-
1
-
-
84880866093
-
Construction of small RNA-mediated gene regulatory networks in the roots of rice (Oryza sativa)
-
Ma X., Shao C., Wang H., Jin Y., Meng Y. Construction of small RNA-mediated gene regulatory networks in the roots of rice (Oryza sativa). BMC Genomics 2013, 14:510.
-
(2013)
BMC Genomics
, vol.14
, pp. 510
-
-
Ma, X.1
Shao, C.2
Wang, H.3
Jin, Y.4
Meng, Y.5
-
2
-
-
81255210925
-
Construction of MicroRNA- and MicroRNA*-mediated regulatory networks in plants
-
Meng Y., Shao C., Gou L., Jin Y., Chen M. Construction of MicroRNA- and MicroRNA*-mediated regulatory networks in plants. RNA Biol 2011, 8:1124-1148.
-
(2011)
RNA Biol
, vol.8
, pp. 1124-1148
-
-
Meng, Y.1
Shao, C.2
Gou, L.3
Jin, Y.4
Chen, M.5
-
3
-
-
84876826470
-
Gene similarity networks provide tools for understanding eukaryote origins and evolution
-
Alvarez-Ponce D., Lopez P., Bapteste E., McInerney J.O. Gene similarity networks provide tools for understanding eukaryote origins and evolution. Proc Natl Acad Sci 2013, 110:E1594-E1603.
-
(2013)
Proc Natl Acad Sci
, vol.110
-
-
Alvarez-Ponce, D.1
Lopez, P.2
Bapteste, E.3
McInerney, J.O.4
-
4
-
-
84861706209
-
Gene-sharing networks reveal organizing principles of transcriptomes in Arabidopsis and other multicellular organisms
-
Li S., Pandey S., Gookin T.E., Zhao Z., Wilson L., Assmann S.M. Gene-sharing networks reveal organizing principles of transcriptomes in Arabidopsis and other multicellular organisms. Plant Cell 2012, 24:1362-1378.
-
(2012)
Plant Cell
, vol.24
, pp. 1362-1378
-
-
Li, S.1
Pandey, S.2
Gookin, T.E.3
Zhao, Z.4
Wilson, L.5
Assmann, S.M.6
-
5
-
-
84873505245
-
Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol
-
Lu F., Lipka A.E., Glaubitz J., Elshire R., Cherney J.H., Casler M.D., Buckler E.S., Costich D.E. Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genet 2013, 9:e1003215.
-
(2013)
PLoS Genet
, vol.9
-
-
Lu, F.1
Lipka, A.E.2
Glaubitz, J.3
Elshire, R.4
Cherney, J.H.5
Casler, M.D.6
Buckler, E.S.7
Costich, D.E.8
-
6
-
-
84880506145
-
The Mycobacterium tuberculosis regulatory network and hypoxia
-
Galagan J.E., Minch K., Peterson M., Lyubetskaya A., Azizi E., Sweet L., Gomes A., Rustad T., Dolganov G., Glotova I., et al. The Mycobacterium tuberculosis regulatory network and hypoxia. Nature 2013, 499:178-183.
-
(2013)
Nature
, vol.499
, pp. 178-183
-
-
Galagan, J.E.1
Minch, K.2
Peterson, M.3
Lyubetskaya, A.4
Azizi, E.5
Sweet, L.6
Gomes, A.7
Rustad, T.8
Dolganov, G.9
Glotova, I.10
-
7
-
-
70349873824
-
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
-
Lieberman-Aiden E., van Berkum N.L., Williams L., Imakaev M., Ragoczy T., Telling A., Amit I., Lajoie B.R., Sabo P.J., Dorschner M.O., et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009, 326:289-293.
-
(2009)
Science
, vol.326
, pp. 289-293
-
-
Lieberman-Aiden, E.1
Van Berkum, N.L.2
Williams, L.3
Imakaev, M.4
Ragoczy, T.5
Telling, A.6
Amit, I.7
Lajoie, B.R.8
Sabo, P.J.9
Dorschner, M.O.10
-
8
-
-
84869054051
-
A travel guide to Cytoscape plugins
-
Saito R., Smoot M.E., Ono K., Ruscheinski J., Wang P.L., Lotia S., Pico A.R., Bader G.D., Ideker T. A travel guide to Cytoscape plugins. Nat Methods 2012, 9:1069-1076.
-
(2012)
Nat Methods
, vol.9
, pp. 1069-1076
-
-
Saito, R.1
Smoot, M.E.2
Ono, K.3
Ruscheinski, J.4
Wang, P.L.5
Lotia, S.6
Pico, A.R.7
Bader, G.D.8
Ideker, T.9
-
9
-
-
0025886455
-
A genetic and physiological analysis of late flowering mutants in Arabidopsis thaliana
-
Koornneef M., Hanhart C.J., van der Veen J.H. A genetic and physiological analysis of late flowering mutants in Arabidopsis thaliana. Mol Gen Genet 1991, 229:57-66.
-
(1991)
Mol Gen Genet
, vol.229
, pp. 57-66
-
-
Koornneef, M.1
Hanhart, C.J.2
van der Veen, J.H.3
-
10
-
-
75649111192
-
The genetic landscape of a cell
-
Costanzo M., Baryshnikova A., Bellay J., Kim Y., Spear E.D., Sevier C.S., Ding H., Koh J.L.Y., Toufighi K., Mostafavi S., et al. The genetic landscape of a cell. Science 2010, 327:425-431.
-
(2010)
Science
, vol.327
, pp. 425-431
-
-
Costanzo, M.1
Baryshnikova, A.2
Bellay, J.3
Kim, Y.4
Spear, E.D.5
Sevier, C.S.6
Ding, H.7
Koh, J.L.Y.8
Toufighi, K.9
Mostafavi, S.10
-
11
-
-
84877854757
-
PLANEX: the plant co-expression database
-
Yim W.C., Yu Y., Song K., Jang C.S., Lee B.-M. PLANEX: the plant co-expression database. BMC Plant Biol 2013, 13:83.
-
(2013)
BMC Plant Biol
, vol.13
, pp. 83
-
-
Yim, W.C.1
Yu, Y.2
Song, K.3
Jang, C.S.4
Lee, B.-M.5
-
12
-
-
80054969308
-
Functional network construction in Arabidopsis using rule-based machine learning on large-scale data sets
-
Bassel G.W., Glaab E., Marquez J., Holdsworth M.J., Bacardit J. Functional network construction in Arabidopsis using rule-based machine learning on large-scale data sets. Plant Cell 2011, 23:3101-3116.
-
(2011)
Plant Cell
, vol.23
, pp. 3101-3116
-
-
Bassel, G.W.1
Glaab, E.2
Marquez, J.3
Holdsworth, M.J.4
Bacardit, J.5
-
13
-
-
79960657553
-
Gene coexpression network analysis as a source of functional annotation for rice genes
-
Childs K.L., Davidson R.M., Buell C.R. Gene coexpression network analysis as a source of functional annotation for rice genes. PLoS ONE 2011, 6:e22196.
-
(2011)
PLoS ONE
, vol.6
-
-
Childs, K.L.1
Davidson, R.M.2
Buell, C.R.3
-
14
-
-
84859336922
-
Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches
-
Fukushima A., Nishizawa T., Hayakumo M., Hikosaka S., Saito K., Goto E., Kusano M. Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches. Plant Physiol 2012, 158:1487-1502.
-
(2012)
Plant Physiol
, vol.158
, pp. 1487-1502
-
-
Fukushima, A.1
Nishizawa, T.2
Hayakumo, M.3
Hikosaka, S.4
Saito, K.5
Goto, E.6
Kusano, M.7
-
15
-
-
84861179768
-
'Guilt by association' is the exception rather than the rule in gene networks
-
Gillis J., Pavlidis P. 'Guilt by association' is the exception rather than the rule in gene networks. PLoS Comput Biol 2012, 8:e1002444.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Gillis, J.1
Pavlidis, P.2
-
16
-
-
84873054720
-
Systematic identification of functional modules and cis-regulatory elements in Arabidopsis thaliana
-
Ruan J., Perez J., Hernandez B., Lei C., Sunter G., Sponsel V.M. Systematic identification of functional modules and cis-regulatory elements in Arabidopsis thaliana. BMC Bioinform 2011, 12(Suppl 12):S2.
-
(2011)
BMC Bioinform
, vol.12
, Issue.SUPPL 12
-
-
Ruan, J.1
Perez, J.2
Hernandez, B.3
Lei, C.4
Sunter, G.5
Sponsel, V.M.6
-
17
-
-
79951767774
-
Large cliques in Arabidopsis gene coexpression network and motif discovery
-
Zheng X., Liu T., Yang Z., Wang J. Large cliques in Arabidopsis gene coexpression network and motif discovery. J Plant Physiol 2011, 168:611-618.
-
(2011)
J Plant Physiol
, vol.168
, pp. 611-618
-
-
Zheng, X.1
Liu, T.2
Yang, Z.3
Wang, J.4
-
18
-
-
77957110013
-
Advantages and limitations of current network inference methods
-
De Smet R., Marchal K. Advantages and limitations of current network inference methods. Nat Rev Microbiol 2010, 8:717-729.
-
(2010)
Nat Rev Microbiol
, vol.8
, pp. 717-729
-
-
De Smet, R.1
Marchal, K.2
-
19
-
-
84870305264
-
Wisdom of crowds for robust gene network inference
-
Marbach D., Costello J.C., Küffner R., Vega N.M., Prill R.J., Camacho D.M., Allison K.R., The DREAM5 Consortium, Kellis M., Collins J.J., et al. Wisdom of crowds for robust gene network inference. Nat Methods 2012, 9:796-804.
-
(2012)
Nat Methods
, vol.9
, pp. 796-804
-
-
Marbach, D.1
Costello, J.C.2
Küffner, R.3
Vega, N.M.4
Prill, R.J.5
Camacho, D.M.6
Allison, K.R.7
The DREAM5 Consortium8
Kellis, M.9
Collins, J.J.10
-
20
-
-
77956848298
-
Identification of transcription factor's targets using tissue-specific transcriptomic data in Arabidopsis thaliana
-
Srivastava G.P., Li P., Liu J., Xu D. Identification of transcription factor's targets using tissue-specific transcriptomic data in Arabidopsis thaliana. BMC Syst Biol 2010, 4(Suppl 2):S2.
-
(2010)
BMC Syst Biol
, vol.4
, Issue.SUPPL 2
-
-
Srivastava, G.P.1
Li, P.2
Liu, J.3
Xu, D.4
-
21
-
-
84876518387
-
Plant protein interactomes
-
Braun P., Aubourg S., Van Leene J., De Jaeger G., Lurin C. Plant protein interactomes. Annu Rev Plant Biol 2013, 64:161-187.
-
(2013)
Annu Rev Plant Biol
, vol.64
, pp. 161-187
-
-
Braun, P.1
Aubourg, S.2
Van Leene, J.3
De Jaeger, G.4
Lurin, C.5
-
22
-
-
77953186504
-
Functional modules in the Arabidopsis core cell cycle binary protein-protein interaction network
-
Boruc J., Van den Daele H., Hollunder J., Rombauts S., Mylle E., Hilson P., Inzé D., De Veylder L., Russinova E. Functional modules in the Arabidopsis core cell cycle binary protein-protein interaction network. Plant Cell 2010, 22:1264-1280.
-
(2010)
Plant Cell
, vol.22
, pp. 1264-1280
-
-
Boruc, J.1
Van Den Daele, H.2
Hollunder, J.3
Rombauts, S.4
Mylle, E.5
Hilson, P.6
Inzé, D.7
De Veylder, L.8
Russinova, E.9
-
23
-
-
79952454507
-
A kaleidoscopic view of the Arabidopsis core cell cycle interactome
-
Van Leene J., Boruc J., De Jaeger G., Russinova E., De Veylder L. A kaleidoscopic view of the Arabidopsis core cell cycle interactome. Trends Plant Sci 2011, 16:141-150.
-
(2011)
Trends Plant Sci
, vol.16
, pp. 141-150
-
-
Van Leene, J.1
Boruc, J.2
De Jaeger, G.3
Russinova, E.4
De Veylder, L.5
-
24
-
-
78651323089
-
PAIR: the predicted Arabidopsis interactome resource
-
Lin M., Shen X., Chen X. PAIR: the predicted Arabidopsis interactome resource. Nucleic Acids Res 2011, 39:D1134-D1140.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Lin, M.1
Shen, X.2
Chen, X.3
-
25
-
-
84857780876
-
Evidence for network evolution in an Arabidopsis interactome map
-
Consortium A.I.M. Evidence for network evolution in an Arabidopsis interactome map. Science 2011, 333:601-607.
-
(2011)
Science
, vol.333
, pp. 601-607
-
-
Consortium, A.I.M.1
-
26
-
-
84875153533
-
Unfoldase-mediated protein translocation through an α-hemolysin nanopore
-
Nivala J., Marks D.B., Akeson M. Unfoldase-mediated protein translocation through an α-hemolysin nanopore. Nat Biotechnol 2013, 31:247-250.
-
(2013)
Nat Biotechnol
, vol.31
, pp. 247-250
-
-
Nivala, J.1
Marks, D.B.2
Akeson, M.3
-
27
-
-
84859224260
-
Metabolic profiling of a mapping population exposes new insights in the regulation of seed metabolism and seed, fruit, and plant relations
-
Toubiana D., Semel Y., Tohge T., Beleggia R., Cattivelli L., Rosental L., Nikoloski Z., Zamir D., Fernie A.R., Fait A. Metabolic profiling of a mapping population exposes new insights in the regulation of seed metabolism and seed, fruit, and plant relations. PLoS Genet 2012, 8:e1002612.
-
(2012)
PLoS Genet
, vol.8
-
-
Toubiana, D.1
Semel, Y.2
Tohge, T.3
Beleggia, R.4
Cattivelli, L.5
Rosental, L.6
Nikoloski, Z.7
Zamir, D.8
Fernie, A.R.9
Fait, A.10
-
28
-
-
84877063533
-
Impact of the carbon and nitrogen supply on relationships and connectivity between metabolism and biomass in a broad panel of Arabidopsis accessions
-
Sulpice R., Nikoloski Z., Tschoep H., Antonio C., Kleessen S., Larhlimi A., Selbig J., Ishihara H., Gibon Y., Fernie A.R., et al. Impact of the carbon and nitrogen supply on relationships and connectivity between metabolism and biomass in a broad panel of Arabidopsis accessions. Plant Physiol 2013, 162:347-363.
-
(2013)
Plant Physiol
, vol.162
, pp. 347-363
-
-
Sulpice, R.1
Nikoloski, Z.2
Tschoep, H.3
Antonio, C.4
Kleessen, S.5
Larhlimi, A.6
Selbig, J.7
Ishihara, H.8
Gibon, Y.9
Fernie, A.R.10
-
29
-
-
84934437712
-
Genome-scale models of plant metabolism
-
Simons M., Misra A., Sriram G. Genome-scale models of plant metabolism. Methods Mol Biol Clifton, NJ 2014, 1083:213-230.
-
(2014)
Methods Mol Biol Clifton, NJ
, vol.1083
, pp. 213-230
-
-
Simons, M.1
Misra, A.2
Sriram, G.3
-
30
-
-
77956696072
-
High-throughput generation, optimization and analysis of genome-scale metabolic models
-
Henry C.S., DeJongh M., Best A.A., Frybarger P.M., Linsay B., Stevens R.L. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol 2010, 28:977-982.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 977-982
-
-
Henry, C.S.1
DeJongh, M.2
Best, A.A.3
Frybarger, P.M.4
Linsay, B.5
Stevens, R.L.6
-
31
-
-
75149129569
-
A protocol for generating a high-quality genome-scale metabolic reconstruction
-
Thiele I., Palsson B.Ø. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 2010, 5:93-121.
-
(2010)
Nat Protoc
, vol.5
, pp. 93-121
-
-
Thiele, I.1
Palsson, B.Ø.2
-
33
-
-
84874971922
-
The challenges of cellular compartmentalization in plant metabolic engineering
-
Heinig U., Gutensohn M., Dudareva N., Aharoni A. The challenges of cellular compartmentalization in plant metabolic engineering. Curr Opin Biotechnol 2013, 24:239-246.
-
(2013)
Curr Opin Biotechnol
, vol.24
, pp. 239-246
-
-
Heinig, U.1
Gutensohn, M.2
Dudareva, N.3
Aharoni, A.4
-
34
-
-
84856015478
-
Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity
-
Mintz-Oron S., Meir S., Malitsky S., Ruppin E., Aharoni A., Shlomi T. Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity. Proc Natl Acad Sci U S A 2012, 109:339-344.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 339-344
-
-
Mintz-Oron, S.1
Meir, S.2
Malitsky, S.3
Ruppin, E.4
Aharoni, A.5
Shlomi, T.6
-
35
-
-
1242264487
-
TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics
-
Yu H., Zhu X., Greenbaum D., Karro J., Gerstein M. TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics. Nucleic Acids Res 2004, 32:328-337.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 328-337
-
-
Yu, H.1
Zhu, X.2
Greenbaum, D.3
Karro, J.4
Gerstein, M.5
-
36
-
-
84875159954
-
Comparative study of RNA-seq- and microarray-derived coexpression networks in Arabidopsis thaliana
-
Giorgi F.M., Del Fabbro C., Licausi F. Comparative study of RNA-seq- and microarray-derived coexpression networks in Arabidopsis thaliana. Bioinforma Oxf Engl 2013, 29:717-724.
-
(2013)
Bioinforma Oxf Engl
, vol.29
, pp. 717-724
-
-
Giorgi, F.M.1
Del Fabbro, C.2
Licausi, F.3
-
37
-
-
78649703966
-
Rewiring of genetic networks in response to DNA damage
-
Bandyopadhyay S., Mehta M., Kuo D., Sung M.K., Chuang R., Jaehnig E.J., Bodenmiller B., Licon K., Copeland W., Shales M., et al. Rewiring of genetic networks in response to DNA damage. Science 2010, 330:1385-1389.
-
(2010)
Science
, vol.330
, pp. 1385-1389
-
-
Bandyopadhyay, S.1
Mehta, M.2
Kuo, D.3
Sung, M.K.4
Chuang, R.5
Jaehnig, E.J.6
Bodenmiller, B.7
Licon, K.8
Copeland, W.9
Shales, M.10
-
38
-
-
79952659846
-
Boosting signal-to-noise in complex biology: prior knowledge is power
-
Ideker T., Dutkowski J., Hood L. Boosting signal-to-noise in complex biology: prior knowledge is power. Cell 2011, 144:860-863.
-
(2011)
Cell
, vol.144
, pp. 860-863
-
-
Ideker, T.1
Dutkowski, J.2
Hood, L.3
-
39
-
-
84878438199
-
Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study
-
Feltus F.A., Ficklin S.P., Gibson S.M., Smith M.C. Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study. BMC Syst Biol 2013, 7:44.
-
(2013)
BMC Syst Biol
, vol.7
, pp. 44
-
-
Feltus, F.A.1
Ficklin, S.P.2
Gibson, S.M.3
Smith, M.C.4
-
40
-
-
84880273715
-
Biosynthesis of antinutritional alkaloids in solanaceous crops is mediated by clustered genes
-
Itkin M., Heinig U., Tzfadia O., Bhide A.J., Shinde B., Cardenas P.D., Bocobza S.E., Unger T., Malitsky S., Finkers R., et al. Biosynthesis of antinutritional alkaloids in solanaceous crops is mediated by clustered genes. Science 2013, 341:175-179.
-
(2013)
Science
, vol.341
, pp. 175-179
-
-
Itkin, M.1
Heinig, U.2
Tzfadia, O.3
Bhide, A.J.4
Shinde, B.5
Cardenas, P.D.6
Bocobza, S.E.7
Unger, T.8
Malitsky, S.9
Finkers, R.10
-
41
-
-
84881086101
-
Systems approaches map regulatory networks downstream of the auxin receptor AFB3 in the nitrate response of Arabidopsis thaliana roots
-
Vidal E.A., Moyano T.C., Riveras E., Contreras-López O., Gutiérrez R.A. Systems approaches map regulatory networks downstream of the auxin receptor AFB3 in the nitrate response of Arabidopsis thaliana roots. Proc Natl Acad Sci U S A 2013, 110:12840-12845.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. 12840-12845
-
-
Vidal, E.A.1
Moyano, T.C.2
Riveras, E.3
Contreras-López, O.4
Gutiérrez, R.A.5
-
42
-
-
79957754723
-
Coordinated gene networks regulating Arabidopsis plant metabolism in response to various stresses and nutritional cues
-
Less H., Angelovici R., Tzin V., Galili G. Coordinated gene networks regulating Arabidopsis plant metabolism in response to various stresses and nutritional cues. Plant Cell 2011, 23:1264-1271.
-
(2011)
Plant Cell
, vol.23
, pp. 1264-1271
-
-
Less, H.1
Angelovici, R.2
Tzin, V.3
Galili, G.4
-
43
-
-
44149121700
-
Extracting expression modules from perturbational gene expression compendia
-
Maere S., Dijck P.V., Kuiper M. Extracting expression modules from perturbational gene expression compendia. BMC Syst Biol 2008, 2:33.
-
(2008)
BMC Syst Biol
, vol.2
, pp. 33
-
-
Maere, S.1
Dijck, P.V.2
Kuiper, M.3
-
44
-
-
38549123986
-
AtPID: Arabidopsis thaliana protein interactome database - an integrative platform for plant systems biology
-
Cui J., Li P., Li G., Xu F., Zhao C., Li Y., Yang Z., Wang G., Yu Q., Li Y., et al. AtPID: Arabidopsis thaliana protein interactome database - an integrative platform for plant systems biology. Nucleic Acids Res 2008, 36:D999-D1008.
-
(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
Li, Y.10
-
45
-
-
79551644334
-
Integrative identification of Arabidopsis mitochondrial proteome and its function exploitation through protein interaction network
-
Cui J., Liu J., Li Y., Shi T. Integrative identification of Arabidopsis mitochondrial proteome and its function exploitation through protein interaction network. PLoS ONE 2011, 6:e16022.
-
(2011)
PLoS ONE
, vol.6
-
-
Cui, J.1
Liu, J.2
Li, Y.3
Shi, T.4
-
46
-
-
76349125292
-
Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana
-
Lee I., Ambaru B., Thakkar P., Marcotte E.M., Rhee S.Y. Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat Biotechnol 2010, 28:149-156.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 149-156
-
-
Lee, I.1
Ambaru, B.2
Thakkar, P.3
Marcotte, E.M.4
Rhee, S.Y.5
-
47
-
-
84879984347
-
Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato
-
Koenig D., Jimenez-Gomez J.M., Kimura S., Fulop D., Chitwood D.H., Headland L.R., Kumar R., Covington M.F., Devisetty U.K., Tat A.V., et al. Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proc Natl Acad Sci U S A 2013, 110:E2655-E2662.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
-
-
Koenig, D.1
Jimenez-Gomez, J.M.2
Kimura, S.3
Fulop, D.4
Chitwood, D.H.5
Headland, L.R.6
Kumar, R.7
Covington, M.F.8
Devisetty, U.K.9
Tat, A.V.10
-
48
-
-
79959970191
-
Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in arabidopsis and rice
-
Movahedi S., Peer Y.V., de Vandepoele K. Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in arabidopsis and rice. Plant Physiol 2011, 156:1316-1330.
-
(2011)
Plant Physiol
, vol.156
, pp. 1316-1330
-
-
Movahedi, S.1
Peer, Y.V.2
de Vandepoele, K.3
-
49
-
-
79551521494
-
Measuring the evolutionary rewiring of biological networks
-
Shou C., Bhardwaj N., Lam H.Y.K., Yan K.-K., Kim P.M., Snyder M., Gerstein M.B. Measuring the evolutionary rewiring of biological networks. PLoS Comput Biol 2011, 7:e1001050.
-
(2011)
PLoS Comput Biol
, vol.7
-
-
Shou, C.1
Bhardwaj, N.2
Lam, H.Y.K.3
Yan, K.-K.4
Kim, P.M.5
Snyder, M.6
Gerstein, M.B.7
-
50
-
-
84859896621
-
Towards understanding how molecular networks evolve in plants
-
Chae L., Lee I., Shin J., Rhee S.Y. Towards understanding how molecular networks evolve in plants. Curr Opin Plant Biol 2012, 15:177-184.
-
(2012)
Curr Opin Plant Biol
, vol.15
, pp. 177-184
-
-
Chae, L.1
Lee, I.2
Shin, J.3
Rhee, S.Y.4
-
51
-
-
84859890901
-
Redundancy and rewiring of genetic networks following genome-wide duplication events
-
De Smet R., Van de Peer Y. Redundancy and rewiring of genetic networks following genome-wide duplication events. Curr Opin Plant Biol 2012, 15:168-176.
-
(2012)
Curr Opin Plant Biol
, vol.15
, pp. 168-176
-
-
De Smet, R.1
Van de Peer, Y.2
-
52
-
-
33847134760
-
Identification of QTLs controlling gene expression networks defined a priori
-
Kliebenstein D.J., West M.A., Leeuwen H., van Loudet O., Doerge R.W., Clair D.A.S. Identification of QTLs controlling gene expression networks defined a priori. BMC Bioinform 2006, 7:1-17.
-
(2006)
BMC Bioinform
, vol.7
, pp. 1-17
-
-
Kliebenstein, D.J.1
West, M.A.2
Leeuwen, H.3
van Loudet, O.4
Doerge, R.W.5
Clair, D.A.S.6
-
53
-
-
33846818896
-
Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci
-
Keurentjes J.J.B., Fu J., Terpstra I.R., Garcia J.M., van den Ackerveken G., Snoek L.B., Peeters A.J.M., Vreugdenhil D., Koornneef M., Jansen R.C. Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. Proc Natl Acad Sci U S A 2007, 104:1708-1713.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 1708-1713
-
-
Keurentjes, J.J.B.1
Fu, J.2
Terpstra, I.R.3
Garcia, J.M.4
Van Den Ackerveken, G.5
Snoek, L.B.6
Peeters, A.J.M.7
Vreugdenhil, D.8
Koornneef, M.9
Jansen, R.C.10
-
54
-
-
77649242421
-
Evidence for widespread adaptive evolution of gene expression in budding yeast
-
Fraser H.B., Moses A.M., Schadt E.E. Evidence for widespread adaptive evolution of gene expression in budding yeast. Proc Natl Acad Sci 2010, 10.1073/pnas.0912245107.
-
(2010)
Proc Natl Acad Sci
-
-
Fraser, H.B.1
Moses, A.M.2
Schadt, E.E.3
-
55
-
-
84862908459
-
Rate of meristem maturation determines inflorescence architecture in tomato
-
Park S.J., Jiang K., Schatz M.C., Lippman Z.B. Rate of meristem maturation determines inflorescence architecture in tomato. Proc Natl Acad Sci U S A 2012, 109:639-644.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 639-644
-
-
Park, S.J.1
Jiang, K.2
Schatz, M.C.3
Lippman, Z.B.4
-
56
-
-
80052338881
-
Combining genome-wide association mapping and transcriptional networks to identify novel genes controlling glucosinolates in Arabidopsis thaliana
-
Chan E.K.F., Rowe H.C., Corwin J.A., Joseph B., Kliebenstein D.J. Combining genome-wide association mapping and transcriptional networks to identify novel genes controlling glucosinolates in Arabidopsis thaliana. PLoS Biol 2011, 9:e1001125.
-
(2011)
PLoS Biol
, vol.9
-
-
Chan, E.K.F.1
Rowe, H.C.2
Corwin, J.A.3
Joseph, B.4
Kliebenstein, D.J.5
-
57
-
-
77952367484
-
Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus
-
Drost D.R., Benedict C.I., Berg A., Novaes E., Novaes C.R.D.B., Yu Q., Dervinis C., Maia J.M., Yap J., Miles B., et al. Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus. Proc Natl Acad Sci 2010, 107:8492-8497.
-
(2010)
Proc Natl Acad Sci
, vol.107
, pp. 8492-8497
-
-
Drost, D.R.1
Benedict, C.I.2
Berg, A.3
Novaes, E.4
Novaes, C.R.D.B.5
Yu, Q.6
Dervinis, C.7
Maia, J.M.8
Yap, J.9
Miles, B.10
-
58
-
-
78049415019
-
Network analysis identifies ELF3 as a QTL for the shade avoidance response in Arabidopsis
-
Jiménez-Gómez J.M., Wallace A.D., Maloof J.N. Network analysis identifies ELF3 as a QTL for the shade avoidance response in Arabidopsis. PLoS Genet 2010, 6:e1001100.
-
(2010)
PLoS Genet
, vol.6
-
-
Jiménez-Gómez, J.M.1
Wallace, A.D.2
Maloof, J.N.3
-
59
-
-
45149106353
-
Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks
-
Zhu J., Zhang B., Smith E.N., Drees B., Brem R.B., Kruglyak L., Bumgarner R.E., Schadt E.E. Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet 2008, 40:854-861.
-
(2008)
Nat Genet
, vol.40
, pp. 854-861
-
-
Zhu, J.1
Zhang, B.2
Smith, E.N.3
Drees, B.4
Brem, R.B.5
Kruglyak, L.6
Bumgarner, R.E.7
Schadt, E.E.8
-
60
-
-
84859959092
-
Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation
-
Zhu J., Sova P., Xu Q., Dombek K.M., Xu E.Y., Vu H., Tu Z., Brem R.B., Bumgarner R.E., Schadt E.E. Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation. PLoS Biol 2012, 10:e1001301.
-
(2012)
PLoS Biol
, vol.10
-
-
Zhu, J.1
Sova, P.2
Xu, Q.3
Dombek, K.M.4
Xu, E.Y.5
Vu, H.6
Tu, Z.7
Brem, R.B.8
Bumgarner, R.E.9
Schadt, E.E.10
-
61
-
-
79955583542
-
Mapping and analysis of chromatin state dynamics in nine human cell types
-
Ernst J., Kheradpour P., Mikkelsen T.S., Shoresh N., Ward L.D., Epstein C.B., Zhang X., Wang L., Issner R., Coyne M., et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 2011, 473:43-49.
-
(2011)
Nature
, vol.473
, pp. 43-49
-
-
Ernst, J.1
Kheradpour, P.2
Mikkelsen, T.S.3
Shoresh, N.4
Ward, L.D.5
Epstein, C.B.6
Zhang, X.7
Wang, L.8
Issner, R.9
Coyne, M.10
-
62
-
-
84865822182
-
Systematic localization of common disease-associated variation in regulatory DNA
-
Maurano M.T., Humbert R., Rynes E., Thurman R.E., Haugen E., Wang H., Reynolds A.P., Sandstrom R., Qu H., Brody J., et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 2012, 337:1190-1195.
-
(2012)
Science
, vol.337
, pp. 1190-1195
-
-
Maurano, M.T.1
Humbert, R.2
Rynes, E.3
Thurman, R.E.4
Haugen, E.5
Wang, H.6
Reynolds, A.P.7
Sandstrom, R.8
Qu, H.9
Brody, J.10
-
63
-
-
81055141350
-
Epigenome characterization at single base-pair resolution
-
Henikoff J.G., Belsky J.A., Krassovsky K., MacAlpine D.M., Henikoff S. Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci 2011, 10.1073/pnas.1110731108.
-
(2011)
Proc Natl Acad Sci
-
-
Henikoff, J.G.1
Belsky, J.A.2
Krassovsky, K.3
MacAlpine, D.M.4
Henikoff, S.5
-
64
-
-
63849308888
-
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
-
Hesselberth J.R., Chen X., Zhang Z., Sabo P.J., Sandstrom R., Reynolds A.P., Thurman R.E., Neph S., Kuehn M.S., Noble W.S., et al. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods 2009, 6:283-289.
-
(2009)
Nat Methods
, vol.6
, pp. 283-289
-
-
Hesselberth, J.R.1
Chen, X.2
Zhang, Z.3
Sabo, P.J.4
Sandstrom, R.5
Reynolds, A.P.6
Thurman, R.E.7
Neph, S.8
Kuehn, M.S.9
Noble, W.S.10
-
65
-
-
84896039897
-
-
Pacific Biosciences. The New Biology. This documentary gathers interviews with the leading scientists in the field of genomics and fantastic examples of how network analyses can help modern society. A must watch.
-
Pacific Biosciences. The New Biology. 2011. This documentary gathers interviews with the leading scientists in the field of genomics and fantastic examples of how network analyses can help modern society. A must watch. http://www.youtube.com/watch%3Fv=sjTQD6E3lH4%26feature=youtu.be.
-
(2011)
-
-
-
66
-
-
79955130092
-
Using graph theory to analyze biological networks
-
Pavlopoulos G.A., Secrier M., Moschopoulos C.N., Soldatos T.G., Kossida S., Aerts J., Schneider R., Bagos P.G. Using graph theory to analyze biological networks. BioData Min 2011, 4:10.
-
(2011)
BioData Min
, vol.4
, pp. 10
-
-
Pavlopoulos, G.A.1
Secrier, M.2
Moschopoulos, C.N.3
Soldatos, T.G.4
Kossida, S.5
Aerts, J.6
Schneider, R.7
Bagos, P.G.8
-
67
-
-
0038483826
-
Emergence of scaling in random networks
-
Barabási A.-L., Albert R. Emergence of scaling in random networks. Science 1999, 286:509-512.
-
(1999)
Science
, vol.286
, pp. 509-512
-
-
Barabási, A.-L.1
Albert, R.2
-
68
-
-
84862588489
-
Gene duplications contribute to the overrepresentation of interactions between proteins of a similar age
-
Fokkens L., Hogeweg P., Snel B. Gene duplications contribute to the overrepresentation of interactions between proteins of a similar age. BMC Evol Biol 2012, 12:99.
-
(2012)
BMC Evol Biol
, vol.12
, pp. 99
-
-
Fokkens, L.1
Hogeweg, P.2
Snel, B.3
-
69
-
-
0032482432
-
Collective dynamics of "small-world" networks
-
Watts D.J., Strogatz S.H. Collective dynamics of "small-world" networks. Nature 1998, 393:440-442.
-
(1998)
Nature
, vol.393
, pp. 440-442
-
-
Watts, D.J.1
Strogatz, S.H.2
-
70
-
-
50949092459
-
Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality
-
Zotenko E., Mestre J., O'Leary D.P., Przytycka T.M. Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLoS Comput Biol 2008, 4:e1000140.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Zotenko, E.1
Mestre, J.2
O'Leary, D.P.3
Przytycka, T.M.4
-
71
-
-
78650486587
-
Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana
-
Hanada K., Sawada Y., Kuromori T., Klausnitzer R., Saito K., Toyoda T., Shinozaki K., Li W.-H., Hirai M.Y. Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana. Mol Biol Evol 2011, 28:377-382.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 377-382
-
-
Hanada, K.1
Sawada, Y.2
Kuromori, T.3
Klausnitzer, R.4
Saito, K.5
Toyoda, T.6
Shinozaki, K.7
Li, W.-H.8
Hirai, M.Y.9
-
72
-
-
84865571240
-
Network context and selection in the evolution to enzyme specificity
-
Nam H., Lewis N.E., Lerman J.A., Lee D.-H., Chang R.L., Kim D., Palsson B.O. Network context and selection in the evolution to enzyme specificity. Science 2012, 337:1101-1104.
-
(2012)
Science
, vol.337
, pp. 1101-1104
-
-
Nam, H.1
Lewis, N.E.2
Lerman, J.A.3
Lee, D.-H.4
Chang, R.L.5
Kim, D.6
Palsson, B.O.7
-
73
-
-
84865600428
-
Systems biology beyond degree, hubs and scale-free networks: the case for multiple metrics in complex networks
-
Roy S. Systems biology beyond degree, hubs and scale-free networks: the case for multiple metrics in complex networks. Syst Synth Biol 2012, 6:31-34.
-
(2012)
Syst Synth Biol
, vol.6
, pp. 31-34
-
-
Roy, S.1
-
74
-
-
84876009220
-
Interpretation of genomic variants using a unified biological network approach
-
Khurana E., Fu Y., Chen J., Gerstein M. Interpretation of genomic variants using a unified biological network approach. PLoS Comput Biol 2013, 9:e1002886.
-
(2013)
PLoS Comput Biol
, vol.9
-
-
Khurana, E.1
Fu, Y.2
Chen, J.3
Gerstein, M.4
|