Analysis of Antisense Expression by Whole Genome Tiling Microarrays and siRNAs Suggests Mis-Annotation of Arabidopsis Orphan Protein-Coding Genes

Evolution, biogenesis and function of promoter-associated RNAs

(2011) Ryan J. Taft et al.   CELL CYCLE

Transcriptional Control of Gene Expression by MicroRNAs

(2010) Basel Khraiwesh et al.   CELL

Long antisense non-coding RNAs function to direct epigenetic complexes that regulate transcription in human cells

(2010) Kevin V. Morris   Epigenetics

Distinct Phases of siRNA Synthesis in an Endogenous RNAi Pathway in C. elegans Soma

(2010) Jonathan I. Gent et al.   MOLECULAR CELL

Control of female gamete formation by a small RNA pathway in Arabidopsis

(2010) Vianey Olmedo-Monfil et al.   NATURE

Small RNAs - secrets and surprises of the genome

(2010) Xuemei Chen   PLANT JOURNAL

Short-Read Sequencing Technologies for Transcriptional Analyses

(2009) Stacey A. Simon et al.   Annual Review of Plant Biology

Aberrant epigenetic reprogramming of imprinted microRNA-127 and Rtl1 in cloned mouse embryos

(2009) Xiang-Shun Cui et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Computational prediction of novel non-coding RNAs in Arabidopsis thaliana

(2009) Dandan Song et al.   BMC BIOINFORMATICS

MicroPC (μPC): A comprehensive resource for predicting and comparing plant microRNAs

(2009) Wuttichai Mhuantong et al.   BMC GENOMICS

Ars2 Regulates Both miRNA- and siRNA- Dependent Silencing and Suppresses RNA Virus Infection in Drosophila

(2009) Leah R. Sabin et al.   CELL

Ars2 Links the Nuclear Cap-Binding Complex to RNA Interference and Cell Proliferation

(2009) Joshua J. Gruber et al.   CELL

Small RNAs as Guardians of the Genome

(2009) Colin D. Malone et al.   CELL

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Origins and Mechanisms of miRNAs and siRNAs

(2009) Richard W. Carthew et al.   CELL

Riboactivators: Transcription activation by noncoding RNA

(2009) Aseem Z. Ansari   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

The long and the short of noncoding RNAs

(2009) Christopher A Brosnan et al.   CURRENT OPINION IN CELL BIOLOGY

Pervasive transcription constitutes a new level of eukaryotic genome regulation

(2009) Julia Berretta et al.   EMBO REPORTS

Clusters and superclusters of phased small RNAs in the developing inflorescence of rice

(2009) C. Johnson et al.   GENOME RESEARCH

Bursts of retrotransposition reproduced in Arabidopsis

(2009) Sayuri Tsukahara et al.   NATURE

Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis

(2009) Rebecca A. Mosher et al.   NATURE

Histone H2A.Z cooperates with RNAi and heterochromatin factors to suppress antisense RNAs

(2009) Martin Zofall et al.   NATURE

Selective epigenetic control of retrotransposition in Arabidopsis

(2009) Marie Mirouze et al.   NATURE

Regulatory roles of natural antisense transcripts

(2009) Mohammad Ali Faghihi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A distinct class of small RNAs arises from pre-miRNA–proximal regions in a simple chordate

(2009) Weiyang Shi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Integrative analysis of the human cis -antisense gene pairs, miRNAs and their transcription regulation patterns

(2009) Oleg V. Grinchuk et al.   NUCLEIC ACIDS RESEARCH

Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana

(2009) Leonardo Alves-Junior et al.   NUCLEIC ACIDS RESEARCH

Current tools for the identification of miRNA genes and their targets

(2009) N. D. Mendes et al.   NUCLEIC ACIDS RESEARCH

Conservation and divergence of microRNAs and their functions in Euphorbiaceous plants

(2009) Changying Zeng et al.   NUCLEIC ACIDS RESEARCH

Transcriptome Analyses Revealed Diverse Expression Changes in ago1 and hyl1 Arabidopsis Mutants

(2009) Yukio Kurihara et al.   PLANT AND CELL PHYSIOLOGY

Stress-induced changes in theArabidopsis thalianatranscriptome analyzed using whole-genome tiling arrays

(2009) Georg Zeller et al.   PLANT JOURNAL

Conserved and novel miRNAs in the legume Phaseolus vulgaris in response to stress

(2009) Catalina Arenas-Huertero et al.   PLANT MOLECULAR BIOLOGY

Expansion Mechanisms and Functional Annotations of Hypothetical Genes in the Rice Genome

(2009) S.-Y. Jiang et al.   PLANT PHYSIOLOGY

Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis

(2009) Y. Kurihara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of an RNA-dependent RNA polymerase in Drosophila involved in RNAi and transposon suppression

(2009) C. Lipardi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microarray analysis of cytoplasmic versus whole cell RNA reveals a considerable number of missed and false positive mRNAs

(2009) H. W. Trask et al.   RNA

Extensive Demethylation of Repetitive Elements During Seed Development Underlies Gene Imprinting

(2009) M. Gehring et al.   SCIENCE

Genome-Wide Demethylation of Arabidopsis Endosperm

(2009) T.-F. Hsieh et al.   SCIENCE

Evidence for Antisense Transcription Associated with MicroRNA Target mRNAs in Arabidopsis

(2009) Qing-Jun Luo et al.   PLoS Genetics

Identification of the candidate genes regulated by RNA-directed DNA methylation in Arabidopsis

(2008) Yukio Kurihara et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Identification of cold-inducible microRNAs in plants by transcriptome analysis

(2008) X ZHOU et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Identification of microRNA regulatory modules in Arabidopsis via a probabilistic graphical model

(2008) Je-Gun Joung et al.   BIOINFORMATICS

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

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

(2008) Hailing Jin et al.   BMC MOLECULAR BIOLOGY

Identification of precursor transcripts for 6 novel miRNAs expands the diversity on the genomic organisation and expression of miRNA genes in rice

(2008) Séverine Lacombe et al.   BMC PLANT BIOLOGY

In silico identification of conserved microRNAs in large number of diverse plant species

(2008) Ramanjulu Sunkar et al.   BMC PLANT BIOLOGY

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

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

(2008) Shijun Mi et al.   CELL

Getting to the Root of miRNA-Mediated Gene Silencing

(2008) Ana Eulalio et al.   CELL

Multifaceted mammalian transcriptome

(2008) Piero Carninci et al.   CURRENT OPINION IN CELL BIOLOGY

Post-transcriptional RNA silencing in plant–microbe interactions: a touch of robustness and versatility

(2008) Olivier Voinnet   CURRENT OPINION IN PLANT BIOLOGY

A Link between RNA Metabolism and Silencing Affecting Arabidopsis Development

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

Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci

(2008) D. M. Tyler et al.   GENES & DEVELOPMENT

A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands

(2008) A. Stark et al.   GENES & DEVELOPMENT

Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening

(2008) S. Moxon et al.   GENOME RESEARCH

Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses

(2008) B. Ben Amor et al.   GENOME RESEARCH

siRNA-Mediated Heterochromatin Establishment Requires HP1 and Is Associated with Antisense Transcription

(2008) Tetsushi Iida et al.   MOLECULAR CELL

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

(2008) Oliver H. Tam et al.   NATURE

Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends

(2008) Marcelo A German et al.   NATURE BIOTECHNOLOGY

Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?

(2008) Witold Filipowicz et al.   NATURE REVIEWS GENETICS

Antisense transcripts are targets for activating small RNAs

(2008) Jacob C Schwartz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Retrotransposons and siRNA have a role in the evolution of desiccation tolerance leading to resurrection of the plantCraterostigma plantagineum

(2008) Tobias Hilbricht et al.   NEW PHYTOLOGIST

Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation

(2008) Jiong-Tang Li et al.   NUCLEIC ACIDS RESEARCH

pssRNAMiner: a plant short small RNA regulatory cascade analysis server

(2008) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

Evolution of Arabidopsis MIR genes generates novel microRNA classes

(2008) Franck Vazquez et al.   NUCLEIC ACIDS RESEARCH

Characterization and expression profiles of miRNAs in rice seeds

(2008) Liang-Jiao Xue et al.   NUCLEIC ACIDS RESEARCH

S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum

(2008) Gaëlle André et al.   NUCLEIC ACIDS RESEARCH

AthaMap, integrating transcriptional and post-transcriptional data

(2008) L. Bulow et al.   NUCLEIC ACIDS RESEARCH

Arabidopsis Transcriptome Analysis under Drought, Cold, High-Salinity and ABA Treatment Conditions using a Tiling Array

(2008) A. Matsui et al.   PLANT AND CELL PHYSIOLOGY

Transcriptome-Wide Analysis of Uncapped mRNAs in Arabidopsis Reveals Regulation of mRNA Degradation

(2008) Y. Jiao et al.   PLANT CELL

Criteria for Annotation of Plant MicroRNAs

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

Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs)

(2008) C. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery and revision of Arabidopsis genes by proteogenomics

(2008) N. E. Castellana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MicroRNAs and the advent of vertebrate morphological complexity

(2008) A. M. Heimberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana

(2008) S. Laubinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of Arabidopsis thaliana microRNAs from random sequences

(2008) F. Fenselau de Felippes et al.   RNA

An Epigenetic Role for Maternally Inherited piRNAs in Transposon Silencing

(2008) J. Brennecke et al.   SCIENCE

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

The Epigenetic Landscape of Plants

(2008) X. Zhang   SCIENCE

Widespread Translational Inhibition by Plant miRNAs and siRNAs

(2008) P. Brodersen et al.   SCIENCE

The Antisense Transcriptomes of Human Cells

(2008) Yiping He et al.   SCIENCE

Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics

(2008) K. Baerenfaller et al.   SCIENCE

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

(2008) Pascal Preker et al.   SCIENCE

Suppression of the MicroRNA Pathway by Bacterial Effector Proteins

(2008) L. Navarro et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

Small RNAs in viral infection and host defense

(2008) Sizolwenkosi Mlotshwa et al.   TRENDS IN PLANT SCIENCE

MicroRNA-directed regulation: to cleave or not to cleave

(2008) Allison C. Mallory et al.   TRENDS IN PLANT SCIENCE

Diamonds in the rough: mRNA-like non-coding RNAs

(2008) Linda A. Rymarquis et al.   TRENDS IN PLANT SCIENCE