The biosynthetic pathways and biological scopes of plant small RNAs, Trends Plant Sci, vol.15, pp.337-382, 2010. ,
The 'how' and 'where' of plant microRNAs, New Phytol, vol.216, pp.1002-1019, 2017. ,
Evolution of Arabidopsis MIR genes generates novel microRNA classes, Nucleic Acids Res, p.670, 2008. ,
siRNAs from miRNA sites mediate DNA methylation of target genes, Nucleic Acids Res, vol.38, pp.6883-94, 2010. ,
DNA methylation mediated by a microRNA pathway, Mol Cell, vol.38, pp.465-75, 2010. ,
Vive la différence: biogenesis and evolution of microRNAs in plants and animals, Genome Biol, vol.12, p.221, 2011. ,
miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants, Bioinforma Oxf Engl, vol.27, pp.2614-2619, 2011. ,
miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data, BMC Bioinformatics, vol.15, p.275, 2014. ,
miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data, Bioinforma Oxf Engl, vol.30, pp.2837-2846, 2014. ,
Improved placement of multimapping small RNAs, G3 Bethesda Md, vol.6, pp.2103-2114, 2016. ,
Computational tools for plant small RNA detection and categorization. Brief Bioinform, 2017. ,
Criteria for annotation of plant MicroRNAs, Plant Cell, vol.20, pp.3186-90, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00369966
Characterization of statistical features for plant microRNA prediction, BMC Genomics, vol.12, p.108, 2011. ,
Revisiting criteria for plant MicroRNA annotation in the era of big data, Plant Cell, vol.30, pp.272-84, 2018. ,
Aligning short sequencing reads with bowtie. Curr Protoc Bioinforma Ed Board Andreas Baxevanis Al, vol.CHAPTER, 2010. ,
Fast and accurate short read alignment with burrowswheeler transform, Bioinforma Oxf Engl, vol.25, pp.1754-60, 2009. ,
annotating high confidence microRNAs using deep sequencing data, Nucleic Acids Res, vol.42, pp.68-73, 2014. ,
ViennaRNA Package 2.0, Algorithms Mol Biol, vol.6, p.26, 2011. ,
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences, Bioinforma Oxf Engl, vol.20, pp.2911-2918, 2004. ,
Arabidopsis micro-RNA biogenesis through dicerlike 1 protein functions, Proc Natl Acad Sci U S A, vol.101, pp.12753-12761, 2004. ,
Computational prediction of the localization of microRNAs within their pre-miRNA, Nucleic Acids Res, vol.41, pp.7200-7211, 2013. ,
Approximate search of short patterns with high error rates using the 01?0 lossless seeds, J Discrete Algorithms, vol.37, pp.3-16, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01360485
Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions, Plant J Cell Mol Biol, vol.67, pp.292-304, 2011. ,
Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet.journal, vol.17, pp.10-12, 2011. ,
Quality control and preprocessing of metagenomic datasets, Bioinforma Oxf Engl, vol.27, pp.863-867, 2011. ,
,
, The Arabidopsis Information Resource
Automated generation of heuristics for biological sequence comparison, BMC Bioinformatics, vol.6, p.31, 2005. ,
Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes, p.368985, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02265374
Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5? terminal nucleotide, Cell, vol.133, pp.116-143, 2008. ,
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