Analysis of RDR1 /RDR2 /RDR6 -independent small RNAs in Arabidopsis thaliana improves MIRNA annotations and reveals unexplained types of short interfering RNA loci

Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data

(2018) Michael J. Axtell et al.   PLANT CELL

Differential expression of cucumber RNA-dependent RNA polymerase 1 genes during antiviral defence and resistance

(2017) Diana Leibman et al.   MOLECULAR PLANT PATHOLOGY

De Novo Genes Arise at a Slow but Steady Rate along the Primate Lineage and Have Been Subject to Incomplete Lineage Sorting

(2016) Daniele Guerzoni et al.   Genome Biology and Evolution

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

(2015) Jixian Zhai et al.   CELL

Suppression of endogenous gene silencing by bidirectional cytoplasmic RNA decay in Arabidopsis

(2015) X. Zhang et al.   SCIENCE

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

Seeing the forest for the trees: annotating small RNA producing genes in plants

(2014) Ceyda Coruh et al.   CURRENT OPINION IN PLANT BIOLOGY

Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis

(2014) H. Wang et al.   GENOME RESEARCH

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

Evolutionary history of plant microRNAs

(2014) Richard S. Taylor et al.   TRENDS IN PLANT SCIENCE

Mechanisms of Small RNA Generation from Cis-NATs in Response to Environmental and Developmental Cues

(2013) Xiaoming Zhang et al.   Molecular Plant

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

(2013) Annabelle Haudry et al.   NATURE GENETICS

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Phased, Secondary, Small Interfering RNAs in Posttranscriptional Regulatory Networks

(2013) Q. Fei et al.   PLANT CELL

The Tomato Yellow Leaf Curl Virus Resistance Genes Ty-1 and Ty-3 Are Allelic and Code for DFDGD-Class RNA–Dependent RNA Polymerases

(2013) Maarten G. Verlaan et al.   PLoS Genetics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

RDR1 and SGS3, Components of RNA-Mediated Gene Silencing, Are Required for the Regulation of Cuticular Wax Biosynthesis in Developing Inflorescence Stems of Arabidopsis

(2012) P. Lam et al.   PLANT PHYSIOLOGY

Cotranscriptional Role for Arabidopsis DICER-LIKE 4 in Transcription Termination

(2012) F. Liu et al.   SCIENCE

Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function

(2012) Xiaoming Zhang et al.   GENOME BIOLOGY

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

PlantNATsDB: a comprehensive database of plant natural antisense transcripts

(2011) D. Chen et al.   NUCLEIC ACIDS RESEARCH

ARGONAUTE2 Mediates RNA-Silencing Antiviral Defenses against Potato virus X in Arabidopsis

(2011) M. Jaubert et al.   PLANT PHYSIOLOGY

An Antiviral Defense Role of AGO2 in Plants

(2011) Jagger J. W. Harvey et al.   PLoS One

A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions

(2010) Chuan-Yun Li et al.   PLoS Computational Biology

RNA-mediated chromatin-based silencing in plants

(2009) Marjori Matzke et al.   CURRENT OPINION IN CELL BIOLOGY

Darwinian alchemy: Human genes from noncoding DNA

(2009) A. Siepel   GENOME RESEARCH

Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis

(2008) Hailing Jin et al.   BMC MOLECULAR BIOLOGY

Kill the messenger: mRNA decay and plant development

(2008) Dmitry A Belostotsky et al.   CURRENT OPINION IN PLANT BIOLOGY

A Link between RNA Metabolism and Silencing Affecting Arabidopsis Development

(2008) Brian D. Gregory et al.   DEVELOPMENTAL CELL

Criteria for Annotation of Plant MicroRNAs

(2008) B. C. Meyers et al.   PLANT CELL