-
1
-
-
66349129975
-
Toward a gold standard for promoter prediction evaluation
-
Abeel, T., Van de Peer, Y., and Saeys, Y. (2009). Toward a gold standard for promoter prediction evaluation. Bioinformatics 25: i313-i320.
-
(2009)
Bioinformatics
, vol.25
-
-
Abeel, T.1
Van de Peer, Y.2
Saeys, Y.3
-
2
-
-
37849020261
-
Network inference, analysis, and modeling in systems biology
-
Albert, R. (2007). Network inference, analysis, and modeling in systems biology. Plant Cell 19: 3327-3338.
-
(2007)
Plant Cell
, vol.19
, pp. 3327-3338
-
-
Albert, R.1
-
4
-
-
0042768158
-
Genome-wide insertional mutagenesis of Arabidopsis thaliana
-
Alonso, J.M., et al. (2003). Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301: 653-657.
-
(2003)
Science
, vol.301
, pp. 653-657
-
-
Alonso, J.M.1
-
5
-
-
84875994305
-
Dissection of regulatory networks that are altered in disease via differential co-expression
-
Amar, D., Safer, H., and Shamir, R. (2013). Dissection of regulatory networks that are altered in disease via differential co-expression. PLOS Comput. Biol. 9: e1002955.
-
(2013)
PLOS Comput. Biol.
, vol.9
-
-
Amar, D.1
Safer, H.2
Shamir, R.3
-
6
-
-
50349090461
-
Convergent energy and stress signaling
-
Baena-González, E., and Sheen, J. (2008). Convergent energy and stress signaling. Trends Plant Sci. 13: 474-482.
-
(2008)
Trends Plant Sci.
, vol.13
, pp. 474-482
-
-
Baena-González, E.1
Sheen, J.2
-
7
-
-
78649703966
-
Rewiring of genetic networks in response to DNA damage
-
Bandyopadhyay, S., et al. (2010). Rewiring of genetic networks in response to DNA damage. Science 330: 1385-1389.
-
(2010)
Science
, vol.330
, pp. 1385-1389
-
-
Bandyopadhyay, S.1
-
8
-
-
33847055114
-
How to infer gene networks from expression profiles
-
Bansal, M., Belcastro, V., Ambesi-Impiombato, A., and di Bernardo, D. (2007). How to infer gene networks from expression profiles. Mol. Syst. Biol. 3: 78.
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 78
-
-
Bansal, M.1
Belcastro, V.2
Ambesi-Impiombato, A.3
di Bernardo, D.4
-
9
-
-
0742305866
-
Network biology: Understanding the cell's functional organization
-
Barabási, A.L., and Oltvai, Z.N. (2004). Network biology: Understanding the cell's functional organization. Nat. Rev. Genet. 5: 101-113.
-
(2004)
Nat. Rev. Genet.
, vol.5
, pp. 101-113
-
-
Barabási, A.L.1
Oltvai, Z.N.2
-
10
-
-
84870724279
-
Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks
-
Bassel, G.W., Gaudinier, A., Brady, S.M., Hennig, L., Rhee, S.Y., and De Smet, I. (2012). Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. Plant Cell 24: 3859-3875.
-
(2012)
Plant Cell
, vol.24
, pp. 3859-3875
-
-
Bassel, G.W.1
Gaudinier, A.2
Brady, S.M.3
Hennig, L.4
Rhee, S.Y.5
De Smet, I.6
-
11
-
-
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., and Bacardit, J. (2011). Functional network construction in Arabidopsis using rule-based machine learning on large-scale data sets. Plant Cell 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
-
12
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57: 289-300.
-
(1995)
J. R. Stat. Soc. B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
13
-
-
35148833196
-
Some unique properties of eigenvector centrality
-
Bonacich, P. (2007). Some unique properties of eigenvector centrality. Soc. Networks 29: 555-564.
-
(2007)
Soc. Networks
, vol.29
, pp. 555-564
-
-
Bonacich, P.1
-
14
-
-
69249085408
-
Stability and aggregation of ranked gene lists
-
Boulesteix, A.L., and Slawski, M. (2009). Stability and aggregation of ranked gene lists. Brief. Bioinform. 10: 556-568.
-
(2009)
Brief. Bioinform.
, vol.10
, pp. 556-568
-
-
Boulesteix, A.L.1
Slawski, M.2
-
15
-
-
0035478854
-
Random forests
-
Breiman, L. (2001). Random forests. Mach. Learn. 45: 5-32.
-
(2001)
Mach. Learn.
, vol.45
, pp. 5-32
-
-
Breiman, L.1
-
16
-
-
84949130891
-
Rewiring makes the difference
-
Califano, A. (2011). Rewiring makes the difference. Mol. Syst. Biol. 7: 463.
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 463
-
-
Califano, A.1
-
17
-
-
34247218627
-
Modulation of ethylene responses affects plant salt-stress responses
-
Cao, W.H., Liu, J., He, X.J., Mu, R.L., Zhou, H.L., Chen, S.Y., and Zhang, J.S. (2007). Modulation of ethylene responses affects plant salt-stress responses. Plant Physiol. 143: 707-719.
-
(2007)
Plant Physiol.
, vol.143
, pp. 707-719
-
-
Cao, W.H.1
Liu, J.2
He, X.J.3
Mu, R.L.4
Zhou, H.L.5
Chen, S.Y.6
Zhang, J.S.7
-
18
-
-
5044245707
-
Gene co-expression network topology provides a framework for molecular characterization of cellular state
-
Carter, S.L., Brechbühler, C.M., Griffin, M., and Bond, A.T. (2004). Gene co-expression network topology provides a framework for molecular characterization of cellular state. Bioinformatics 20: 2242-2250.
-
(2004)
Bioinformatics
, vol.20
, pp. 2242-2250
-
-
Carter, S.L.1
Brechbühler, C.M.2
Griffin, M.3
Bond, A.T.4
-
19
-
-
28944444652
-
Differential coexpression analysis using microarray data and its application to human cancer
-
Choi, J.K., Yu, U., Yoo, O.J., and Kim, S. (2005). Differential coexpression analysis using microarray data and its application to human cancer. Bioinformatics 21: 4348-4355.
-
(2005)
Bioinformatics
, vol.21
, pp. 4348-4355
-
-
Choi, J.K.1
Yu, U.2
Yoo, O.J.3
Kim, S.4
-
20
-
-
0037276175
-
Statistical tests for differential expression in cDNA microarray experiments
-
Cui, X., and Churchill, G.A. (2003). Statistical tests for differential expression in cDNA microarray experiments. Genome Biol. 4: 210.
-
(2003)
Genome Biol.
, vol.4
, pp. 210
-
-
Cui, X.1
Churchill, G.A.2
-
21
-
-
77953913791
-
From 'differential expression' to 'differential networking'-Identification of dysfunctional regulatory networks in diseases
-
de la Fuente, A. (2010). From 'differential expression' to 'differential networking'-Identification of dysfunctional regulatory networks in diseases. Trends Genet. 26: 326-333.
-
(2010)
Trends Genet.
, vol.26
, pp. 326-333
-
-
de la Fuente, A.1
-
22
-
-
77957110013
-
Advantages and limitations of current network inference methods
-
De Smet, R., and Marchal, K. (2010). Advantages and limitations of current network inference methods. Nat. Rev. Microbiol. 8: 717-729.
-
(2010)
Nat. Rev. Microbiol.
, vol.8
, pp. 717-729
-
-
De Smet, R.1
Marchal, K.2
-
23
-
-
30644464444
-
Gene selection and classification of microarray data using random forest
-
Díaz-Uriarte, R., and Alvarez de Andrés, S. (2006). Gene selection and classification of microarray data using random forest. BMC Bioinformatics 7: 3.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 3
-
-
Díaz-Uriarte, R.1
Alvarez de Andrés, S.2
-
24
-
-
34548550573
-
Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process
-
Elo, L.L., Järvenpää, H., Oresic, M., Lahesmaa, R., and Aittokallio, T. (2007). Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process. Bioinformatics 23: 2096-2103.
-
(2007)
Bioinformatics
, vol.23
, pp. 2096-2103
-
-
Elo, L.L.1
Järvenpää, H.2
Oresic, M.3
Lahesmaa, R.4
Aittokallio, T.5
-
25
-
-
79954414422
-
Arabidopsis paves the way: Genomic and network analyses in crops
-
Ferrier, T., Matus, J.T., Jin, J., and Riechmann, J.L. (2011). Arabidopsis paves the way: Genomic and network analyses in crops. Curr. Opin. Biotechnol. 22: 260-270.
-
(2011)
Curr. Opin. Biotechnol.
, vol.22
, pp. 260-270
-
-
Ferrier, T.1
Matus, J.T.2
Jin, J.3
Riechmann, J.L.4
-
26
-
-
33750177351
-
Centrality in social networks: Concept clarification
-
Freeman, L.C. (1978). Centrality in social networks: Concept clarification. Soc. Networks 1: 215-239.
-
(1978)
Soc. Networks
, vol.1
, pp. 215-239
-
-
Freeman, L.C.1
-
27
-
-
84883162998
-
Reverse engineering: A key component of systems biology to unravel global abiotic stress cross-talk
-
Friedel, S., Usadel, B., von Wirén, N., and Sreenivasulu, N. (2012). Reverse engineering: A key component of systems biology to unravel global abiotic stress cross-talk. Front. Plant Sci. 3: 294.
-
(2012)
Front. Plant Sci.
, vol.3
, pp. 294
-
-
Friedel, S.1
Usadel, B.2
von Wirén, N.3
Sreenivasulu, N.4
-
28
-
-
33745210764
-
Crosstalk between abiotic and biotic stress responses: A current view from the points of convergence in the stress signaling networks
-
Fujita, M., Fujita, Y., Noutoshi, Y., Takahashi, F., Narusaka, Y., Yamaguchi-Shinozaki, K., and Shinozaki, K. (2006). Crosstalk between abiotic and biotic stress responses: A current view from the points of convergence in the stress signaling networks. Curr. Opin. Plant Biol. 9: 436-442.
-
(2006)
Curr. Opin. Plant Biol.
, vol.9
, pp. 436-442
-
-
Fujita, M.1
Fujita, Y.2
Noutoshi, Y.3
Takahashi, F.4
Narusaka, Y.5
Yamaguchi-Shinozaki, K.6
Shinozaki, K.7
-
29
-
-
34548442971
-
Weighted gene coexpression network analysis strategies applied to mouse weight
-
Fuller, T.F., Ghazalpour, A., Aten, J.E., Drake, T.A., Lusis, A.J., and Horvath, S. (2007). Weighted gene coexpression network analysis strategies applied to mouse weight. Mamm. Genome 18: 463-472.
-
(2007)
Mamm. Genome
, vol.18
, pp. 463-472
-
-
Fuller, T.F.1
Ghazalpour, A.2
Aten, J.E.3
Drake, T.A.4
Lusis, A.J.5
Horvath, S.6
-
30
-
-
77950544798
-
A statistical framework for differential network analysis from microarray data
-
Gill, R., Datta, S., and Datta, S. (2010). A statistical framework for differential network analysis from microarray data. BMC Bioinformatics 11: 95.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 95
-
-
Gill, R.1
Datta, S.2
Datta, S.3
-
31
-
-
47249163800
-
Functional meta-analysis of double connectivity in gene coexpression networks in mammals
-
Gustin, M.P., Paultre, C.Z., Randon, J., Bricca, G., and Cerutti, C. (2008). Functional meta-analysis of double connectivity in gene coexpression networks in mammals. Physiol. Genomics 34: 34-41.
-
(2008)
Physiol. Genomics
, vol.34
, pp. 34-41
-
-
Gustin, M.P.1
Paultre, C.Z.2
Randon, J.3
Bricca, G.4
Cerutti, C.5
-
32
-
-
0007265820
-
Eccentricity and centrality in networks
-
Hage, P., and Harary, F. (1995). Eccentricity and centrality in networks. Soc. Networks 17: 57-63.
-
(1995)
Soc. Networks
, vol.17
, pp. 57-63
-
-
Hage, P.1
Harary, F.2
-
33
-
-
34547131280
-
A robust measure of correlation between two genes on a microarray
-
Hardin, J., Mitani, A., Hicks, L., and VanKoten, B. (2007). A robust measure of correlation between two genes on a microarray. BMC Bioinformatics 8: 220.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 220
-
-
Hardin, J.1
Mitani, A.2
Hicks, L.3
VanKoten, B.4
-
34
-
-
32344446535
-
AtNAC2, a transcription factor downstream of ethylene and auxin signaling pathways, is involved in salt stress response and lateral root development
-
He, X.J., Mu, R.L., Cao, W.H., Zhang, Z.G., Zhang, J.S., and Chen, S.Y. (2005). AtNAC2, a transcription factor downstream of ethylene and auxin signaling pathways, is involved in salt stress response and lateral root development. Plant J. 44: 903-916.
-
(2005)
Plant J.
, vol.44
, pp. 903-916
-
-
He, X.J.1
Mu, R.L.2
Cao, W.H.3
Zhang, Z.G.4
Zhang, J.S.5
Chen, S.Y.6
-
35
-
-
50949084896
-
Geometric interpretation of gene coexpression network analysis
-
Horvath, S., and Dong, J. (2008). Geometric interpretation of gene coexpression network analysis. PLOS Comput. Biol. 4: e1000117.
-
(2008)
PLOS Comput. Biol.
, vol.4
-
-
Horvath, S.1
Dong, J.2
-
36
-
-
84864374040
-
Beyond differential expression: The quest for causal mutations and effector molecules
-
Hudson, N.J., Dalrymple, B.P., and Reverter, A. (2012). Beyond differential expression: The quest for causal mutations and effector molecules. BMC Genomics 13: 356.
-
(2012)
BMC Genomics
, vol.13
, pp. 356
-
-
Hudson, N.J.1
Dalrymple, B.P.2
Reverter, A.3
-
37
-
-
67049159812
-
A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation
-
Hudson, N.J., Reverter, A., and Dalrymple, B.P. (2009). A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation. PLOS Comput. Biol. 5: e1000382.
-
(2009)
PLOS Comput. Biol.
, vol.5
-
-
Hudson, N.J.1
Reverter, A.2
Dalrymple, B.P.3
-
38
-
-
80052394788
-
Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network
-
Hwang, S., Rhee, S.Y., Marcotte, E.M., and Lee, I. (2011). Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network. Nat. Protoc. 6: 1429-1442.
-
(2011)
Nat. Protoc.
, vol.6
, pp. 1429-1442
-
-
Hwang, S.1
Rhee, S.Y.2
Marcotte, E.M.3
Lee, I.4
-
39
-
-
84863509940
-
Utilizing RNA-Seq data for de novo coexpression network inference
-
Iancu, O.D., Kawane, S., Bottomly, D., Searles, R., Hitzemann, R., and McWeeney, S. (2012). Utilizing RNA-Seq data for de novo coexpression network inference. Bioinformatics 28: 1592-1597.
-
(2012)
Bioinformatics
, vol.28
, pp. 1592-1597
-
-
Iancu, O.D.1
Kawane, S.2
Bottomly, D.3
Searles, R.4
Hitzemann, R.5
McWeeney, S.6
-
40
-
-
84856094560
-
Differential network biology
-
Ideker, T., and Krogan, N.J. (2012). Differential network biology. Mol. Syst. Biol. 8: 565.
-
(2012)
Mol. Syst. Biol.
, vol.8
, pp. 565
-
-
Ideker, T.1
Krogan, N.J.2
-
41
-
-
0036840274
-
Salt-stressinduced ABA accumulation is more sensitively triggered in roots than in shoots
-
Jia, W., Wang, Y., Zhang, S., and Zhang, J. (2002). Salt-stressinduced ABA accumulation is more sensitively triggered in roots than in shoots. J. Exp. Bot. 53: 2201-2206.
-
(2002)
J. Exp. Bot.
, vol.53
, pp. 2201-2206
-
-
Jia, W.1
Wang, Y.2
Zhang, S.3
Zhang, J.4
-
42
-
-
34547596338
-
MiPred: Classification of real and pseudo microRNA precursors using random forest prediction model with combined features
-
Jiang, P., Wu, H., Wang, W., Ma, W., Sun, X., and Lu, Z. (2007). MiPred: Classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res. 35: W339-W344.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Jiang, P.1
Wu, H.2
Wang, W.3
Ma, W.4
Sun, X.5
Lu, Z.6
-
43
-
-
33750367871
-
Comprehensive transcriptional profiling of NaCl-stressed Arabidopsis roots reveals novel classes of responsive genes
-
Jiang, Y., and Deyholos, M.K. (2006). Comprehensive transcriptional profiling of NaCl-stressed Arabidopsis roots reveals novel classes of responsive genes. BMC Plant Biol. 6: 25.
-
(2006)
BMC Plant Biol.
, vol.6
, pp. 25
-
-
Jiang, Y.1
Deyholos, M.K.2
-
44
-
-
84855183279
-
Dragon PolyA Spotter: Predictor of poly(A) motifs within human genomic DNA sequences
-
Kalkatawi, M., Rangkuti, F., Schramm, M., Jankovic, B.R., Kamau, A., Chowdhary, R., Archer, J.A., and Bajic, V.B. (2012). Dragon PolyA Spotter: Predictor of poly(A) motifs within human genomic DNA sequences. Bioinformatics 28: 127-129.
-
(2012)
Bioinformatics
, vol.28
, pp. 127-129
-
-
Kalkatawi, M.1
Rangkuti, F.2
Schramm, M.3
Jankovic, B.R.4
Kamau, A.5
Chowdhary, R.6
Archer, J.A.7
Bajic, V.B.8
-
45
-
-
34247200577
-
The AtGenExpress global stress expression data set: Protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses
-
Kilian, J., Whitehead, D., Horak, J., Wanke, D., Weinl, S., Batistic, O., D'Angelo, C., Bornberg-Bauer, E., Kudla, J., and Harter, K. (2007). The AtGenExpress global stress expression data set: Protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J. 50: 347-363.
-
(2007)
Plant J.
, vol.50
, pp. 347-363
-
-
Kilian, J.1
Whitehead, D.2
Horak, J.3
Wanke, D.4
Weinl, S.5
Batistic, O.6
D'Angelo, C.7
Bornberg-Bauer, E.8
Kudla, J.9
Harter, K.10
-
46
-
-
84880943554
-
Data integration through proximity-based networks provides biological principles of organization across scales
-
Kleessen, S., Klie, S., and Nikoloski, Z. (2013). Data integration through proximity-based networks provides biological principles of organization across scales. Plant Cell 25: 1917-1927.
-
(2013)
Plant Cell
, vol.25
, pp. 1917-1927
-
-
Kleessen, S.1
Klie, S.2
Nikoloski, Z.3
-
47
-
-
78650335757
-
Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate
-
Krouk, G., Mirowski, P., LeCun, Y., Shasha, D.E., and Coruzzi, G.M. (2010). Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate. Genome Biol. 11: R123.
-
(2010)
Genome Biol.
, vol.11
-
-
Krouk, G.1
Mirowski, P.2
LeCun, Y.3
Shasha, D.E.4
Coruzzi, G.M.5
-
48
-
-
80054106797
-
Role of DREBs in regulation of abiotic stress responses in plants
-
Lata, C., and Prasad, M. (2011). Role of DREBs in regulation of abiotic stress responses in plants. J. Exp. Bot. 62: 4731-4748.
-
(2011)
J. Exp. Bot.
, vol.62
, pp. 4731-4748
-
-
Lata, C.1
Prasad, M.2
-
49
-
-
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., and Rhee, S.Y. (2010). Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat. Biotechnol. 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
-
50
-
-
79957754723
-
Coordinated gene networks regulating Arabidopsis plant metabolism in response to various stresses and nutritional cues
-
Less, H., Angelovici, R., Tzin, V., and Galili, G. (2011). Coordinated gene networks regulating Arabidopsis plant metabolism in response to various stresses and nutritional cues. Plant Cell 23: 1264-1271.
-
(2011)
Plant Cell
, vol.23
, pp. 1264-1271
-
-
Less, H.1
Angelovici, R.2
Tzin, V.3
Galili, G.4
-
51
-
-
80052776231
-
A dynamic programming algorithm for identification of triplex-forming sequences
-
Lexa, M., Martínek, T., Burgetová, I., Kopecek, D., and Brázdová, M. (2011). A dynamic programming algorithm for identification of triplex-forming sequences. Bioinformatics 27: 2510-2517.
-
(2011)
Bioinformatics
, vol.27
, pp. 2510-2517
-
-
Lexa, M.1
Martínek, T.2
Burgetová, I.3
Kopecek, D.4
Brázdová, M.5
-
52
-
-
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., and Assmann, S.M. (2012). Gene-sharing networks reveal organizing principles of transcriptomes in Arabidopsis and other multicellular organisms. Plant Cell 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
-
53
-
-
77957813589
-
DCGL: An R package for identifying differentially coexpressed genes and links from gene expression microarray data
-
Liu, B.H., Yu, H., Tu, K., Li, C., Li, Y.X., and Li, Y.Y. (2010). DCGL: An R package for identifying differentially coexpressed genes and links from gene expression microarray data. Bioinformatics 26: 2637-2638.
-
(2010)
Bioinformatics
, vol.26
, pp. 2637-2638
-
-
Liu, B.H.1
Yu, H.2
Tu, K.3
Li, C.4
Li, Y.X.5
Li, Y.Y.6
-
54
-
-
55849151275
-
Systems approaches to identifying gene regulatory networks in plants
-
Long, T.A., Brady, S.M., and Benfey, P.N. (2008). Systems approaches to identifying gene regulatory networks in plants. Annu. Rev. Cell Dev. Biol. 24: 81-103.
-
(2008)
Annu. Rev. Cell Dev. Biol.
, vol.24
, pp. 81-103
-
-
Long, T.A.1
Brady, S.M.2
Benfey, P.N.3
-
55
-
-
84884518215
-
Biostatistical approaches for the reconstruction of gene co-expression networks based on transcriptomic data
-
López-Kleine, L., Leal, L., and López, C. (2013). Biostatistical approaches for the reconstruction of gene co-expression networks based on transcriptomic data. Brief Funct. Genomics 12: 457-467.
-
(2013)
Brief Funct. Genomics
, vol.12
, pp. 457-467
-
-
López-Kleine, L.1
Leal, L.2
López, C.3
-
56
-
-
84879137062
-
Linking genes of unknown function with abiotic stress responses by high-throughput phenotype screening
-
Luhua, S., et al. (2013). Linking genes of unknown function with abiotic stress responses by high-throughput phenotype screening. Physiol. Plant. 148: 322-333.
-
(2013)
Physiol. Plant.
, vol.148
, pp. 322-333
-
-
Luhua, S.1
-
57
-
-
84865842920
-
Application of the Gini correlation coefficient to infer regulatory relationships in transcriptome analysis
-
Ma, C., and Wang, X. (2012). Application of the Gini correlation coefficient to infer regulatory relationships in transcriptome analysis. Plant Physiol. 160: 192-203.
-
(2012)
Plant Physiol.
, vol.160
, pp. 192-203
-
-
Ma, C.1
Wang, X.2
-
58
-
-
24044440971
-
BiNGO: A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
-
Maere, S., Heymans, K., and Kuiper, M. (2005). BiNGO: A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21: 3448-3449.
-
(2005)
Bioinformatics
, vol.21
, pp. 3448-3449
-
-
Maere, S.1
Heymans, K.2
Kuiper, M.3
-
59
-
-
28444441250
-
Cold, salinity and drought stresses: An overview
-
Mahajan, S., and Tuteja, N. (2005). Cold, salinity and drought stresses: An overview. Arch. Biochem. Biophys. 444: 139-158.
-
(2005)
Arch. Biochem. Biophys.
, vol.444
, pp. 139-158
-
-
Mahajan, S.1
Tuteja, N.2
-
60
-
-
84870305264
-
Wisdom of crowds for robust gene network inference
-
DREAM5 Consortium
-
Marbach, D., et al; DREAM5 Consortium (2012). Wisdom of crowds for robust gene network inference. Nat. Methods 9: 796-804.
-
(2012)
Nat. Methods
, vol.9
, pp. 796-804
-
-
Marbach, D.1
-
61
-
-
78649775562
-
Enrichment map: A network-based method for gene-set enrichment visualization and interpretation
-
Merico, D., Isserlin, R., Stueker, O., Emili, A., and Bader, G.D. (2010). Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS ONE 5: e13984.
-
(2010)
PLoS ONE
, vol.5
-
-
Merico, D.1
Isserlin, R.2
Stueker, O.3
Emili, A.4
Bader, G.D.5
-
62
-
-
0035860537
-
Machine learning for science: State of the art and future prospects
-
Mjolsness, E., and DeCoste, D. (2001). Machine learning for science: State of the art and future prospects. Science 293: 2051-2055.
-
(2001)
Science
, vol.293
, pp. 2051-2055
-
-
Mjolsness, E.1
DeCoste, D.2
-
63
-
-
77951168442
-
Omics meet networks-Using systems approaches to infer regulatory networks in plants
-
Moreno-Risueno, M.A., Busch, W., and Benfey, P.N. (2010). Omics meet networks-Using systems approaches to infer regulatory networks in plants. Curr. Opin. Plant Biol. 13: 126-131.
-
(2010)
Curr. Opin. Plant Biol.
, vol.13
, pp. 126-131
-
-
Moreno-Risueno, M.A.1
Busch, W.2
Benfey, P.N.3
-
64
-
-
0003780986
-
-
(Stanford, CA: Stanford InfoLab)
-
Page, L., Brin, S., Motwani, R., and Winograd, T. (1999). The PageRank Citation Ranking: Bring Order to the Web. (Stanford, CA: Stanford InfoLab).
-
(1999)
The PageRank Citation Ranking: Bring Order to the Web
-
-
Page, L.1
Brin, S.2
Motwani, R.3
Winograd, T.4
-
65
-
-
84870790399
-
An ensemble correlation-based gene selection algorithm for cancer classification with gene expression data
-
Piao, Y., Piao, M., Park, K., and Ryu, K.H. (2012). An ensemble correlation-based gene selection algorithm for cancer classification with gene expression data. Bioinformatics 28: 3306-3315.
-
(2012)
Bioinformatics
, vol.28
, pp. 3306-3315
-
-
Piao, Y.1
Piao, M.2
Park, K.3
Ryu, K.H.4
-
66
-
-
44449145580
-
A comparative study of different machine learning methods on microarray gene expression data
-
Pirooznia, M., Yang, J.Y., Yang, M.Q., and Deng, Y. (2008). A comparative study of different machine learning methods on microarray gene expression data. BMC Genomics 9 (suppl. 1): S13.
-
(2008)
BMC Genomics
, vol.9
, Issue.SUPPL. 1
-
-
Pirooznia, M.1
Yang, J.Y.2
Yang, M.Q.3
Deng, Y.4
-
67
-
-
84883644707
-
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
-
Rapaport, F., Khanin, R., Liang, Y., Pirun, M., Krek, A., Zumbo, P., Mason, C.E., Socci, N.D., and Betel, D. (2013). Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol. 14: R95.
-
(2013)
Genome Biol.
, vol.14
-
-
Rapaport, F.1
Khanin, R.2
Liang, Y.3
Pirun, M.4
Krek, A.5
Zumbo, P.6
Mason, C.E.7
Socci, N.D.8
Betel, D.9
-
68
-
-
84875741316
-
Transcriptome responses to combinations of stresses in Arabidopsis
-
Rasmussen, S., Barah, P., Suarez-Rodriguez, M.C., Bressendorff, S., Friis, P., Costantino, P., Bones, A.M., Nielsen, H.B., and Mundy, J. (2013). Transcriptome responses to combinations of stresses in Arabidopsis. Plant Physiol. 161: 1783-1794.
-
(2013)
Plant Physiol.
, vol.161
, pp. 1783-1794
-
-
Rasmussen, S.1
Barah, P.2
Suarez-Rodriguez, M.C.3
Bressendorff, S.4
Friis, P.5
Costantino, P.6
Bones, A.M.7
Nielsen, H.B.8
Mundy, J.9
-
69
-
-
83755163018
-
Detecting novel associations in large data sets
-
Reshef, D.N., Reshef, Y.A., Finucane, H.K., Grossman, S.R., McVean, G., Turnbaugh, P.J., Lander, E.S., Mitzenmacher, M., and Sabeti, P.C. (2011). Detecting novel associations in large data sets. Science 334: 1518-1524.
-
(2011)
Science
, vol.334
, pp. 1518-1524
-
-
Reshef, D.N.1
Reshef, Y.A.2
Finucane, H.K.3
Grossman, S.R.4
McVean, G.5
Turnbaugh, P.J.6
Lander, E.S.7
Mitzenmacher, M.8
Sabeti, P.C.9
-
70
-
-
33745477457
-
Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression
-
Sakuma, Y., Maruyama, K., Osakabe, Y., Qin, F., Seki, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2006). Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression. Plant Cell 18: 1292-1309.
-
(2006)
Plant Cell
, vol.18
, pp. 1292-1309
-
-
Sakuma, Y.1
Maruyama, K.2
Osakabe, Y.3
Qin, F.4
Seki, M.5
Shinozaki, K.6
Yamaguchi-Shinozaki, K.7
-
71
-
-
0033421491
-
On the proper bounds of the Gini correlation
-
Schechtman, E., and Yitzhaki, S. (1999). On the proper bounds of the Gini correlation. Econ. Lett. 63: 6.
-
(1999)
Econ. Lett.
, vol.63
, pp. 6
-
-
Schechtman, E.1
Yitzhaki, S.2
-
72
-
-
4544341015
-
Linear models and empirical bayes methods for assessing differential expression in microarray experiments
-
Smyth, G.K. (2004). Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3: e3.
-
(2004)
Stat. Appl. Genet. Mol. Biol.
, vol.3
-
-
Smyth, G.K.1
-
73
-
-
74249118093
-
Aging mice show a decreasing correlation of gene expression within genetic modules
-
Southworth, L.K., Owen, A.B., and Kim, S.K. (2009). Aging mice show a decreasing correlation of gene expression within genetic modules. PLoS Genet. 5: e1000776.
-
(2009)
PLoS Genet.
, vol.5
-
-
Southworth, L.K.1
Owen, A.B.2
Kim, S.K.3
-
74
-
-
30144433499
-
Enhanced tolerance to environmental stress in transgenic plants expressing the transcriptional coactivator multiprotein bridging factor 1c
-
Suzuki, N., Rizhsky, L., Liang, H., Shuman, J., Shulaev, V., and Mittler, R. (2005). Enhanced tolerance to environmental stress in transgenic plants expressing the transcriptional coactivator multiprotein bridging factor 1c. Plant Physiol. 139: 1313-1322.
-
(2005)
Plant Physiol.
, vol.139
, pp. 1313-1322
-
-
Suzuki, N.1
Rizhsky, L.2
Liang, H.3
Shuman, J.4
Shulaev, V.5
Mittler, R.6
-
75
-
-
84871787691
-
Data mining in the Life Sciences with Random Forest: A walk in the park or lost in the jungle? Brief
-
Touw, W.G., Bayjanov, J.R., Overmars, L., Backus, L., Boekhorst, J., Wels, M., and van Hijum, S.A. (2013). Data mining in the Life Sciences with Random Forest: A walk in the park or lost in the jungle? Brief. Bioinform. 14: 315-326.
-
(2013)
Bioinform.
, vol.14
, pp. 315-326
-
-
Touw, W.G.1
Bayjanov, J.R.2
Overmars, L.3
Backus, L.4
Boekhorst, J.5
Wels, M.6
van Hijum, S.A.7
-
76
-
-
0035942271
-
Significance analysis of microarrays applied to the ionizing radiation response
-
Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 98: 5116-5121.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
77
-
-
77951687828
-
'Omics' analyses of regulatory networks in plant abiotic stress responses
-
Urano, K., Kurihara, Y., Seki, M., and Shinozaki, K. (2010). 'Omics' analyses of regulatory networks in plant abiotic stress responses. Curr. Opin. Plant Biol. 13: 132-138.
-
(2010)
Curr. Opin. Plant Biol.
, vol.13
, pp. 132-138
-
-
Urano, K.1
Kurihara, Y.2
Seki, M.3
Shinozaki, K.4
-
78
-
-
70449115789
-
Co-expression tools for plant biology: Opportunities for hypothesis generation and caveats
-
Usadel, B., Obayashi, T., Mutwil, M., Giorgi, F.M., Bassel, G.W., Tanimoto, M., Chow, A., Steinhauser, D., Persson, S., and Provart, N.J. (2009). Co-expression tools for plant biology: Opportunities for hypothesis generation and caveats. Plant Cell Environ. 32: 1633-1651.
-
(2009)
Plant Cell Environ.
, vol.32
, pp. 1633-1651
-
-
Usadel, B.1
Obayashi, T.2
Mutwil, M.3
Giorgi, F.M.4
Bassel, G.W.5
Tanimoto, M.6
Chow, A.7
Steinhauser, D.8
Persson, S.9
Provart, N.J.10
-
79
-
-
84876760070
-
The potential of text mining in data integration and network biology for plant research: A case study on Arabidopsis
-
Van Landeghem, S., De Bodt, S., Drebert, Z.J., Inzé, D., and Van de Peer, Y. (2013). The potential of text mining in data integration and network biology for plant research: A case study on Arabidopsis. Plant Cell 25: 794-807.
-
(2013)
Plant Cell
, vol.25
, pp. 794-807
-
-
Van Landeghem, S.1
De Bodt, S.2
Drebert, Z.J.3
Inzé, D.4
Van de Peer, Y.5
-
80
-
-
33750416896
-
PSoL: A positive sample only learning algorithm for finding non-coding RNA genes
-
Wang, C., Ding, C., Meraz, R.F., and Holbrook, S.R. (2006). PSoL: A positive sample only learning algorithm for finding non-coding RNA genes. Bioinformatics 22: 2590-2596.
-
(2006)
Bioinformatics
, vol.22
, pp. 2590-2596
-
-
Wang, C.1
Ding, C.2
Meraz, R.F.3
Holbrook, S.R.4
-
81
-
-
84868288164
-
Arabidopsis defense against Botrytis cinerea: Chronology and regulation deciphered by high-resolution temporal transcriptomic analysis
-
Windram, O., et al. (2012). Arabidopsis defense against Botrytis cinerea: Chronology and regulation deciphered by high-resolution temporal transcriptomic analysis. Plant Cell 24: 3530-3557.
-
(2012)
Plant Cell
, vol.24
, pp. 3530-3557
-
-
Windram, O.1
-
82
-
-
80655128625
-
Average rank-based score to measure deregulation of molecular pathway gene sets
-
Yang, H., Cheng, C., and Zhang, W. (2011). Average rank-based score to measure deregulation of molecular pathway gene sets. PLoS ONE 6: e27579.
-
(2011)
PLoS ONE
, vol.6
-
-
Yang, H.1
Cheng, C.2
Zhang, W.3
-
83
-
-
33744725160
-
Gini's mean difference: A superior measure of variability for non-normal distributions
-
Yitzhaki, S. (2003). Gini's mean difference: A superior measure of variability for non-normal distributions. METRON LXI: 285-316.
-
(2003)
METRON
, vol.61
, pp. 285-316
-
-
Yitzhaki, S.1
-
84
-
-
79960892858
-
Linkbased quantitative methods to identify differentially coexpressed genes and gene pairs
-
Yu, H., Liu, B.H., Ye, Z.Q., Li, C., Li, Y.X., and Li, Y.Y. (2011). Linkbased quantitative methods to identify differentially coexpressed genes and gene pairs. BMC Bioinformatics 12: 315.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 315
-
-
Yu, H.1
Liu, B.H.2
Ye, Z.Q.3
Li, C.4
Li, Y.X.5
Li, Y.Y.6
-
85
-
-
0036999615
-
Salt and drought stress signal transduction in plants
-
Zhu, J.K. (2002). Salt and drought stress signal transduction in plants. Annu. Rev. Plant Biol. 53: 247-273.
-
(2002)
Annu. Rev. Plant Biol.
, vol.53
, pp. 247-273
-
-
Zhu, J.K.1
|