A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing

RNA editing in nascent RNA affects pre-mRNA splicing

(2018) Yun-Hua Esther Hsiao et al.   GENOME RESEARCH

A-to-I RNA editing — immune protector and transcriptome diversifier

(2018) Eli Eisenberg et al.   NATURE REVIEWS GENETICS

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

SRSF9 selectively represses ADAR2-mediated editing of brain-specific sites in primates

(2018) Raghuvaran Shanmugam et al.   NUCLEIC ACIDS RESEARCH

Primary transcriptome analysis reveals importance of IS elements for the shaping of the transcriptional landscape of Bordetella pertussis

(2018) Fabian Amman et al.   RNA Biology

Organ-wide profiling in mouse reveals high editing levels of Filamin B mRNA in the musculoskeletal system

(2018) Philipp Czermak et al.   RNA Biology

Inosine induces context-dependent recoding and translational stalling

(2018) Konstantin Licht et al.   NUCLEIC ACIDS RESEARCH

Adenosine Deaminase That Acts on RNA 3 (ADAR3) Binding to Glutamate Receptor Subunit B Pre-mRNA Inhibits RNA Editing in Glioblastoma

(2017) Eimile Oakes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Dynamic landscape and regulation of RNA editing in mammals

(2017) Meng How Tan et al.   NATURE

Alternative splicing as a regulator of development and tissue identity

(2017) Francisco E. Baralle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2017) Sarah N Deffit et al.   eLife

RDDpred: a condition-specific RNA-editing prediction model from RNA-seq data

(2016) Min-su Kim et al.   BMC GENOMICS

Complex regulation of ADAR-mediated RNA-editing across tissues

(2016) Melanie A. Huntley et al.   BMC GENOMICS

Rapid and dynamic transcriptome regulation by RNA editing and RNA modifications

(2016) Konstantin Licht et al.   JOURNAL OF CELL BIOLOGY

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

(2016) Ernesto Picardi et al.   NUCLEIC ACIDS RESEARCH

Adenosine to Inosine editing frequency controlled by splicing efficiency

(2016) Konstantin Licht et al.   NUCLEIC ACIDS RESEARCH

NOVA2-mediated RNA regulation is required for axonal pathfinding during development

(2016) Yuhki Saito et al.   eLife

Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams

(2015) Peter Kerpedjiev et al.   BIOINFORMATICS

The dynamic epitranscriptome: A to I editing modulates genetic information

(2015) Mansoureh Tajaddod et al.   CHROMOSOMA

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

(2015) Kathleen Pestal et al.   IMMUNITY

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

(2015) Kazuko Nishikura   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles

(2015) Bushra Raj et al.   NEURON

Genome-wide identification and characterization of tissue-specific RNA editing events inD. melanogasterand their potential role in regulating alternative splicing

(2015) Alborz Mazloomian et al.   RNA Biology

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

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

Profiling RNA editing in human tissues: towards the inosinome Atlas

(2015) Ernesto Picardi et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

Optimal guideRNAs for re-directing deaminase activity of hADAR1 and hADAR2 in trans

(2014) Marius F. Schneider et al.   NUCLEIC ACIDS RESEARCH

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

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

RNA-DNA Differences Are Generated in Human Cells within Seconds after RNA Exits Polymerase II

(2014) Isabel X. Wang et al.   Cell Reports

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

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

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

pLogo: a probabilistic approach to visualizing sequence motifs

(2013) Joseph P O'Shea et al.   NATURE METHODS

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

A high-throughput screen to identify enhancers of ADAR-mediated RNA-editing

(2013) Wojciech Garncarz et al.   RNA Biology

Spatio-temporal profiling of Filamin A RNA-editing reveals ADAR preferences and high editing levels outside neuronal tissues

(2013) Maja Stulić et al.   RNA Biology

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

(2013) O. Solomon et al.   RNA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

Comparison of Splicing Factor 3b Inhibitors in Human Cells

(2012) Yang Gao et al.   CHEMBIOCHEM

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

Nascent-Seq Indicates Widespread Cotranscriptional RNA Editing in Drosophila

(2012) Joseph Rodriguez et al.   MOLECULAR CELL

Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

(2012) Zhiyu Peng et al.   NATURE BIOTECHNOLOGY

Accurate identification of human Alu and non-Alu RNA editing sites

(2012) Gokul Ramaswami et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

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

RNA-interacting proteins act as site-specific repressors of ADAR2-mediated RNA editing and fluctuate upon neuronal stimulation

(2012) Aamira Tariq et al.   NUCLEIC ACIDS RESEARCH

Steric antisense inhibition of AMPA receptor Q/R editing reveals tight coupling to intronic editing sites and splicing

(2012) Andrew C. Penn et al.   NUCLEIC ACIDS RESEARCH

Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

(2012) Jerome S Menet et al.   eLife

ViennaRNA Package 2.0

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

Fast accessibility-based prediction of RNA–RNA interactions

(2011) Hakim Tafer et al.   BIOINFORMATICS

Pin1 and WWP2 regulateGluR2Q/R site RNA editing by ADAR2 with opposing effects

(2011) Roberto Marcucci et al.   EMBO JOURNAL

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

Predicting sites of ADAR editing in double-stranded RNA

(2011) Julie M. Eggington et al.   Nature Communications

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Large-scale mRNA sequencing determines global regulation of RNA editing during brain development

(2009) H. Wahlstedt et al.   GENOME RESEARCH

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

(2009) J. B. Li et al.   SCIENCE

The Preparation of Primary Hematopoietic Cell Cultures From Murine Bone Marrow for Electroporation

(2009) Kelly Kroeger et al.   Jove-Journal of Visualized Experiments

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

(2008) Jochen C Hartner et al.   NATURE IMMUNOLOGY