-
1
-
-
43449091567
-
Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome
-
Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ. 2008. Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Current Biology 18: 758-762.
-
(2008)
Current Biology
, vol.18
, pp. 758-762
-
-
Addo-Quaye, C.1
Eshoo, T.W.2
Bartel, D.P.3
Axtell, M.J.4
-
2
-
-
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
-
3
-
-
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
-
4
-
-
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
-
5
-
-
1642366133
-
A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development
-
Chen X. 2004. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303: 2022-2025.
-
(2004)
Science
, vol.303
, pp. 2022-2025
-
-
Chen, X.1
-
6
-
-
79951774269
-
Molecular cloning - a laboratory manual, 3rd edn
-
Chong L. 2001. Molecular cloning - a laboratory manual, 3rd edn. Science 292: 547-610.
-
(2001)
Science
, vol.292
, pp. 547-610
-
-
Chong, L.1
-
7
-
-
79953086307
-
Evolution and functional diversification of MIRNA genes
-
Cuperus JT, Fahlgren N, Carrington JC. 2011. Evolution and functional diversification of MIRNA genes. Plant Cell 23: 431-442.
-
(2011)
Plant Cell
, vol.23
, pp. 431-442
-
-
Cuperus, J.T.1
Fahlgren, N.2
Carrington, J.C.3
-
8
-
-
79959967431
-
psRNATarget: a plant small RNA target analysis server
-
Dai X, Zhao PX. 2011. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Research 39: W155-W159.
-
(2011)
Nucleic Acids Research
, vol.39
-
-
Dai, X.1
Zhao, P.X.2
-
9
-
-
48249142558
-
Sequence variation of microRNAs and their binding sites in Arabidopsis
-
Ehrenreich IM, Purugganan MD. 2008. Sequence variation of microRNAs and their binding sites in Arabidopsis. Plant Physiology 146: 1974-1982.
-
(2008)
Plant Physiology
, vol.146
, pp. 1974-1982
-
-
Ehrenreich, I.M.1
Purugganan, M.D.2
-
10
-
-
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 et al. 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
-
11
-
-
77953214518
-
MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana
-
Fahlgren N, Jogdeo S, Kasschau KD, Sullivan CM, Chapman EJ, Laubinger S, Smith LM, Dasenko M, Givan SA, Weigel D et al. 2010. MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. Plant Cell 22: 1074-1089.
-
(2010)
Plant Cell
, vol.22
, pp. 1074-1089
-
-
Fahlgren, N.1
Jogdeo, S.2
Kasschau, K.D.3
Sullivan, C.M.4
Chapman, E.J.5
Laubinger, S.6
Smith, L.M.7
Dasenko, M.8
Givan, S.A.9
Weigel, D.10
-
12
-
-
0033911640
-
Hitchhiking under positive Darwinian selection
-
Fay JC, Wu CI. 2000. Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
-
(2000)
Genetics
, vol.155
, pp. 1405-1413
-
-
Fay, J.C.1
Wu, C.I.2
-
13
-
-
49449118943
-
Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends
-
German MA, Pillay M, Jeong DH, Hetawal A, Luo SJ, Janardhanan P, Kannan V, Rymarquis LA, Nobuta K, German R et al. 2008. Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nature Biotechnology 26: 941-946.
-
(2008)
Nature Biotechnology
, vol.26
, pp. 941-946
-
-
German, M.A.1
Pillay, M.2
Jeong, D.H.3
Hetawal, A.4
Luo, S.J.5
Janardhanan, P.6
Kannan, V.7
Rymarquis, L.A.8
Nobuta, K.9
German, R.10
-
14
-
-
54049108505
-
Selection and mutation on microRNA target sequences during rice evolution
-
Guo X, Gui Y, Wang Y, Zhu QH, Helliwell C, Fan L. 2008. Selection and mutation on microRNA target sequences during rice evolution. BMC Genomics 9: 454.
-
(2008)
BMC Genomics
, vol.9
, pp. 454
-
-
Guo, X.1
Gui, Y.2
Wang, Y.3
Zhu, Q.H.4
Helliwell, C.5
Fan, L.6
-
15
-
-
77950346035
-
Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids
-
He G, Zhu X, Elling AA, Chen L, Wang X, Guo L, Liang M, He H, Zhang H, Chen F et al. 2010. Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 22: 17-33.
-
(2010)
Plant Cell
, vol.22
, pp. 17-33
-
-
He, G.1
Zhu, X.2
Elling, A.A.3
Chen, L.4
Wang, X.5
Guo, L.6
Liang, M.7
He, H.8
Zhang, H.9
Chen, F.10
-
16
-
-
0043123153
-
Vienna RNA secondary structure server
-
Hofacker IL. 2003. Vienna RNA secondary structure server. Nucleic Acids Research 31: 3429-3431.
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 3429-3431
-
-
Hofacker, I.L.1
-
17
-
-
84863012576
-
Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage
-
Jeong DH, Park S, Zhai J, Gurazada SG, De Paoli E, Meyers BC, Green PJ. 2011. Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage. Plant Cell 23: 4185-4207.
-
(2011)
Plant Cell
, vol.23
, pp. 4185-4207
-
-
Jeong, D.H.1
Park, S.2
Zhai, J.3
Gurazada, S.G.4
De Paoli, E.5
Meyers, B.C.6
Green, P.J.7
-
18
-
-
77952821615
-
Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice
-
Jiao Y, Wang Y, Xue D, Wang J, Yan M, Liu G, Dong G, Zeng D, Lu Z, Zhu X et al. 2010. Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nature Genetics 42: 541-544.
-
(2010)
Nature Genetics
, vol.42
, pp. 541-544
-
-
Jiao, Y.1
Wang, Y.2
Xue, D.3
Wang, J.4
Yan, M.5
Liu, G.6
Dong, G.7
Zeng, D.8
Lu, Z.9
Zhu, X.10
-
19
-
-
33744830059
-
An SNP caused loss of seed shattering during rice domestication
-
Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y, Sasaki T, Yano M. 2006. An SNP caused loss of seed shattering during rice domestication. Science 312: 1392-1396.
-
(2006)
Science
, vol.312
, pp. 1392-1396
-
-
Konishi, S.1
Izawa, T.2
Lin, S.Y.3
Ebana, K.4
Fukuta, Y.5
Sasaki, T.6
Yano, M.7
-
20
-
-
78651293534
-
miRBase: integrating microRNA annotation and deep-sequencing data
-
Kozomara A, Griffiths-Jones S. 2011. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Research 39: D152-D157.
-
(2011)
Nucleic Acids Research
, vol.39
-
-
Kozomara, A.1
Griffiths-Jones, S.2
-
21
-
-
78649479141
-
Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection
-
Lam HM, Xu X, Liu X, Chen W, Yang G, Wong FL, Li MW, He W, Qin N, Wang B et al. 2010. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nature Genetics 42: 1053-1059.
-
(2010)
Nature Genetics
, vol.42
, pp. 1053-1059
-
-
Lam, H.M.1
Xu, X.2
Liu, X.3
Chen, W.4
Yang, G.5
Wong, F.L.6
Li, M.W.7
He, W.8
Qin, N.9
Wang, B.10
-
22
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
23
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009a. The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
24
-
-
67650711615
-
SOAP2: an improved ultrafast tool for short read alignment
-
Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. 2009b. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966-1967.
-
(2009)
Bioinformatics
, vol.25
, pp. 1966-1967
-
-
Li, R.1
Yu, C.2
Li, Y.3
Lam, T.W.4
Yiu, S.M.5
Kristiansen, K.6
Wang, J.7
-
25
-
-
75649124547
-
De novo assembly of human genomes with massively parallel short read sequencing
-
Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K et al. 2010a. De novo assembly of human genomes with massively parallel short read sequencing. Genome Research 20: 265-272.
-
(2010)
Genome Research
, vol.20
, pp. 265-272
-
-
Li, R.1
Zhu, H.2
Ruan, J.3
Qian, W.4
Fang, X.5
Shi, Z.6
Li, Y.7
Li, S.8
Shan, G.9
Kristiansen, K.10
-
26
-
-
77952832325
-
Transcriptome-wide identification of microRNA targets in rice
-
Li YF, Zheng Y, Addo-Quaye C, Zhang L, Saini A, Jagadeeswaran G, Axtell MJ, Zhang W, Sunkar R. 2010b. Transcriptome-wide identification of microRNA targets in rice. Plant Journal 62: 742-759.
-
(2010)
Plant Journal
, vol.62
, pp. 742-759
-
-
Li, Y.F.1
Zheng, Y.2
Addo-Quaye, C.3
Zhang, L.4
Saini, A.5
Jagadeeswaran, G.6
Axtell, M.J.7
Zhang, W.8
Sunkar, R.9
-
28
-
-
73449113271
-
Identification of microRNA processing determinants by random mutagenesis of Arabidopsis MIR172a precursor
-
Mateos JL, Bologna NG, Chorostecki U, Palatnik JF. 2010. Identification of microRNA processing determinants by random mutagenesis of Arabidopsis MIR172a precursor. Current Biology 20: 49-54.
-
(2010)
Current Biology
, vol.20
, pp. 49-54
-
-
Mateos, J.L.1
Bologna, N.G.2
Chorostecki, U.3
Palatnik, J.F.4
-
29
-
-
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 et al. 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
-
30
-
-
77952885074
-
OsSPL14 promotes panicle branching and higher grain productivity in rice
-
Miura K, Ikeda M, Matsubara A, Song XJ, Ito M, Asano K, Matsuoka M, Kitano H, Ashikari M. 2010. OsSPL14 promotes panicle branching and higher grain productivity in rice. Nature Genetics 42: 545-549.
-
(2010)
Nature Genetics
, vol.42
, pp. 545-549
-
-
Miura, K.1
Ikeda, M.2
Matsubara, A.3
Song, X.J.4
Ito, M.5
Asano, K.6
Matsuoka, M.7
Kitano, H.8
Ashikari, M.9
-
31
-
-
75249099173
-
inGAP: an integrated next-generation genome analysis pipeline
-
Qi J, Zhao F, Buboltz A, Schuster SC. 2010. inGAP: an integrated next-generation genome analysis pipeline. Bioinformatics 26: 127-129.
-
(2010)
Bioinformatics
, vol.26
, pp. 127-129
-
-
Qi, J.1
Zhao, F.2
Buboltz, A.3
Schuster, S.C.4
-
32
-
-
73449126830
-
RNA secondary structural determinants of miRNA precursor processing in Arabidopsis
-
Song L, Axtell MJ, Fedoroff NV. 2010. RNA secondary structural determinants of miRNA precursor processing in Arabidopsis. Current Biology 20: 37-41.
-
(2010)
Current Biology
, vol.20
, pp. 37-41
-
-
Song, L.1
Axtell, M.J.2
Fedoroff, N.V.3
-
33
-
-
0024313579
-
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism
-
Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
-
(1989)
Genetics
, vol.123
, pp. 585-595
-
-
Tajima, F.1
-
34
-
-
60149086351
-
Origin, biogenesis, and activity of plant microRNAs
-
Voinnet O. 2009. Origin, biogenesis, and activity of plant microRNAs. Cell 136: 669-687.
-
(2009)
Cell
, vol.136
, pp. 669-687
-
-
Voinnet, O.1
-
35
-
-
34548683235
-
Molecular evolution and selection of a gene encoding two tandem microRNAs in rice
-
Wang S, Zhu QH, Guo X, Gui Y, Bao J, Helliwell C, Fan L. 2007. Molecular evolution and selection of a gene encoding two tandem microRNAs in rice. FEBS Letters 581: 4789-4793.
-
(2007)
FEBS Letters
, vol.581
, pp. 4789-4793
-
-
Wang, S.1
Zhu, Q.H.2
Guo, X.3
Gui, Y.4
Bao, J.5
Helliwell, C.6
Fan, L.7
-
36
-
-
77951593590
-
Sequence variation and selection of small RNAs in domesticated rice
-
Wang Y, Shen D, Bo S, Chen H, Zheng J, Zhu QH, Cai D, Helliwell C, Fan L. 2010. Sequence variation and selection of small RNAs in domesticated rice. BMC Evolutionary Biology 10: 119.
-
(2010)
BMC Evolutionary Biology
, vol.10
, pp. 119
-
-
Wang, Y.1
Shen, D.2
Bo, S.3
Chen, H.4
Zheng, J.5
Zhu, Q.H.6
Cai, D.7
Helliwell, C.8
Fan, L.9
-
37
-
-
73449136828
-
Structure determinants for accurate processing of miR172a in Arabidopsis thaliana
-
Werner S, Wollmann H, Schneeberger K, Weigel D. 2010. Structure determinants for accurate processing of miR172a in Arabidopsis thaliana. Current Biology 20: 42-48.
-
(2010)
Current Biology
, vol.20
, pp. 42-48
-
-
Werner, S.1
Wollmann, H.2
Schneeberger, K.3
Weigel, D.4
-
38
-
-
73249125240
-
Rice MicroRNA effector complexes and targets
-
Wu L, Zhang Q, Zhou H, Ni F, Wu X, Qi Y. 2009. Rice MicroRNA effector complexes and targets. Plant Cell 21: 3421-3435.
-
(2009)
Plant Cell
, vol.21
, pp. 3421-3435
-
-
Wu, L.1
Zhang, Q.2
Zhou, H.3
Ni, F.4
Wu, X.5
Qi, Y.6
-
39
-
-
84862936211
-
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes
-
Xu X, Liu X, Ge S, Jensen JD, Hu F, Li X, Dong Y, Gutenkunst RN, Fang L, Huang L et al. 2012. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology 30: 105-111.
-
(2012)
Nature Biotechnology
, vol.30
, pp. 105-111
-
-
Xu, X.1
Liu, X.2
Ge, S.3
Jensen, J.D.4
Hu, F.5
Li, X.6
Dong, Y.7
Gutenkunst, R.N.8
Fang, L.9
Huang, L.10
-
40
-
-
83355173057
-
Evolution of microRNA genes in Oryza sativa and Arabidopsis thaliana: an update of the inverted duplication model
-
Zhang Y, Jiang W, Gao L. 2011. Evolution of microRNA genes in Oryza sativa and Arabidopsis thaliana: an update of the inverted duplication model. PLoS ONE 6: e28073.
-
(2011)
PLoS ONE
, vol.6
-
-
Zhang, Y.1
Jiang, W.2
Gao, L.3
-
41
-
-
33847661877
-
Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice
-
Zhu Q, Zheng X, Luo J, Gaut BS, Ge S. 2007. Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Molecular Biology and Evolution 24: 875-888.
-
(2007)
Molecular Biology and Evolution
, vol.24
, pp. 875-888
-
-
Zhu, Q.1
Zheng, X.2
Luo, J.3
Gaut, B.S.4
Ge, S.5
-
42
-
-
84867401563
-
Functions of miRNAs in rice
-
Sunkar R, ed. Berlin, Heidelberg, Germany: Springer-Verlag
-
Zhu Q-H, Curaba J, Lima JC, Helliwell C 2012. Functions of miRNAs in rice. In: Sunkar R, ed. MicroRNAs in plant development and stress responses. Berlin, Heidelberg, Germany: Springer-Verlag, 149-176.
-
(2012)
MicroRNAs in plant development and stress responses
, pp. 149-176
-
-
Zhu, Q.-H.1
Curaba, J.2
Lima, J.C.3
Helliwell, C.4
-
43
-
-
50649110065
-
A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains
-
Zhu QH, Spriggs A, Matthew L, Fan L, Kennedy G, Gubler F, Helliwell C. 2008. A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Research 18: 1456-1465.
-
(2008)
Genome Research
, vol.18
, pp. 1456-1465
-
-
Zhu, Q.H.1
Spriggs, A.2
Matthew, L.3
Fan, L.4
Kennedy, G.5
Gubler, F.6
Helliwell, C.7
|