Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing

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

(2016) Mikaela Behm et al.   TRENDS IN GENETICS

The Landscape of A-to-I RNA Editome Is Shaped by Both Positive and Purifying Selection

(2016) Yao Yu et al.   PLoS Genetics

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

(2015) Kazuko Nishikura   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genetic mapping uncovers cis-regulatory landscape of RNA editing

(2015) Gokul Ramaswami et al.   Nature Communications

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

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

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

(2014) Z.-X. Chen et al.   GENOME RESEARCH

Human coding RNA editing is generally nonadaptive

(2014) G. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterizing of functional human coding RNA editing from evolutionary, structural, and dynamic perspectives

(2014) Oz Solomon et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The molecular link between inefficient GluA2 Q/R site-RNA editing and TDP-43 pathology in motor neurons of sporadic amyotrophic lateral sclerosis patients

(2013) Takenari Yamashita et al.   BRAIN RESEARCH

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

RNAstructure: web servers for RNA secondary structure prediction and analysis

(2013) Stanislav Bellaousov et al.   NUCLEIC ACIDS RESEARCH

Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9

(2013) X. Ren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Nascent-Seq Indicates Widespread Cotranscriptional RNA Editing in Drosophila

(2012) Joseph Rodriguez et al.   MOLECULAR CELL

Comparative RNA editing in autistic and neurotypical cerebella

(2012) A Eran et al.   MOLECULAR PSYCHIATRY

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

A distant cis acting intronic element induces site-selective RNA editing

(2012) Chammiran Daniel et al.   NUCLEIC ACIDS RESEARCH

Selective Depletion of rRNA Enables Whole Transcriptome Profiling of Archival Fixed Tissue

(2012) John D. Morlan et al.   PLoS One

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Predicting sites of ADAR editing in double-stranded RNA

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

Functions and Regulation of RNA Editing by ADAR Deaminases

(2010) Kazuko Nishikura   Annual Review of Biochemistry

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

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

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

Molecular diversity through RNA editing: a balancing act

(2010) Sanaz Farajollahi et al.   TRENDS IN GENETICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Adenosine deamination in human transcripts generates novel microRNA binding sites

(2009) Glen M. Borchert et al.   HUMAN MOLECULAR GENETICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

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

(2009) J. B. Li et al.   SCIENCE

Regulated RNA Editing and Functional Epistasis inShakerPotassium Channels

(2008) Lindsey Ingleby et al.   JOURNAL OF GENERAL PHYSIOLOGY

Evolution of protein-coding genes in Drosophila

(2008) Amanda M. Larracuente et al.   TRENDS IN GENETICS