Mapping the dsRNA World

Breaching Self-Tolerance to Alu Duplex RNA Underlies MDA5-Mediated Inflammation

(2018) Sadeem Ahmad et al.   CELL

C. elegansADARs antagonize silencing of cellular dsRNAs by the antiviral RNAi pathway

(2018) Daniel P. Reich et al.   GENES & DEVELOPMENT

Repressive Chromatin inCaenorhabditis elegans: Establishment, Composition, and Function

(2018) Julie Ahringer et al.   GENETICS

N 6 -Methyladenosines Modulate A-to-I RNA Editing

(2018) Jian-Feng Xiang et al.   MOLECULAR CELL

Repressive Chromatin inCaenorhabditis elegans: Establishment, Composition, and Function

(2018) Julie Ahringer et al.   GENETICS

Dynamic landscape and regulation of RNA editing in mammals

(2017) Meng How Tan et al.   NATURE

ADAR1 controls apoptosis of stressed cells by inhibiting Staufen1-mediated mRNA decay

(2017) Masayuki Sakurai et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A to I editing in disease is not fake news

(2017) Prajakta Bajad et al.   RNA Biology

Biogenesis and Function of Ago-Associated RNAs

(2017) Iben Daugaard et al.   TRENDS IN GENETICS

ADAR1 controls apoptosis of stressed cells by inhibiting Staufen1-mediated mRNA decay

(2017) Masayuki Sakurai et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis

(2017) Sarah N Deffit et al.   eLife

Identification of the long, edited dsRNAome of LPS-stimulated immune cells

(2016) Matthew G. Blango et al.   GENOME RESEARCH

Ubiquitin-dependent Turnover of Adenosine Deaminase Acting on RNA 1 (ADAR1) Is Required for Efficient Antiviral Activity of Type I Interferon

(2016) Lemin Li et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Editing of Cellular Self-RNAs by Adenosine Deaminase ADAR1 Suppresses Innate Immune Stress Responses

(2016) Cyril X. George et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification of human RNA editing sites: A historical perspective

(2016) Gokul Ramaswami et al.   METHODS

REDIportal: a comprehensive database of A-to-I RNA editing events in humans

(2016) Ernesto Picardi et al.   NUCLEIC ACIDS RESEARCH

RNA-seq of human reference RNA samples using a thermostable group II intron reverse transcriptase

(2016) Ryan M. Nottingham et al.   RNA

RNA Editing: A Contributor to Neuronal Dynamics in the Mammalian Brain

(2016) Mikaela Behm et al.   TRENDS IN GENETICS

RES-Scanner: a software package for genome-wide identification of RNA-editing sites

(2016) Zongji Wang et al.   GigaScience

The Developmental Control of Transposable Elements and the Evolution of Higher Species

(2015) Marc Friedli et al.   Annual Review of Cell and Developmental Biology

Isoforms of RNA-Editing Enzyme ADAR1 Independently Control Nucleic Acid Sensor MDA5-Driven Autoimmunity and Multi-organ Development

(2015) Kathleen Pestal et al.   IMMUNITY

The emerging role of RNA editing in plasticity

(2015) J. J. C. Rosenthal   JOURNAL OF EXPERIMENTAL BIOLOGY

Measles Virus Defective Interfering RNAs Are Generated Frequently and Early in the Absence of C Protein and Can Be Destabilized by Adenosine Deaminase Acting on RNA-1-Like Hypermutations

(2015) Christian K. Pfaller et al.   JOURNAL OF VIROLOGY

Drosophila Dicer-2 Cleavage Is Mediated by Helicase- and dsRNA Termini-Dependent States that Are Modulated by Loquacious-PD

(2015) Niladri K. Sinha et al.   MOLECULAR CELL

Genome sequence–independent identification of RNA editing sites

(2015) Qing Zhang et al.   NATURE METHODS

Transcriptome-wide identification of adenosine-to-inosine editing using the ICE-seq method

(2015) Tsutomu Suzuki et al.   Nature Protocols

A-to-I editing of coding and non-coding RNAs by ADARs

(2015) Kazuko Nishikura   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Diverse selective regimes shape genetic diversity atADARgenes and at their coding targets

(2015) Diego Forni et al.   RNA Biology

Noncoding regions ofC. elegansmRNA undergo selective adenosine to inosine deamination and contain a small number of editing sites per transcript

(2015) Emily C Wheeler et al.   RNA Biology

Genome-wide profiling of theC. elegansdsRNAome

(2015) Joseph M. Whipple et al.   RNA

RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself

(2015) B. J. Liddicoat et al.   SCIENCE

The Epitranscriptome and Innate Immunity

(2015) Mary A. O’Connell et al.   PLoS Genetics

To edit or not to edit: regulation of ADAR editing specificity and efficiency

(2015) Sarah N. Deffit et al.   Wiley Interdisciplinary Reviews-RNA

ATP hydrolysis by the viral RNA sensor RIG-I prevents unintentional recognition of self-RNA

(2015) Charlotte Lässig et al.   eLife

The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing

(2015) Shahar Alon et al.   eLife

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling

(2014) Wei Zhao et al.   BMC GENOMICS

A Variety of Dicer Substrates in Human and C. elegans

(2014) Agnieszka Rybak-Wolf et al.   CELL

Sensing viral invasion by RIG-I like receptors

(2014) Ji-Seung Yoo et al.   CURRENT OPINION IN MICROBIOLOGY

TDP‐1, theCaenorhabditis elegansortholog of TDP‐43, limits the accumulation of double‐stranded RNA

(2014) Tassa K Saldi et al.   EMBO JOURNAL

Profiling the RNA editomes of wild-typeC. elegansand ADAR mutants

(2014) Han-Qing Zhao et al.   GENOME RESEARCH

A biochemical landscape of A-to-I RNA editing in the human brain transcriptome

(2014) M. Sakurai et al.   GENOME RESEARCH

Comparative analysis of metazoan chromatin organization

(2014) Joshua W. K. Ho et al.   NATURE

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

A genome-wide map of hyper-edited RNA reveals numerous new sites

(2014) Hagit T. Porath et al.   Nature Communications

The RNA-Editing Enzyme ADAR1 Controls Innate Immune Responses to RNA

(2014) Niamh M. Mannion et al.   Cell Reports

REDItools: high-throughput RNA editing detection made easy

(2013) Ernesto Picardi et al.   BIOINFORMATICS

Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data

(2013) Changjin Hong et al.   BMC BIOINFORMATICS

Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences

(2013) Shanshan Zhu et al.   BMC GENOMICS

Strand-Specific RNA-Seq Provides Greater Resolution of Transcriptome Profiling

(2013) James Dominic Mills et al.   CURRENT GENOMICS

STAU1 binding 3' UTR IRAlus complements nuclear retention to protect cells from PKR-mediated translational shutdown

(2013) R. A. Elbarbary et al.   GENES & DEVELOPMENT

A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes

(2013) L. Bazak et al.   GENOME RESEARCH

Master sensors of pathogenic RNA – RIG-I like receptors

(2013) Martin Schlee   IMMUNOBIOLOGY

Identifying RNA editing sites using RNA sequencing data alone

(2013) Gokul Ramaswami et al.   NATURE METHODS

Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila

(2013) Georges St Laurent et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RADAR: a rigorously annotated database of A-to-I RNA editing

(2013) Gokul Ramaswami et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Alignment Algorithms for Discovery and Identification of Pathogens Using RNA-Seq

(2013) Ivan Borozan et al.   PLoS One

Consistent Errors in First Strand cDNA Due to Random Hexamer Mispriming

(2013) Thomas P. van Gurp et al.   PLoS One

Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR)

(2013) O. Solomon et al.   RNA

Analysis and design of RNA sequencing experiments for identifying RNA editing and other single-nucleotide variants

(2013) J.-H. Lee et al.   RNA

Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing

(2013) S. Mohr et al.   RNA

RNA editing regulates transposon-mediated heterochromatic gene silencing

(2013) Yiannis A. Savva et al.   Nature Communications

Tertiary structural elements determine the extent and specificity of messenger RNA editing

(2013) Leila E. Rieder et al.   Nature Communications

ADAR Regulates RNA Editing, Transcript Stability, and Gene Expression

(2013) Isabel X. Wang et al.   Cell Reports

Visualizing genomic information across chromosomes with PhenoGram

(2013) Daniel Wolfe et al.   BioData Mining

Effects of ADARs on small RNA processing pathways in C. elegans

(2012) M. B. Warf et al.   GENOME RESEARCH

Darned in 2013: inclusion of model organisms and linking with Wikipedia

(2012) Anmol M. Kiran et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-wide identification of A > I RNA editing sites by inosine specific cleavage

(2012) P. B. Cattenoz et al.   RNA

RNA Editing Underlies Temperature Adaptation in K+ Channels from Polar Octopuses

(2012) S. Garrett et al.   SCIENCE

Global Analysis of RNA Secondary Structure in Two Metazoans

(2012) Fan Li et al.   Cell Reports

The birth of the Epitranscriptome: deciphering the function of RNA modifications

(2012) Yogesh Saletore et al.   GENOME BIOLOGY

Comparative analysis of algorithms for next-generation sequencing read alignment

(2011) M. Ruffalo et al.   BIOINFORMATICS

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing

(2011) J. H. Bahn et al.   GENOME RESEARCH

DICER1 deficit induces Alu RNA toxicity in age-related macular degeneration

(2011) Hiroki Kaneko et al.   NATURE

Competition between ADAR and RNAi pathways for an extensive class of RNA targets

(2011) Diane Wu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

(2011) J. B. Lucks et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adenosine deaminases acting on RNA (ADARs) are both antiviral and proviral

(2011) Charles E. Samuel   VIROLOGY

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

Functions and Regulation of RNA Editing by ADAR Deaminases

(2010) Kazuko Nishikura   Annual Review of Biochemistry

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Effects of Organic Solvents on the Reverse Transcription Reaction Catalyzed by Reverse Transcriptases from Avian Myeloblastosis Virus and Moloney Murine Leukemia Virus

(2010) Kiyoshi YASUKAWA et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

The Solution Structure of the ADAR2 dsRBM-RNA Complex Reveals a Sequence-Specific Readout of the Minor Groove

(2010) Richard Stefl et al.   CELL

Broad chromosomal domains of histone modification patterns in C. elegans

(2010) T. Liu et al.   GENOME RESEARCH

A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing

(2010) Peng Cui et al.   GENOMICS

Inosine cyanoethylation identifies A-to-I RNA editing sites in the human transcriptome

(2010) Masayuki Sakurai et al.   Nature Chemical Biology

Sequence based identification of RNA editing sites

(2010) Eli Eisenberg et al.   RNA Biology

The Origins of the RNA World

(2010) M. P. Robertson et al.   Cold Spring Harbor Perspectives in Biology

The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing

(2009) Nathan L. Clement et al.   BIOINFORMATICS

Adenosine-to-Inosine Genetic Recoding Is Required in the Adult Stage Nervous System for Coordinated Behavior in Drosophila

(2009) James E. C. Jepson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing

(2009) J. B. Li et al.   SCIENCE

A real-time PCR method for the quantitative analysis of RNA editing at specific sites

(2008) Yu-Chia Chen et al.   ANALYTICAL BIOCHEMISTRY

Autoinhibition of Human Dicer by Its Internal Helicase Domain

(2008) Enbo Ma et al.   JOURNAL OF MOLECULAR BIOLOGY

dsRNA Binding Properties of RDE-4 and TRBP Reflect Their Distinct Roles in RNAi

(2008) Greg S. Parker et al.   JOURNAL OF MOLECULAR BIOLOGY

ADAR1 is essential for the maintenance of hematopoiesis and suppression of interferon signaling

(2008) Jochen C Hartner et al.   NATURE IMMUNOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

A starvation-induced noncoding RNA modulates expression of Dicer-regulated genes

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