-
1
-
-
58049220318
-
CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets
-
Addo-Quaye C, Miller W, Axtell MJ (2009) CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics 25: 130-131.
-
(2009)
Bioinformatics
, vol.25
, pp. 130-131
-
-
Addo-Quaye, C.1
Miller, W.2
Axtell, M.J.3
-
2
-
-
4644309196
-
The functions of animal microRNAs
-
Ambros V (2004) The functions of animal microRNAs. Nature 431: 350-355.
-
(2004)
Nature
, vol.431
, pp. 350-355
-
-
Ambros, V.1
-
3
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
-
(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
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
4
-
-
0242361521
-
Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes
-
Aukerman MJ, Sakai H (2003) Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 15: 2730-2741.
-
(2003)
Plant Cell
, vol.15
, pp. 2730-2741
-
-
Aukerman, M.J.1
Sakai, H.2
-
5
-
-
0347444723
-
MicroRNAs: genomics, biogenesis, mechanism, and function
-
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
-
(2004)
Cell
, vol.116
, pp. 281-297
-
-
Bartel, D.P.1
-
6
-
-
3843089328
-
Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes
-
Bonnet E, Wuyts J, Rouze P, van de Peer Y (2004) Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci USA 101: 11511-11516.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 11511-11516
-
-
Bonnet, E.1
Wuyts, J.2
Rouze, P.3
van de Peer, Y.4
-
7
-
-
77954184918
-
TAPIR, a web server for the prediction of plant microRNA targets, including target mimics
-
Bonnet E, He Y, Billiau K, van de Peer Y (2010) TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics 26: 1566-1568.
-
(2010)
Bioinformatics
, vol.26
, pp. 1566-1568
-
-
Bonnet, E.1
He, Y.2
Billiau, K.3
van de Peer, Y.4
-
8
-
-
40649090437
-
MicroRNA metabolism in plants
-
Chen X (2008) MicroRNA metabolism in plants. Curr Top Microbiol Immunol 320: 117-136.
-
(2008)
Curr Top Microbiol Immunol
, vol.320
, pp. 117-136
-
-
Chen, X.1
-
9
-
-
29144470346
-
Real-time quantification of microRNAs by stem-loop RT-PCR
-
Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33: e179.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Chen, C.1
Ridzon, D.A.2
Broomer, A.J.3
Zhou, Z.4
Lee, D.H.5
Nguyen, J.T.6
Barbisin, M.7
Xu, N.L.8
Mahuvakar, V.R.9
Andersen, M.R.10
Lao, K.Q.11
Livak, K.J.12
Guegler, K.J.13
-
10
-
-
77953140972
-
Argonaute proteins at a glance
-
Ender C, Meister G (2010) Argonaute proteins at a glance. J Cell Sci 123: 1819-1823.
-
(2010)
J Cell Sci
, vol.123
, pp. 1819-1823
-
-
Ender, C.1
Meister, G.2
-
11
-
-
34547115664
-
High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes
-
Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC (2007) High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PloS one 2: e219.
-
(2007)
PloS One
, vol.2
-
-
Fahlgren, N.1
Howell, M.D.2
Kasschau, K.D.3
Chapman, E.J.4
Sullivan, C.M.5
Cumbie, J.S.6
Givan, S.A.7
Law, T.F.8
Grant, S.R.9
Dangl, J.L.10
Carrington, J.C.11
-
12
-
-
41849084855
-
Discovering microRNAs from deep sequencing data using miRDeep
-
Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, Rajewsky N (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 26: 407-415.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 407-415
-
-
Friedlander, M.R.1
Chen, W.2
Adamidi, C.3
Maaskola, J.4
Einspanier, R.5
Knespel, S.6
Rajewsky, N.7
-
13
-
-
21344438211
-
Identification of human fetal liver miRNAs by a novel method
-
Fu H, Tie Y, Xu C, Zhang Z, Zhu J, Shi Y, Jiang H, Sun Z, Zheng X (2005) Identification of human fetal liver miRNAs by a novel method. FEBS Lett 579: 3849-3854.
-
(2005)
FEBS Lett
, vol.579
, pp. 3849-3854
-
-
Fu, H.1
Tie, Y.2
Xu, C.3
Zhang, Z.4
Zhu, J.5
Shi, Y.6
Jiang, H.7
Sun, Z.8
Zheng, X.9
-
14
-
-
27844526222
-
A miRNA involved in phosphate-starvation response in Arabidopsis
-
Fujii H, Chiou TJ, Lin SI, Aung K, Zhu JK (2005) A miRNA involved in phosphate-starvation response in Arabidopsis. Curr Biol 15: 2038-2043.
-
(2005)
Curr Biol
, vol.15
, pp. 2038-2043
-
-
Fujii, H.1
Chiou, T.J.2
Lin, S.I.3
Aung, K.4
Zhu, J.K.5
-
15
-
-
58149191274
-
Rfam: updates to the RNA families database
-
Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A (2009) Rfam: updates to the RNA families database. Nucleic Acids Res 37: D136-D140.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Gardner, P.P.1
Daub, J.2
Tate, J.G.3
Nawrocki, E.P.4
Kolbe, D.L.5
Lindgreen, S.6
Wilkinson, A.C.7
Finn, R.D.8
Griffiths-Jones, S.9
Eddy, S.R.10
Bateman, A.11
-
16
-
-
0038054470
-
Computational and experimental identification of C. elegans microRNAs
-
Grad Y, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun G, Kim J (2003) Computational and experimental identification of C. elegans microRNAs. Mol Cell 11: 1253-1263.
-
(2003)
Mol Cell
, vol.11
, pp. 1253-1263
-
-
Grad, Y.1
Aach, J.2
Hayes, G.D.3
Reinhart, B.J.4
Church, G.M.5
Ruvkun, G.6
Kim, J.7
-
18
-
-
24944510549
-
MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for arabidopsis lateral root development
-
Guo HS, Xie Q, Fei JF, Chua NH (2005) MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for arabidopsis lateral root development. Plant Cell 17: 1376-1386.
-
(2005)
Plant Cell
, vol.17
, pp. 1376-1386
-
-
Guo, H.S.1
Xie, Q.2
Fei, J.F.3
Chua, N.H.4
-
19
-
-
67849114241
-
miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments
-
Hackenberg M, Sturm M, Langenberger D, Falcon-Perez JM, Aransay AM (2009) miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res 37: W68-W76.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Hackenberg, M.1
Sturm, M.2
Langenberger, D.3
Falcon-Perez, J.M.4
Aransay, A.M.5
-
20
-
-
26944452405
-
Pathways through the small RNA world of plants
-
Herr AJ (2005) Pathways through the small RNA world of plants. FEBS Lett 579: 5879-5888.
-
(2005)
FEBS Lett
, vol.579
, pp. 5879-5888
-
-
Herr, A.J.1
-
21
-
-
0043123153
-
Vienna RNA secondary structure server
-
Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31: 3429-3431.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3429-3431
-
-
Hofacker, I.L.1
-
22
-
-
71049136041
-
Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing
-
Hsieh LC, Lin SI, Shih AC, Chen JW, Lin WY, Tseng CY, Li WH, Chiou TJ (2009) Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiol 151: 2120-2132.
-
(2009)
Plant Physiol
, vol.151
, pp. 2120-2132
-
-
Hsieh, L.C.1
Lin, S.I.2
Shih, A.C.3
Chen, J.W.4
Lin, W.Y.5
Tseng, C.Y.6
Li, W.H.7
Chiou, T.J.8
-
23
-
-
77954304695
-
DSAP: deep-sequencing small RNA analysis pipeline
-
Huang PJ, Liu YC, Lee CC, Lin WC, Gan RR, Lyu PC, Tang P (2010) DSAP: deep-sequencing small RNA analysis pipeline. Nucleic Acids Res 38(Suppl): W385-W391.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.SUPPL.
-
-
Huang, P.J.1
Liu, Y.C.2
Lee, C.C.3
Lin, W.C.4
Gan, R.R.5
Lyu, P.C.6
Tang, P.7
-
24
-
-
0033982936
-
KEGG: kyoto encyclopedia of genes and genomes
-
Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
25
-
-
18344369543
-
MicroRNA biogenesis: coordinated cropping and dicing
-
Kim VN (2005) MicroRNA biogenesis: coordinated cropping and dicing. Natl Rev Mol Cell Biol 6: 376-385.
-
(2005)
Natl Rev Mol Cell Biol
, vol.6
, pp. 376-385
-
-
Kim, V.N.1
-
26
-
-
0027751663
-
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
-
Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.
-
(1993)
Cell
, vol.75
, pp. 843-854
-
-
Lee, R.C.1
Feinbaum, R.L.2
Ambros, V.3
-
27
-
-
77956508095
-
MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data
-
Mathelier A, Carbone A (2010) MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. Bioinformatics 26: 2226-2234.
-
(2010)
Bioinformatics
, vol.26
, pp. 2226-2234
-
-
Mathelier, A.1
Carbone, A.2
-
28
-
-
60149090481
-
Criteria for annotation of plant MicroRNAs
-
Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, Griffiths-Jones S, Jacobsen SE, Mallory AC, Martienssen RA, Poethig RS, Qi Y, Vaucheret H, Voinnet O, Watanabe Y, Weigel D, Zhu JK (2008) Criteria for annotation of plant MicroRNAs. Plant Cell 20: 3186-3190.
-
(2008)
Plant Cell
, vol.20
, pp. 3186-3190
-
-
Meyers, B.C.1
Axtell, M.J.2
Bartel, B.3
Bartel, D.P.4
Baulcombe, D.5
Bowman, J.L.6
Cao, X.7
Carrington, J.C.8
Chen, X.9
Green, P.J.10
Griffiths-Jones, S.11
Jacobsen, S.E.12
Mallory, A.C.13
Martienssen, R.A.14
Poethig, R.S.15
Qi, Y.16
Vaucheret, H.17
Voinnet, O.18
Watanabe, Y.19
Weigel, D.20
Zhu, J.K.21
more..
-
29
-
-
52949088691
-
A toolkit for analysing large-scale plant small RNA datasets
-
Moxon S, Schwach F, Dalmay T, Maclean D, Studholme DJ, Moulton V (2008) A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics 24: 2252-2253.
-
(2008)
Bioinformatics
, vol.24
, pp. 2252-2253
-
-
Moxon, S.1
Schwach, F.2
Dalmay, T.3
Maclean, D.4
Studholme, D.J.5
Moulton, V.6
-
32
-
-
0034708122
-
The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans
-
Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901-906.
-
(2000)
Nature
, vol.403
, pp. 901-906
-
-
Reinhart, B.J.1
Slack, F.J.2
Basson, M.3
Pasquinelli, A.E.4
Bettinger, J.C.5
Rougvie, A.E.6
Horvitz, H.R.7
Ruvkun, G.8
-
33
-
-
16244398080
-
Specific effects of microRNAs on the plant transcriptome
-
Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D (2005) Specific effects of microRNAs on the plant transcriptome. Dev Cell 8: 517-527.
-
(2005)
Dev Cell
, vol.8
, pp. 517-527
-
-
Schwab, R.1
Palatnik, J.F.2
Riester, M.3
Schommer, C.4
Schmid, M.5
Weigel, D.6
-
34
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol 147: 195-197.
-
(1981)
J Mol Biol
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
35
-
-
42149157716
-
Identification of novel and candidate miRNAs in rice by high throughput sequencing
-
Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu JK (2008) Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol 8: 25.
-
(2008)
BMC Plant Biol
, vol.8
, pp. 25
-
-
Sunkar, R.1
Zhou, X.2
Zheng, Y.3
Zhang, W.4
Zhu, J.K.5
-
36
-
-
70449639806
-
miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression
-
Wang WC, Lin FM, Chang WC, Lin KY, Huang HD, Lin NS (2009) miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics 10: 328.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 328
-
-
Wang, W.C.1
Lin, F.M.2
Chang, W.C.3
Lin, K.Y.4
Huang, H.D.5
Lin, N.S.6
-
37
-
-
78449293356
-
Target-align: a tool for plant microRNA target identification
-
Xie F, Zhang B (2010) Target-align: a tool for plant microRNA target identification. Bioinformatics 26: 3002-3003.
-
(2010)
Bioinformatics
, vol.26
, pp. 3002-3003
-
-
Xie, F.1
Zhang, B.2
-
38
-
-
33947411951
-
Computational identification of novel microRNAs and targets in Brassica napus
-
Xie FL, Huang SQ, Guo K, Xiang AL, Zhu YY, Nie L, Yang ZM (2007) Computational identification of novel microRNAs and targets in Brassica napus. FEBS Lett 581: 1464-1474.
-
(2007)
FEBS Lett
, vol.581
, pp. 1464-1474
-
-
Xie, F.L.1
Huang, S.Q.2
Guo, K.3
Xiang, A.L.4
Zhu, Y.Y.5
Nie, L.6
Yang, Z.M.7
-
39
-
-
77953683331
-
Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum)
-
Xie F, Frazier TP, Zhang B (2010) Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum). Planta 232: 417-434.
-
(2010)
Planta
, vol.232
, pp. 417-434
-
-
Xie, F.1
Frazier, T.P.2
Zhang, B.3
-
40
-
-
79951570957
-
MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features
-
Xu J, Li CX, Li YS, Lv JY, Ma Y, Shao TT, Xu LD, Wang YY, Du L, Zhang YP, Jiang W, Li CQ, Xiao Y, Li X (2011) MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features. Nucleic Acids Res 39: 825-836.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 825-836
-
-
Xu, J.1
Li, C.X.2
Li, Y.S.3
Lv, J.Y.4
Ma, Y.5
Shao, T.T.6
Xu, L.D.7
Wang, Y.Y.8
Du, L.9
Zhang, Y.P.10
Jiang, W.11
Li, C.Q.12
Xiao, Y.13
Li, X.14
-
41
-
-
23144458275
-
miRU: an automated plant miRNA target prediction server
-
Zhang Y (2005) miRU: an automated plant miRNA target prediction server. Nucleic Acids Res 33: W701-W704.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Zhang, Y.1
-
42
-
-
33646830110
-
Conservation and divergence of plant microRNA genes
-
Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA (2006) Conservation and divergence of plant microRNA genes. Plant J 46: 243-259.
-
(2006)
Plant J
, vol.46
, pp. 243-259
-
-
Zhang, B.1
Pan, X.2
Cannon, C.H.3
Cobb, G.P.4
Anderson, T.A.5
-
43
-
-
56649120500
-
Identification of soybean microRNAs and their targets
-
Zhang B, Pan X, Stellwag EJ (2008) Identification of soybean microRNAs and their targets. Planta 229: 161-182.
-
(2008)
Planta
, vol.229
, pp. 161-182
-
-
Zhang, B.1
Pan, X.2
Stellwag, E.J.3
-
44
-
-
77954330416
-
mirTools: microRNA profiling and discovery based on high-throughput sequencing
-
Zhu E, Zhao F, Xu G, Hou H, Zhou L, Li X, Sun Z, Wu J (2010) mirTools: microRNA profiling and discovery based on high-throughput sequencing. Nucleic Acids Res 38(Suppl): W392-W397.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.SUPPL.
-
-
Zhu, E.1
Zhao, F.2
Xu, G.3
Hou, H.4
Zhou, L.5
Li, X.6
Sun, Z.7
Wu, J.8
-
45
-
-
0019876473
-
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
-
Zuker M, Stiegler P (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 9: 133-148.
-
(1981)
Nucleic Acids Res
, vol.9
, pp. 133-148
-
-
Zuker, M.1
Stiegler, P.2
|