-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
-
(1990)
J. Mol. Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
2
-
-
84964913549
-
ATTED-II in 2016: A plant coexpression database towards lineage-specific coexpression
-
Aoki, Y., Okamura, Y., Tadaka, S., Kinoshita, K. and Obayashi, T. (2015) ATTED-II in 2016: a plant coexpression database towards lineage-specific coexpression. Plant Cell Physiol. 57: XXX-XXX.
-
(2015)
Plant Cell Physiol
, vol.57
, pp. XXX-XXX
-
-
Aoki, Y.1
Okamura, Y.2
Tadaka, S.3
Kinoshita, K.4
Obayashi, T.5
-
3
-
-
84874271270
-
NCBI GEO: Archive for functional genomics data sets - Update
-
Barrett, T., Wilhite, S.E., Ledoux, P., Evangelista, C., Kim, I.F., Tomashevsky, M., et al. (2013) NCBI GEO: archive for functional genomics data sets - update. Nucleic Acids Res. 41: D991-D995.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D991-D995
-
-
Barrett, T.1
Wilhite, S.E.2
Ledoux, P.3
Evangelista, C.4
Kim, I.F.5
Tomashevsky, M.6
-
4
-
-
84860566258
-
Arabidopsis WRKY33 is a key transcriptional regulator of hormonal and metabolic responses toward Botrytis cinerea infection
-
Birkenbihl, R.P., Diezel, C. and Somssich, I.E. (2012) Arabidopsis WRKY33 is a key transcriptional regulator of hormonal and metabolic responses toward Botrytis cinerea infection. Plant Physiol. 159: 266-285.
-
(2012)
Plant Physiol
, vol.159
, pp. 266-285
-
-
Birkenbihl, R.P.1
Diezel, C.2
Somssich, I.E.3
-
5
-
-
75449092046
-
AtPIN: Arabidopsis thaliana protein interaction network
-
Brandao, M., Dantas, L. and Silva-Filho, M. (2009) AtPIN: Arabidopsis thaliana protein interaction network. BMC Bioinformatics 10: 454.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 454
-
-
Brandao, M.1
Dantas, L.2
Silva-Filho, M.3
-
6
-
-
84941145210
-
The BioGRID interaction database: 2015 update
-
Chatr-aryamontri, A., Breitkreutz, B.-J., Oughtred, R., Boucher, L., Heinicke, S., Chen, D., et al. (2015) The BioGRID interaction database: 2015 update. Nucleic Acids Res. 43: D470-D478.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. D470-D478
-
-
Chatr-Aryamontri, A.1
Breitkreutz, B.-J.2
Oughtred, R.3
Boucher, L.4
Heinicke, S.5
Chen, D.6
-
8
-
-
34547843643
-
A new systematic computational approach to predicting target genes of transcription factors
-
Dai, X., He, J. and Zhao, X. (2007) A new systematic computational approach to predicting target genes of transcription factors. Nucleic Acids Res. 35: 4433-4440.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 4433-4440
-
-
Dai, X.1
He, J.2
Zhao, X.3
-
9
-
-
48449098051
-
PssRNAMiner: A plant short small RNA regulatory cascade analysis server
-
Dai, X. and Zhao, P.X. (2008) pssRNAMiner: a plant short small RNA regulatory cascade analysis server. Nucleic Acids Res. 36: W114-W118.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. W114-W118
-
-
Dai, X.1
Zhao, P.X.2
-
10
-
-
79959967431
-
PsRNATarget: A plant small RNA target analysis server
-
Dai, X. and Zhao, P.X. (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res. 39: W155-W159.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. W155-W159
-
-
Dai, X.1
Zhao, P.X.2
-
11
-
-
21344458139
-
Plant development is regulated by a family of auxin receptor F box proteins
-
Dharmasiri, N., Dharmasiri, S., Weijers, D., Lechner, E., Yamada, M., Hobbie, L., et al. (2005) Plant development is regulated by a family of auxin receptor F box proteins. Dev. Cell 9: 109-119.
-
(2005)
Dev. Cell
, vol.9
, pp. 109-119
-
-
Dharmasiri, N.1
Dharmasiri, S.2
Weijers, D.3
Lechner, E.4
Yamada, M.5
Hobbie, L.6
-
12
-
-
22044450951
-
A statistical analysis of the TRANSFAC database
-
Fogel, G.B., Weekes, D.G., Varga, G., Dow, E.R., Craven, A.M., Harlow, H.B., et al. (2005) A statistical analysis of the TRANSFAC database. Biosystems 81: 137-154.
-
(2005)
Biosystems
, vol.81
, pp. 137-154
-
-
Fogel, G.B.1
Weekes, D.G.2
Varga, G.3
Dow, E.R.4
Craven, A.M.5
Harlow, H.B.6
-
13
-
-
84945475714
-
Araport: An application platform for data discovery
-
Hanlon, M.R., Vaughn, M., Mock, S., Dooley, R., Moreira, W., Stubbs, J., et al. (2015) Araport: an application platform for data discovery. Concurrency Computat. Pract. Exper. 27: 4412-4422.
-
(2015)
Concurrency Computat. Pract. Exper
, vol.27
, pp. 4412-4422
-
-
Hanlon, M.R.1
Vaughn, M.2
Mock, S.3
Dooley, R.4
Moreira, W.5
Stubbs, J.6
-
14
-
-
56949095288
-
Functional characterization of Arabidopsis NaCl-inducible WRKY25 and WRKY33 transcription factors in abiotic stresses
-
Jiang, Y. and Deyholos, M.K. (2009) Functional characterization of Arabidopsis NaCl-inducible WRKY25 and WRKY33 transcription factors in abiotic stresses. Plant Mol. Biol. 69: 91-105.
-
(2009)
Plant Mol. Biol
, vol.69
, pp. 91-105
-
-
Jiang, Y.1
Deyholos, M.K.2
-
15
-
-
78651270438
-
AHD2.0: An update version of Arabidopsis Hormone Database for plant systematic studies
-
Jiang, Z., Liu, X., Peng, Z., Wan, Y., Ji, Y., He, W., et al. (2011) AHD2.0: an update version of Arabidopsis Hormone Database for plant systematic studies. Nucleic Acids Res. 39: D1123-D1129.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D1123-D1129
-
-
Jiang, Z.1
Liu, X.2
Peng, Z.3
Wan, Y.4
Ji, Y.5
He, W.6
-
16
-
-
84891760956
-
Data, information, knowledge and principle: Back to metabolism in KEGG
-
Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M. and Tanabe, M. (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42: D199-D205.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D199-D205
-
-
Kanehisa, M.1
Goto, S.2
Sato, Y.3
Kawashima, M.4
Furumichi, M.5
Tanabe, M.6
-
17
-
-
84941103248
-
ArrayExpress update - Simplifying data submissions
-
Kolesnikov, N., Hastings, E., Keays, M., Melnichuk, O., Tang, Y.A., Williams, E., et al. (2015) ArrayExpress update - simplifying data submissions. Nucleic Acids Res. 43: D1113-D1116.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. D1113-D1116
-
-
Kolesnikov, N.1
Hastings, E.2
Keays, M.3
Melnichuk, O.4
Tang, Y.A.5
Williams, E.6
-
18
-
-
84891818318
-
MiRBase: Annotating high confidence microRNAs using deep sequencing data
-
Kozomara, A. and Griffiths-Jones, S. (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 42: D68-D73.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D68-D73
-
-
Kozomara, A.1
Griffiths-Jones, S.2
-
19
-
-
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
-
20
-
-
75149162948
-
TransportTP: A two-phase classification approach for membrane transporter prediction and characterization
-
Li, H., Benedito, V.A., Udvardi, M.K. and Zhao, P.X. (2009) TransportTP: a two-phase classification approach for membrane transporter prediction and characterization. BMC Bioinformatics 10: 418.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 418
-
-
Li, H.1
Benedito, V.A.2
Udvardi, M.K.3
Zhao, P.X.4
-
21
-
-
42649092537
-
A nearest neighbor approach for automated transporter prediction and categorization from protein sequences
-
Li, H., Dai, X. and Zhao, X. (2008) A nearest neighbor approach for automated transporter prediction and categorization from protein sequences. Bioinformatics 24: 1129-1136.
-
(2008)
Bioinformatics
, vol.24
, pp. 1129-1136
-
-
Li, H.1
Dai, X.2
Zhao, X.3
-
22
-
-
80655139075
-
Large-scale protein-protein interaction analysis in Arabidopsis mesophyll protoplasts by split firefly luciferase complementation
-
Li, J.-F., Bush, J., Xiong, Y., Li, L. and McCormack, M. (2011) Large-scale protein-protein interaction analysis in Arabidopsis mesophyll protoplasts by split firefly luciferase complementation. PLoS One 6: e27364.
-
(2011)
PLoS One
, vol.6
-
-
Li, J.-F.1
Bush, J.2
Xiong, Y.3
Li, L.4
McCormack, M.5
-
23
-
-
84891466538
-
GPLEXUS: Enabling genome-scale gene association network reconstruction and analysis for very largescale expression data
-
Li, J., Wei, H., Liu, T. and Zhao, P.X. (2014) GPLEXUS: enabling genome-scale gene association network reconstruction and analysis for very largescale expression data. Nucleic Acids Res. 42: e32.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. e32
-
-
Li, J.1
Wei, H.2
Liu, T.3
Zhao, P.X.4
-
24
-
-
84903386038
-
Prediction of membrane transport proteins and their substrate specificities using primary sequence information
-
Mishra, N.K., Chang, J. and Zhao, P.X. (2014) Prediction of membrane transport proteins and their substrate specificities using primary sequence information. PLoS One 9: e100278.
-
(2014)
PLoS One
, vol.9
-
-
Mishra, N.K.1
Chang, J.2
Zhao, P.X.3
-
25
-
-
84892736334
-
ATTED-II in 2014: Evaluation of gene coexpression in agriculturally important plants
-
Obayashi, T., Okamura, Y., Ito, S., Tadaka, S., Aoki, Y., Shirota, M., et al. (2014) ATTED-II in 2014: evaluation of gene coexpression in agriculturally important plants. Plant Cell Physiol. 55: e6.
-
(2014)
Plant Cell Physiol
, vol.55
, pp. e6
-
-
Obayashi, T.1
Okamura, Y.2
Ito, S.3
Tadaka, S.4
Aoki, Y.5
Shirota, M.6
-
26
-
-
33846039701
-
ArrayExpress - A public database of microarray experiments and gene expression profiles
-
Parkinson, H., Kapushesky, M., Shojatalab, M., Abeygunawardena, N., Coulson, R., Farne, A., et al. (2007) ArrayExpress - a public database of microarray experiments and gene expression profiles. Nucleic Acids Res. 35: D747-D750.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. D747-D750
-
-
Parkinson, H.1
Kapushesky, M.2
Shojatalab, M.3
Abeygunawardena, N.4
Coulson, R.5
Farne, A.6
-
27
-
-
56049107695
-
Downstream targets of WRKY33
-
Petersen, K., Fiil, B.K., Mundy, J. and Petersen, M. (2008) Downstream targets of WRKY33. Plant Signal. Behav. 3: 1033-1034.
-
(2008)
Plant Signal. Behav
, vol.3
, pp. 1033-1034
-
-
Petersen, K.1
Fiil, B.K.2
Mundy, J.3
Petersen, M.4
-
28
-
-
84872562284
-
NetCAD: A network analysis tool for coronary artery disease-associated PPI network
-
Ren, G. and Liu, Z. (2013) NetCAD: a network analysis tool for coronary artery disease-associated PPI network. Bioinformatics 29: 279-280.
-
(2013)
Bioinformatics
, vol.29
, pp. 279-280
-
-
Ren, G.1
Liu, Z.2
-
29
-
-
84891779616
-
The transporter classification database
-
Saier, M.H., Reddy, V.S., Tamang, D.G. and Västermark, Å. (2014) The transporter classification database. Nucleic Acids Re. 42: D251-D258.
-
(2014)
Nucleic Acids Re
, vol.42
, pp. D251-D258
-
-
Saier, M.H.1
Reddy, V.S.2
Tamang, D.G.3
Västermark, Å.4
-
30
-
-
84933055824
-
Network reconstruction based on proteomic data and prior knowledge of protein connectivity using graph theory
-
Stavrakas, V., Melas, I.N., Sakellaropoulos, T. and Alexopoulos, L.G. (2015) Network reconstruction based on proteomic data and prior knowledge of protein connectivity using graph theory. PLoS One 10: e0128411.
-
(2015)
PLoS One
, vol.10
-
-
Stavrakas, V.1
Melas, I.N.2
Sakellaropoulos, T.3
Alexopoulos, L.G.4
-
31
-
-
84890920646
-
Genetic networks involved in poplar root response to low nitrogen
-
Wei, H., Yordanov, Y., Kumari, S., Georgieva, T. and Busov, V. (2013) Genetic networks involved in poplar root response to low nitrogen. Plant Signal. Behav. 8: e27211.
-
(2013)
Plant Signal. Behav
, vol.8
-
-
Wei, H.1
Yordanov, Y.2
Kumari, S.3
Georgieva, T.4
Busov, V.5
-
32
-
-
84876517560
-
PhosPhAt goes kinases - Searchable protein kinase target information in the plant phosphorylation site database PhosPhAt
-
Zulawski, M., Braginets, R. and Schulze, W.X. (2013) PhosPhAt goes kinases - searchable protein kinase target information in the plant phosphorylation site database PhosPhAt. Nucleic Acids Res. 41: D1176-D1184.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D1176-D1184
-
-
Zulawski, M.1
Braginets, R.2
Schulze, W.X.3
|