Genome-wide analysis of single non-templated nucleotides in plant endogenous siRNAs and miRNAs

A Dicer-Independent Route for Biogenesis of siRNAs that Direct DNA Methylation in Arabidopsis

(2016) Ruiqiang Ye et al.   MOLECULAR CELL

miTRATA: a web-based tool formicroRNATruncationandTailingAnalysis

(2015) Parth Patel et al.   BIOINFORMATICS

A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis

(2015) Jixian Zhai et al.   CELL

Dicer-independent RNA-directed DNA methylation in Arabidopsis

(2015) Dong-Lei Yang et al.   CELL RESEARCH

More than meets the eye? Factors that affect target selection by plant miRNAs and heterochromatic siRNAs

(2015) Feng Wang et al.   CURRENT OPINION IN PLANT BIOLOGY

The expanding world of small RNAs in plants

(2015) Filipe Borges et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Comprehensive Annotation ofPhyscomitrella patensSmall RNA Loci Reveals That the Heterochromatic Short Interfering RNA Pathway Is Largely Conserved in Land Plants

(2015) Ceyda Coruh et al.   PLANT CELL

Secondary siRNAs fromMedicago NB-LRRsmodulated via miRNA-target interactions and their abundances

(2015) Qili Fei et al.   PLANT JOURNAL

Synergistic and Independent Actions of Multiple Terminal Nucleotidyl Transferases in the 3’ Tailing of Small RNAs in Arabidopsis

(2015) Xiaoyan Wang et al.   PLoS Genetics

Distinct and Cooperative Activities of HESO1 and URT1 Nucleotidyl Transferases in MicroRNA Turnover in Arabidopsis

(2015) Bin Tu et al.   PLoS Genetics

Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis

(2015) Todd Blevins et al.   eLife

Detection of Pol IV/RDR2-dependent transcripts at the genomic scale inArabidopsisreveals features and regulation of siRNA biogenesis

(2014) Shaofang Li et al.   GENOME RESEARCH

Analysis of Complementarity Requirements for Plant MicroRNA Targeting Using a Nicotiana benthamiana Quantitative Transient Assay

(2014) Q. Liu et al.   PLANT CELL

Classification and Comparison of Small RNAs from Plants

(2013) Michael J. Axtell   Annual Review of Plant Biology

Identification and annotation of small RNA genes using ShortStack

(2013) Saima Shahid et al.   METHODS

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Plant MicroRNAs Display Differential 3' Truncation and Tailing Modifications That Are ARGONAUTE1 Dependent and Conserved Across Species

(2013) J. Zhai et al.   PLANT CELL

Biogenesis, Turnover, and Mode of Action of Plant MicroRNAs

(2013) K. Rogers et al.   PLANT CELL

ShortStack: Comprehensive annotation and quantification of small RNA genes

(2013) M. J. Axtell   RNA

Plants regenerated from tissue culture contain stable epigenome changes in rice

(2013) Hume Stroud et al.   eLife

Uridylation of miRNAs by HEN1 SUPPRESSOR1 in Arabidopsis

(2012) Guodong Ren et al.   CURRENT BIOLOGY

The Arabidopsis Nucleotidyl Transferase HESO1 Uridylates Unmethylated Small RNAs to Trigger Their Degradation

(2012) Yuanyuan Zhao et al.   CURRENT BIOLOGY

A MicroRNA Superfamily Regulates Nucleotide Binding Site-Leucine-Rich Repeats and Other mRNAs

(2012) P. V. Shivaprasad et al.   PLANT CELL

Mechanisms that impact microRNA stability in plants

(2012) Yuanyuan Zhao et al.   RNA Biology

Extraordinary transgressive phenotypes of hybrid tomato are influenced by epigenetics and small silencing RNAs

(2011) Padubidri V Shivaprasad et al.   EMBO JOURNAL

Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions

(2011) Huan Wang et al.   PLANT JOURNAL

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

RNA polymerase V transcription guides ARGONAUTE4 to chromatin

(2009) Andrzej T Wierzbicki et al.   NATURE GENETICS

Adenylation of plant miRNAs

(2009) S. Lu et al.   NUCLEIC ACIDS RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Sorting of Small RNAs into Arabidopsis Argonaute Complexes Is Directed by the 5′ Terminal Nucleotide

(2008) Shijun Mi et al.   CELL

Physcomitrella patens DCL3 Is Required for 22–24 nt siRNA Accumulation, Suppression of Retrotransposon-Derived Transcripts, and Normal Development

(2008) Sung Hyun Cho et al.   PLoS Genetics