irCLASH reveals RNA substrates recognized by human ADARs

In vivo RNA editing of point mutations via RNA-guided adenosine deaminases

(2019) Dhruva Katrekar et al.   NATURE METHODS

Precise RNA editing by recruiting endogenous ADARs with antisense oligonucleotides

(2019) Tobias Merkle et al.   NATURE BIOTECHNOLOGY

Regulation of Co-transcriptional Pre-mRNA Splicing by m6A through the Low-Complexity Protein hnRNPG

(2019) Katherine I. Zhou et al.   MOLECULAR CELL

RNA editing in nascent RNA affects pre-mRNA splicing

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

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Efficient and precise editing of endogenous transcripts with SNAP-tagged ADARs

(2018) Paul Vogel et al.   NATURE METHODS

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

(2018) Eli Eisenberg et al.   NATURE REVIEWS GENETICS

bpRNA: large-scale automated annotation and analysis of RNA secondary structure

(2018) Padideh Danaee et al.   NUCLEIC ACIDS RESEARCH

Loss of ADAR1 in tumours overcomes resistance to immune checkpoint blockade

(2018) Jeffrey J. Ishizuka et al.   NATURE

The landscape of miRNA editing in animals and its impact on miRNA biogenesis and targeting

(2017) Lishi Li et al.   GENOME 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

DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome

(2017) Tuğçe Aktaş et al.   NATURE

Dynamic landscape and regulation of RNA editing in mammals

(2017) Meng How Tan et al.   NATURE

Site-directed RNA repair of endogenous Mecp2 RNA in neurons

(2017) John R. Sinnamon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

(2016) Zhipeng Lu et al.   CELL

A-to-I RNA editing promotes developmental stage–specific gene and lncRNA expression

(2016) Boaz Goldstein et al.   GENOME RESEARCH

In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation

(2016) Jong Ghut Ashley Aw et al.   MOLECULAR CELL

Global Mapping of Human RNA-RNA Interactions

(2016) Eesha Sharma et al.   MOLECULAR CELL

Adenosine-to-inosine RNA editing controls cathepsin S expression in atherosclerosis by enabling HuR-mediated post-transcriptional regulation

(2016) Konstantinos Stellos et al.   NATURE MEDICINE

irCLIP platform for efficient characterization of protein–RNA interactions

(2016) Brian J Zarnegar et al.   NATURE METHODS

Genetic Architectures of Quantitative Variation in RNA Editing Pathways

(2015) T. Gu et al.   GENETICS

hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1

(2015) Yoichiro Sugimoto et al.   NATURE

High-throughput determination of RNA structure by proximity ligation

(2015) Vijay Ramani et al.   NATURE BIOTECHNOLOGY

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

(2015) Kazuko Nishikura   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

Genetic mapping uncovers cis-regulatory landscape of RNA editing

(2015) Gokul Ramaswami et al.   Nature Communications

Elevated RNA Editing Activity Is a Major Contributor to Transcriptomic Diversity in Tumors

(2015) Nurit Paz-Yaacov et al.   Cell Reports

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

Mapping the miRNA interactome by cross-linking ligation and sequencing of hybrids (CLASH)

(2014) Aleksandra Helwak et al.   Nature Protocols

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

(2013) Y. Liao et al.   BIOINFORMATICS

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

ADAR1 Forms a Complex with Dicer to Promote MicroRNA Processing and RNA-Induced Gene Silencing

(2013) Hiromitsu Ota et al.   CELL

Identifying RNA editing sites using RNA sequencing data alone

(2013) Gokul Ramaswami et al.   NATURE METHODS

Deciphering the functions and regulation of brain-enriched A-to-I RNA editing

(2013) Jin Billy Li et al.   NATURE NEUROSCIENCE

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

(2013) Gokul Ramaswami et al.   NUCLEIC ACIDS RESEARCH

Correction of mutations within the cystic fibrosis transmembrane conductance regulator by site-directed RNA editing

(2013) M. F. Montiel-Gonzalez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ADAR Regulates RNA Editing, Transcript Stability, and Gene Expression

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

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

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

ViennaRNA Package 2.0

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

Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast

(2011) G. Kudla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functions and Regulation of RNA Editing by ADAR Deaminases

(2010) Kazuko Nishikura   Annual Review of Biochemistry

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH