Dynamic landscape and regulation of RNA editing in mammals

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

Identification of human RNA editing sites: A historical perspective

(2016) Gokul Ramaswami et al.   METHODS

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

Dynamic regulation of RNA editing in human brain development and disease

(2016) Taeyoung Hwang et al.   NATURE NEUROSCIENCE

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

(2016) Mikaela Behm et al.   TRENDS IN GENETICS

Genome sequence–independent identification of RNA editing sites

(2015) Qing Zhang et al.   NATURE METHODS

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

Profiling RNA editing in human tissues: towards the inosinome Atlas

(2015) Ernesto Picardi et al.   Scientific Reports

Cis Regulatory Effects on A-to-I RNA Editing in Related Drosophila Species

(2015) Anne L. Sapiro et al.   Cell Reports

ADAR1 deaminase contributes to scheduled skeletal myogenesis progression via stage-specific functions

(2014) C-L Hsieh et al.   CELL DEATH AND DIFFERENTIATION

Alu elements shape the primate transcriptome by cis-regulation of RNA editing

(2014) Chammiran Daniel et al.   GENOME BIOLOGY

Mammalian conserved ADAR targets comprise only a small fragment of the human editosome

(2014) Yishay Pinto et al.   GENOME BIOLOGY

Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing

(2013) Rui Zhang et al.   NATURE METHODS

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

Drift and conservation of differential exon usage across tissues in primate species

(2013) A. Reyes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development

(2012) M. H. Tan et al.   GENOME RESEARCH

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

A-to-I RNA Editing: Effects on Proteins Key to Neural Excitability

(2012) Joshua J.C. Rosenthal et al.   NEURON

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

The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics

(2012) Lenore Pipes et al.   NUCLEIC ACIDS RESEARCH

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

High levels of RNA-editing site conservation amongst 15 laboratory mouse strains

(2012) Petr Daneck et al.   GENOME BIOLOGY

ViennaRNA Package 2.0

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

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming

(2011) Kengo Sato et al.   BIOINFORMATICS

MissForest--non-parametric missing value imputation for mixed-type data

(2011) D. J. Stekhoven et al.   BIOINFORMATICS

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

(2011) Roberto Marcucci et al.   EMBO JOURNAL

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

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

Sequence-based characterization of structural variation in the mouse genome

(2011) Binnaz Yalcin et al.   NATURE

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

Modulation of dADAR-dependent RNA editing by the Drosophila fragile X mental retardation protein

(2011) Balpreet Bhogal et al.   NATURE NEUROSCIENCE

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

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

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

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS