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Results: 1 to 20 of 108

1.

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets.

Addo-Quaye C, Miller W, Axtell MJ.

Bioinformatics. 2009 Jan 1;25(1):130-1. doi: 10.1093/bioinformatics/btn604. Epub 2008 Nov 18.

PMID:
19017659
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Beyond cleaved small RNA targets: unraveling the complexity of plant RNA degradome data.

Hou CY, Wu MT, Lu SH, Hsing YI, Chen HM.

BMC Genomics. 2014 Jan 10;15:15. doi: 10.1186/1471-2164-15-15.

PMID:
24405808
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Identification of Taxus microRNAs and their targets with high-throughput sequencing and degradome analysis.

Hao DC, Yang L, Xiao PG, Liu M.

Physiol Plant. 2012 Dec;146(4):388-403. doi: 10.1111/j.1399-3054.2012.01668.x. Epub 2012 Jul 25.

PMID:
22708792
[PubMed - indexed for MEDLINE]
4.

Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome.

Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ.

Curr Biol. 2008 May 20;18(10):758-62. doi: 10.1016/j.cub.2008.04.042. Epub 2008 May 8.

PMID:
18472421
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome.

German MA, Luo S, Schroth G, Meyers BC, Green PJ.

Nat Protoc. 2009;4(3):356-62. doi: 10.1038/nprot.2009.8.

PMID:
19247285
[PubMed - indexed for MEDLINE]
6.

starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data.

Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH.

Nucleic Acids Res. 2011 Jan;39(Database issue):D202-9. doi: 10.1093/nar/gkq1056. Epub 2010 Oct 30.

PMID:
21037263
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Small RNA and degradome sequencing reveal complex miRNA regulation during cotton somatic embryogenesis.

Yang X, Wang L, Yuan D, Lindsey K, Zhang X.

J Exp Bot. 2013 Apr;64(6):1521-36. doi: 10.1093/jxb/ert013. Epub 2013 Feb 4.

PMID:
23382553
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets.

Wang XJ, Reyes JL, Chua NH, Gaasterland T.

Genome Biol. 2004;5(9):R65. Epub 2004 Aug 31.

PMID:
15345049
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

SeqTar: an effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants.

Zheng Y, Li YF, Sunkar R, Zhang W.

Nucleic Acids Res. 2012 Feb;40(4):e28. doi: 10.1093/nar/gkr1092. Epub 2011 Dec 2.

PMID:
22140118
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

Plant J. 2010 Jun 1;62(5):742-59. doi: 10.1111/j.1365-313X.2010.04187.x. Epub 2010 Feb 26.

PMID:
20202174
[PubMed - indexed for MEDLINE]
11.

Computational identification of novel microRNAs and targets in Brassica napus.

Xie FL, Huang SQ, Guo K, Xiang AL, Zhu YY, Nie L, Yang ZM.

FEBS Lett. 2007 Apr 3;581(7):1464-74. Epub 2007 Mar 8.

PMID:
17367786
[PubMed - indexed for MEDLINE]
Free Article
12.

Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing.

Shamimuzzaman M, Vodkin L.

BMC Genomics. 2012 Jul 16;13:310. doi: 10.1186/1471-2164-13-310.

PMID:
22799740
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

miRDeepFinder: a miRNA analysis tool for deep sequencing of plant small RNAs.

Xie F, Xiao P, Chen D, Xu L, Zhang B.

Plant Mol Biol. 2012 Jan 31. [Epub ahead of print]

PMID:
22290409
[PubMed - as supplied by publisher]
14.

Genome-wide identification and characterization of cadmium-responsive microRNAs and their target genes in radish (Raphanus sativus L.) roots.

Xu L, Wang Y, Zhai L, Xu Y, Wang L, Zhu X, Gong Y, Yu R, Limera C, Liu L.

J Exp Bot. 2013 Nov;64(14):4271-87. doi: 10.1093/jxb/ert240. Epub 2013 Sep 7.

PMID:
24014874
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Discovery of microRNA regulatory networks by integrating multidimensional high-throughput data.

Yang JH, Qu LH.

Adv Exp Med Biol. 2013;774:251-66. doi: 10.1007/978-94-007-5590-1_13.

PMID:
23377977
[PubMed - indexed for MEDLINE]
16.

Improved genome-wide mapping of uncapped and cleaved transcripts in eukaryotes--GMUCT 2.0.

Willmann MR, Berkowitz ND, Gregory BD.

Methods. 2014 May 1;67(1):64-73. doi: 10.1016/j.ymeth.2013.07.003. Epub 2013 Jul 15.

PMID:
23867340
[PubMed - in process]
17.

Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends.

German MA, Pillay M, Jeong DH, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis LA, Nobuta K, German R, De Paoli E, Lu C, Schroth G, Meyers BC, Green PJ.

Nat Biotechnol. 2008 Aug;26(8):941-6. doi: 10.1038/nbt1417. Epub 2008 Jun 9.

PMID:
18542052
[PubMed - indexed for MEDLINE]
18.

Prediction of novel miRNAs and associated target genes in Glycine max.

Joshi T, Yan Z, Libault M, Jeong DH, Park S, Green PJ, Sherrier DJ, Farmer A, May G, Meyers BC, Xu D, Stacey G.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S14. doi: 10.1186/1471-2105-11-S1-S14.

PMID:
20122185
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach.

Ding J, Li D, Ohler U, Guan J, Zhou S.

BMC Genomics. 2012 Jun 11;13 Suppl 3:S3. doi: 10.1186/1471-2164-13-S3-S3.

PMID:
22759612
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis.

Pantaleo V, Szittya G, Moxon S, Miozzi L, Moulton V, Dalmay T, Burgyan J.

Plant J. 2010 Jun 1;62(6):960-76. doi: 10.1111/j.0960-7412.2010.04208.x.

PMID:
20230504
[PubMed - indexed for MEDLINE]

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