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CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets.
Bioinformatics. 2009 Jan 1;25(1):130-1. doi: 10.1093/bioinformatics/btn604. Epub 2008 Nov 18.
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Beyond cleaved small RNA targets: unraveling the complexity of plant RNA degradome data.
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Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome.
Curr Biol. 2008 May 20;18(10):758-762. doi: 10.1016/j.cub.2008.04.042. Epub 2008 May 8.
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MTide: an integrated tool for the identification of miRNA-target interaction in plants.
Bioinformatics. 2015 Jan 15;31(2):290-1. doi: 10.1093/bioinformatics/btu633. Epub 2014 Sep 24.
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miRNA Digger: a comprehensive pipeline for genome-wide novel miRNA mining.
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Identification of Taxus microRNAs and their targets with high-throughput sequencing and degradome analysis.
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Transcriptome-wide identification of miRNA targets and a TAS3-homologous gene in Populus by degradome sequencing.
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starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data.
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Genome-wide identification, transcriptional profiling, and miRNA-binding site analysis of the gene family in the camphor tree.
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Integrated miRNAome, transcriptome, and degradome analyses reveal the role of miRNA-mRNA modules in the biosynthesis of oridonin in .
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Dynamics of small RNAs in a red-fruited wine grape cultivar infected with Grapevine red blotch virus.
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Identification of the co-regulatory siRNAs of "miRNA→target" in Oryza sativa.
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Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends.
Nat Biotechnol. 2008 Aug;26(8):941-6. doi: 10.1038/nbt1417. Epub 2008 Jun 9.
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MicroRNA-directed regulation: to cleave or not to cleave.
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A link between RNA metabolism and silencing affecting Arabidopsis development.
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Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome.
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Computational analysis of small RNA cloning data.
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Galaxy: a platform for interactive large-scale genome analysis.
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microRNA-directed phasing during trans-acting siRNA biogenesis in plants.
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MicroRNAs: genomics, biogenesis, mechanism, and function.
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Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA.
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