg, D.S.4
Berriz, G.F.5
Zhang, L.V.6
Dupuy, D.7
Walhout, A.J.8
Cusick, M.E.9
Roth, F.P.10
Vidal, M.11
-
33
-
-
13244284551
-
Dynamic complex formation during the yeast cell cycle
-
10.1126/science.1105103, 15692050
-
de Lichtenberg U, Jensen LJ, Brunak S, Bork P. Dynamic complex formation during the yeast cell cycle. Science 2005, 307:724-727. 10.1126/science.1105103, 15692050.
-
(2005)
Science
, vol.307
, pp. 724-727
-
-
de Lichtenberg, U.1
Jensen, L.J.2
Brunak, S.3
Bork, P.4
-
34
-
-
64049086247
-
Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks
-
10.1186/1752-0509-3-32, 2663781, 19284572
-
Lin WH, Liu WC, Hwang MJ. Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks. BMC Syst Biol 2009, 3:32. 10.1186/1752-0509-3-32, 2663781, 19284572.
-
(2009)
BMC Syst Biol
, vol.3
, pp. 32
-
-
Lin, W.H.1
Liu, W.C.2
Hwang, M.J.3
-
35
-
-
64349094767
-
Tissue specificity and the human protein interaction network
-
10.1038/msb.2009.17, 2683721, 19357639
-
Bossi A, Lehner B. Tissue specificity and the human protein interaction network. Mol Syst Biol 2009, 5:260. 10.1038/msb.2009.17, 2683721, 19357639.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 260
-
-
Bossi, A.1
Lehner, B.2
-
36
-
-
44249091879
-
Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics
-
10.1126/science.1157956, 18436743
-
Baerenfaller K, Grossmann J, Grobei MA, Hull R, Hirsch-Hoffmann M, Yalovsky S, Zimmermann P, Grossniklaus U, Gruissem W, Baginsky S. Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 2008, 320:938-941. 10.1126/science.1157956, 18436743.
-
(2008)
Science
, vol.320
, pp. 938-941
-
-
Baerenfaller, K.1
Grossmann, J.2
Grobei, M.A.3
Hull, R.4
Hirsch-Hoffmann, M.5
Yalovsky, S.6
Zimmermann, P.7
Grossniklaus, U.8
Gruissem, W.9
Baginsky, S.10
-
37
-
-
84876732841
-
Biomolecular network analysis and applications
-
John Wiley & Sons, Alterovitz G, Ramoni M
-
Zhang M, Deng J, Fang C, Zhang X, Lu LJ. Biomolecular network analysis and applications. Knowledge-Based Bioinformatics: From analysis to interpretation 2010, 253-288. John Wiley & Sons, Alterovitz G, Ramoni M.
-
(2010)
Knowledge-Based Bioinformatics: From analysis to interpretation
, pp. 253-288
-
-
Zhang, M.1
Deng, J.2
Fang, C.3
Zhang, X.4
Lu, L.J.5
-
38
-
-
0034820537
-
Interrelating different types of genomic data, from proteome to secretome: 'oming in on function
-
10.1101/gr.207401, 11544189
-
Greenbaum D, Luscombe NM, Jansen R, Qian J, Gerstein M. Interrelating different types of genomic data, from proteome to secretome: 'oming in on function. Genome Res 2001, 11:1463-1468. 10.1101/gr.207401, 11544189.
-
(2001)
Genome Res
, vol.11
, pp. 1463-1468
-
-
Greenbaum, D.1
Luscombe, N.M.2
Jansen, R.3
Qian, J.4
Gerstein, M.5
-
39
-
-
33645993265
-
Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling
-
10.1016/j.cell.2006.01.044, 16615898
-
Kislinger T, Cox B, Kannan A, Chung C, Hu P, Ignatchenko A, Scott MS, Gramolini AO, Morris Q, Hallett MT, et al. Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell 2006, 125:173-186. 10.1016/j.cell.2006.01.044, 16615898.
-
(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
-
40
-
-
38549144806
-
The Arabidopsis Information Resource (TAIR): gene structure and function annotation
-
10.1093/nar/gkm965, 2238962, 17986450
-
Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, et al. The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res 2008, 36:D1009-1014. 10.1093/nar/gkm965, 2238962, 17986450.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Swarbreck, D.1
Wilks, C.2
Lamesch, P.3
Berardini, T.Z.4
Garcia-Hernandez, M.5
Foerster, H.6
Li, D.7
Meyer, T.8
Muller, R.9
Ploetz, L.10
-
41
-
-
38549123986
-
AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology
-
10.1093/nar/gkm844, 2238993, 17962307
-
Cui J, Li P, Li G, Xu F, Zhao C, Li Y, Yang Z, Wang G, Yu Q, Shi T. AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology. Nucleic Acids Res 2008, 36:D999-1008. 10.1093/nar/gkm844, 2238993, 17962307.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Cui, J.1
Li, P.2
Li, G.3
Xu, F.4
Zhao, C.5
Li, Y.6
Yang, Z.7
Wang, G.8
Yu, Q.9
Shi, T.10
-
42
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
10.1038/75556, 10802651
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29. 10.1038/75556, 10802651.
-
(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
-
43
-
-
0036733292
-
The vernalization independence 4 gene encodes a novel regulator of flowering locus C
-
10.1046/j.1365-313X.2002.01380.x, 12207655
-
Zhang H, van Nocker S. The vernalization independence 4 gene encodes a novel regulator of flowering locus C. Plant J 2002, 31:663-673. 10.1046/j.1365-313X.2002.01380.x, 12207655.
-
(2002)
Plant J
, vol.31
, pp. 663-673
-
-
Zhang, H.1
van Nocker, S.2
-
44
-
-
44349099751
-
Sorting signals, N-terminal modifications and abundance of the chloroplast proteome
-
10.1371/journal.pone.0001994, 2291561, 18431481
-
Zybailov B, Rutschow H, Friso G, Rudella A, Emanuelsson O, Sun Q, van Wijk KJ. Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. PLoS One 2008, 3:e1994. 10.1371/journal.pone.0001994, 2291561, 18431481.
-
(2008)
PLoS One
, vol.3
-
-
Zybailov, B.1
Rutschow, H.2
Friso, G.3
Rudella, A.4
Emanuelsson, O.5
Sun, Q.6
van Wijk, K.J.7
-
45
-
-
55549091437
-
Quantitative proteomics of a chloroplast SRP54 sorting mutant and its genetic interactions with CLPC1 in Arabidopsis
-
10.1104/pp.108.124545, 2528104, 18633119
-
Rutschow H, Ytterberg AJ, Friso G, Nilsson R, van Wijk KJ. Quantitative proteomics of a chloroplast SRP54 sorting mutant and its genetic interactions with CLPC1 in Arabidopsis. Plant Physiol 2008, 148:156-175. 10.1104/pp.108.124545, 2528104, 18633119.
-
(2008)
Plant Physiol
, vol.148
, pp. 156-175
-
-
Rutschow, H.1
Ytterberg, A.J.2
Friso, G.3
Nilsson, R.4
van Wijk, K.J.5
-
46
-
-
66249092826
-
Information flow analysis of interactome networks
-
10.1371/journal.pcbi.1000350, 2685719, 19503817
-
Missiuro PV, Liu K, Zou L, Ross BC, Zhao G, Liu JS, Ge H. Information flow analysis of interactome networks. PLoS Comput Biol 2009, 5:e1000350. 10.1371/journal.pcbi.1000350, 2685719, 19503817.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Missiuro, P.V.1
Liu, K.2
Zou, L.3
Ross, B.C.4
Zhao, G.5
Liu, J.S.6
Ge, H.7
-
47
-
-
3042672020
-
Functional annotation of the Arabidopsis genome using controlled vocabularies
-
10.1104/pp.104.040071, 514112, 15173566
-
Berardini TZ, Mundodi S, Reiser L, Huala E, Garcia-Hernandez M, Zhang P, Mueller LA, Yoon J, Doyle A, Lander G, et al. Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol 2004, 135:745-755. 10.1104/pp.104.040071, 514112, 15173566.
-
(2004)
Plant Physiol
, vol.135
, pp. 745-755
-
-
Berardini, T.Z.1
Mundodi, S.2
Reiser, L.3
Huala, E.4
Garcia-Hernandez, M.5
Zhang, P.6
Mueller, L.A.7
Yoon, J.8
Doyle, A.9
Lander, G.10
-
48
-
-
20444504323
-
Uncovering the overlapping community structure of complex networks in nature and society
-
10.1038/nature03607, 15944704
-
Palla G, Derenyi I, Farkas I, Vicsek T. Uncovering the overlapping community structure of complex networks in nature and society. Nature 2005, 435:814-818. 10.1038/nature03607, 15944704.
-
(2005)
Nature
, vol.435
, pp. 814-818
-
-
Palla, G.1
Derenyi, I.2
Farkas, I.3
Vicsek, T.4
-
49
-
-
14644396645
-
Functional cartography of complex metabolic networks
-
10.1038/nature03288, 2175124, 15729348
-
Guimera R, Nunes Amaral LA. Functional cartography of complex metabolic networks. Nature 2005, 433:895-900. 10.1038/nature03288, 2175124, 15729348.
-
(2005)
Nature
, vol.433
, pp. 895-900
-
-
Guimera, R.1
Nunes Amaral, L.A.2
-
50
-
-
0037062448
-
Community structure in social and biological networks
-
10.1073/pnas.122653799, 122977, 12060727
-
Girvan M, Newman ME. Community structure in social and biological networks. Proc Natl Acad Sci USA 2002, 99:7821-7826. 10.1073/pnas.122653799, 122977, 12060727.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 7821-7826
-
-
Girvan, M.1
Newman, M.E.2
-
51
-
-
0242268461
-
Predicting protein functions from redundancies in large-scale protein interaction networks
-
10.1073/pnas.2132527100, 240660, 14566057
-
Samanta MP, Liang S. Predicting protein functions from redundancies in large-scale protein interaction networks. Proc Natl Acad Sci USA 2003, 100:12579-12583. 10.1073/pnas.2132527100, 240660, 14566057.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 12579-12583
-
-
Samanta, M.P.1
Liang, S.2
-
52
-
-
34548511546
-
Semantic integration to identify overlapping functional modules in protein interaction networks
-
10.1186/1471-2105-8-265, 1971074, 17650343
-
Cho YR, Hwang W, Ramanathan M, Zhang A. Semantic integration to identify overlapping functional modules in protein interaction networks. BMC Bioinformatics 2007, 8:265. 10.1186/1471-2105-8-265, 1971074, 17650343.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 265
-
-
Cho, Y.R.1
Hwang, W.2
Ramanathan, M.3
Zhang, A.4
-
53
-
-
33645319955
-
Predicting interactions in protein networks by completing defective cliques
-
10.1093/bioinformatics/btl014, 16455753
-
Yu H, Paccanaro A, Trifonov V, Gerstein M. Predicting interactions in protein networks by completing defective cliques. Bioinformatics 2006, 22:823-829. 10.1093/bioinformatics/btl014, 16455753.
-
(2006)
Bioinformatics
, vol.22
, pp. 823-829
-
-
Yu, H.1
Paccanaro, A.2
Trifonov, V.3
Gerstein, M.4
-
54
-
-
53349117774
-
High-quality binary protein interaction map of the yeast interactome network
-
10.1126/science.1158684, 2746753, 18719252
-
Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, et al. High-quality binary protein interaction map of the yeast interactome network. Science 2008, 322:104-110. 10.1126/science.1158684, 2746753, 18719252.
-
(2008)
Science
, vol.322
, pp. 104-110
-
-
Yu, H.1
Braun, P.2
Yildirim, M.A.3
Lemmens, I.4
Venkatesan, K.5
Sahalie, J.6
Hirozane-Kishikawa, T.7
Gebreab, F.8
Li, N.9
Simonis, N.10
-
55
-
-
0037161731
-
Comparative assessment of large-scale data sets of protein-protein interactions
-
10.1038/nature750, 12000970
-
von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417:399-403. 10.1038/nature750, 12000970.
-
(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
-
56
-
-
59549083190
-
Precision and recall estimates for two-hybrid screens
-
10.1093/bioinformatics/btn640, 2639075, 19091773
-
Huang H, Bader JS. Precision and recall estimates for two-hybrid screens. Bioinformatics 2009, 25:372-378. 10.1093/bioinformatics/btn640, 2639075, 19091773.
-
(2009)
Bioinformatics
, vol.25
, pp. 372-378
-
-
Huang, H.1
Bader, J.S.2
-
57
-
-
3543099834
-
Evolution and topology in the yeast protein interaction network
-
10.1101/gr.2300204, 442146, 15231746
-
Wuchty S. Evolution and topology in the yeast protein interaction network. Genome Res 2004, 14:1310-1314. 10.1101/gr.2300204, 442146, 15231746.
-
(2004)
Genome Res
, vol.14
, pp. 1310-1314
-
-
Wuchty, S.1
-
58
-
-
27144509163
-
A network-based analysis of systemic inflammation in humans
-
10.1038/nature03985, 16136080
-
Calvano SE, Xiao W, Richards DR, Felciano RM, Baker HV, Cho RJ, Chen RO, Brownstein BH, Cobb JP, Tschoeke SK, et al. A network-based analysis of systemic inflammation in humans. Nature 2005, 437:1032-1037. 10.1038/nature03985, 16136080.
-
(2005)
Nature
, vol.437
, pp. 1032-1037
-
-
Calvano, S.E.1
Xiao, W.2
Richards, D.R.3
Felciano, R.M.4
Baker, H.V.5
Cho, R.J.6
Chen, R.O.7
Brownstein, B.H.8
Cobb, J.P.9
Tschoeke, S.K.10
-
59
-
-
59849125136
-
Dynamic modularity in protein interaction networks predicts breast cancer outcome
-
10.1038/nbt.1522, 19182785
-
Taylor IW, Linding R, Warde-Farley D, Liu Y, Pesquita C, Faria D, Bull S, Pawson T, Morris Q, Wrana JL. Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol 2009, 27:199-204. 10.1038/nbt.1522, 19182785.
-
(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
Faria, D.6
Bull, S.7
Pawson, T.8
Morris, Q.9
Wrana, J.L.10
-
60
-
-
34347329333
-
In search of the biological significance of modular structures in protein networks
-
10.1371/journal.pcbi.0030107, 1885274,1885274, 17542644
-
Wang Z, Zhang J. In search of the biological significance of modular structures in protein networks. PLoS Comput Biol 2007, 3:e107. 10.1371/journal.pcbi.0030107, 1885274,1885274, 17542644.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Wang, Z.1
Zhang, J.2
-
61
-
-
33750238153
-
Stratus not altocumulus: a new view of the yeast protein interaction network
-
10.1371/journal.pbio.0040317, 1569888,1569888, 16984220
-
Batada NN, Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hurst LD, Tyers M. Stratus not altocumulus: a new view of the yeast protein interaction network. PLoS Biol 2006, 4:e317. 10.1371/journal.pbio.0040317, 1569888,1569888, 16984220.
-
(2006)
PLoS Biol
, vol.4
-
-
Batada, N.N.1
Reguly, T.2
Breitkreutz, A.3
Boucher, L.4
Breitkreutz, B.J.5
Hurst, L.D.6
Tyers, M.7
-
62
-
-
34250345292
-
Confirmation of organized modularity in the yeast interactome
-
10.1371/journal.pbio.0050153, 1892830,1892830, 17564493
-
Bertin N, Simonis N, Dupuy D, Cusick ME, Han JD, Fraser HB, Roth FP, Vidal M. Confirmation of organized modularity in the yeast interactome. PLoS Biol 2007, 5:e153. 10.1371/journal.pbio.0050153, 1892830,1892830, 17564493.
-
(2007)
PLoS Biol
, vol.5
-
-
Bertin, N.1
Simonis, N.2
Dupuy, D.3
Cusick, M.E.4
Han, J.D.5
Fraser, H.B.6
Roth, F.P.7
Vidal, M.8
-
63
-
-
34250361148
-
Still stratus not altocumulus: further evidence against the date/party hub distinction
-
10.1371/journal.pbio.0050154, 1892831,1892831, 17564494
-
Batada NN, Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hurst LD, Tyers M. Still stratus not altocumulus: further evidence against the date/party hub distinction. PLoS Biol 2007, 5:e154. 10.1371/journal.pbio.0050154, 1892831,1892831, 17564494.
-
(2007)
PLoS Biol
, vol.5
-
-
Batada, N.N.1
Reguly, T.2
Breitkreutz, A.3
Boucher, L.4
Breitkreutz, B.J.5
Hurst, L.D.6
Tyers, M.7
-
64
-
-
25144516911
-
Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome
-
10.1186/gb-2005-6-5-r40, 1175952, 15892868
-
Ramani AK, Bunescu RC, Mooney RJ, Marcotte EM. Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol 2005, 6:R40. 10.1186/gb-2005-6-5-r40, 1175952, 15892868.
-
(2005)
Genome Biol
, vol.6
-
-
Ramani, A.K.1
Bunescu, R.C.2
Mooney, R.J.3
Marcotte, E.M.4
-
65
-
-
25144498379
-
A human protein-protein interaction network: a resource for annotating the proteome
-
10.1016/j.cell.2005.08.029, 16169070
-
Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, et al. A human protein-protein interaction network: a resource for annotating the proteome. Cell 2005, 122:957-968. 10.1016/j.cell.2005.08.029, 16169070.
-
(2005)
Cell
, vol.122
, pp. 957-968
-
-
Stelzl, U.1
Worm, U.2
Lalowski, M.3
Haenig, C.4
Brembeck, F.H.5
Goehler, H.6
Stroedicke, M.7
Zenkner, M.8
Schoenherr, A.9
Koeppen, S.10
-
66
-
-
10744224197
-
Development of human protein reference database as an initial platform for approaching systems biology in humans
-
10.1101/gr.1680803, 403728, 14525934
-
Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TK, Gronborg M, et al. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res 2003, 13:2363-2371. 10.1101/gr.1680803, 403728, 14525934.
-
(2003)
Genome Res
, vol.13
, pp. 2363-2371
-
-
Peri, S.1
Navarro, J.D.2
Amanchy, R.3
Kristiansen, T.Z.4
Jonnalagadda, C.K.5
Surendranath, V.6
Niranjan, V.7
Muthusamy, B.8
Gandhi, T.K.9
Gronborg, M.10
-
67
-
-
13444272070
-
The Biomolecular Interaction Network Database and related tools 2005 update
-
10.1093/nar/gki051, 540005, 15608229
-
Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, Betel D, Bobechko B, Boutilier K, Burgess E, et al. The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res 2005, 33:D418-424. 10.1093/nar/gki051, 540005, 15608229.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Alfarano, C.1
Andrade, C.E.2
Anthony, K.3
Bahroos, N.4
Bajec, M.5
Bantoft, K.6
Betel, D.7
Bobechko, B.8
Boutilier, K.9
Burgess, E.10
-
68
-
-
13444259844
-
Reactome: a knowledgebase of biological pathways
-
10.1093/nar/gki072, 540026, 15608231
-
Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath GR, Wu GR, Matthews L, et al. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 2005, 33:D428-432. 10.1093/nar/gki072, 540026, 15608231.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Joshi-Tope, G.1
Gillespie, M.2
Vastrik, I.3
D'Eustachio, P.4
Schmidt, E.5
de Bono, B.6
Jassal, B.7
Gopinath, G.R.8
Wu, G.R.9
Matthews, L.10
-
69
-
-
33749248174
-
HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy
-
10.1002/pmic.200600295, 16927433
-
Hamacher M, Apweiler R, Arnold G, Becker A, Bluggel M, Carrette O, Colvis C, Dunn MJ, Frohlich T, Fountoulakis M, et al. HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy. Proteomics 2006, 6:4890-4898. 10.1002/pmic.200600295, 16927433.
-
(2006)
Proteomics
, vol.6
, pp. 4890-4898
-
-
Hamacher, M.1
Apweiler, R.2
Arnold, G.3
Becker, A.4
Bluggel, M.5
Carrette, O.6
Colvis, C.7
Dunn, M.J.8
Frohlich, T.9
Fountoulakis, M.10
-
70
-
-
34948831564
-
In-depth proteomic profiling of the normal human kidney glomerulus using two-dimensional protein prefractionation in combination with liquid chromatography-tandem mass spectrometry
-
10.1021/pr070203n, 17711322
-
Miyamoto M, Yoshida Y, Taguchi I, Nagasaka Y, Tasaki M, Zhang Y, Xu B, Nameta M, Sezaki H, Cuellar LM, et al. In-depth proteomic profiling of the normal human kidney glomerulus using two-dimensional protein prefractionation in combination with liquid chromatography-tandem mass spectrometry. J Proteome Res 2007, 6:3680-3690. 10.1021/pr070203n, 17711322.
-
(2007)
J Proteome Res
, vol.6
, pp. 3680-3690
-
-
Miyamoto, M.1
Yoshida, Y.2
Taguchi, I.3
Nagasaka, Y.4
Tasaki, M.5
Zhang, Y.6
Xu, B.7
Nameta, M.8
Sezaki, H.9
Cuellar, L.M.10
-
71
-
-
33751375646
-
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks
-
10.1093/bioinformatics/btl488, 17021160
-
Yip KY, Yu H, Kim PM, Schultz M, Gerstein M. The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. Bioinformatics 2006, 22:2968-2970. 10.1093/bioinformatics/btl488, 17021160.
-
(2006)
Bioinformatics
, vol.22
, pp. 2968-2970
-
-
Yip, K.Y.1
Yu, H.2
Kim, P.M.3
Schultz, M.4
Gerstein, M.5
|