Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal

pblat: a multithread blat algorithm speeding up aligning sequences to genomes

(2019) Meng Wang et al.   BMC BIOINFORMATICS

Illuminating spatial A-to-I RNA editing signatures within the Drosophila brain

(2019) Anne L. Sapiro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

“Mining the Epitranscriptome: Detection of RNA editing and RNA modifications”

(2019) Michael F. Jantsch et al.   METHODS

The Cancer Editome Atlas: A Resource for Exploratory Analysis of the Adenosine-to-Inosine RNA Editome in Cancer

(2019) Chui-Hsien Lin et al.   CANCER RESEARCH

RNA editing is abundant and correlates with task performance in a social bumblebee

(2019) Hagit T. Porath et al.   Nature Communications

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

(2018) Eli Eisenberg et al.   NATURE REVIEWS GENETICS

Accurate identification of RNA editing sites from primitive sequence with deep neural networks

(2018) Zhangyi Ouyang et al.   Scientific Reports

Whole transcriptome profiling of Late-Onset Alzheimer’s Disease patients provides insights into the molecular changes involved in the disease

(2018) Anita Annese et al.   Scientific Reports

Widespread RNA editing dysregulation in brains from autistic individuals

(2018) Stephen S. Tran et al.   NATURE NEUROSCIENCE

Genome-wide analysis of differential RNA editing in epilepsy

(2017) Prashant Kumar Srivastava et al.   GENOME RESEARCH

ADAR RNA editing in human disease; more to it than meets the I

(2017) Angela Gallo et al.   HUMAN GENETICS

RNA editing signature during myeloid leukemia cell differentiation

(2017) C Rossetti et al.   LEUKEMIA

Dynamic landscape and regulation of RNA editing in mammals

(2017) Meng How Tan et al.   NATURE

MODOMICS: a database of RNA modification pathways. 2017 update

(2017) Pietro Boccaletto et al.   NUCLEIC ACIDS RESEARCH

Human cancer tissues exhibit reduced A-to-I editing of miRNAs coupled with elevated editing of their targets

(2017) Yishay Pinto et al.   NUCLEIC ACIDS RESEARCH

A-to-I RNA editing is developmentally regulated and generally adaptive for sexual reproduction inNeurospora crassa

(2017) Huiquan Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell transcriptomics reveals specific RNA editing signatures in the human brain

(2017) Ernesto Picardi et al.   RNA

Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum

(2017) Yi Jin Liew et al.   PLoS Genetics

RED-ML: a novel, effective RNA editing detection method based on machine learning

(2017) Heng Xiong et al.   GigaScience

Identification of Symmetrical RNA Editing Events in the Mitochondria of Salvia miltiorrhiza by Strand-specific RNA Sequencing

(2017) Bin Wu et al.   Scientific Reports

Massive transcriptome sequencing of human spinal cord tissues provides new insights into motor neuron degeneration in ALS

(2017) Anna Maria D’Erchia et al.   Scientific Reports

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

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

Transcriptome sequencing reveals aberrant alternative splicing in Huntington's disease

(2016) Lan Lin et al.   HUMAN MOLECULAR GENETICS

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

(2016) Ernesto Picardi et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Zongji Wang et al.   GigaScience

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Genome sequence–independent identification of RNA editing sites

(2015) Qing Zhang et al.   NATURE METHODS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR

(2015) Hui Yang et al.   Nature Protocols

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

(2015) Kazuko Nishikura   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Reduced levels of protein recoding by A-to-I RNA editing in Alzheimer's disease

(2015) Khen Khermesh et al.   RNA

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

Transcription, Epigenetics and Ameliorative Strategies in Huntington’s Disease: a Genome-Wide Perspective

(2014) Luis M. Valor   MOLECULAR NEUROBIOLOGY

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

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

(2014) Yishay Pinto et al.   GENOME BIOLOGY

REDItools: high-throughput RNA editing detection made easy

(2013) Ernesto Picardi 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

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

(2013) Gokul Ramaswami et al.   NUCLEIC ACIDS RESEARCH

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A-to-I editing of protein coding and noncoding RNAs

(2012) Arka Mallela et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

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

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

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

(2012) Yogesh Saletore et al.   GENOME BIOLOGY

Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3′ UTRs

(2011) Brad R Rosenberg et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Alu elements: know the SINEs

(2011) Prescott Deininger   GENOME BIOLOGY

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

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

Paediatric neurology: understanding risk and improving therapeutic choices

(2010) Colin Kennedy   LANCET NEUROLOGY

A myriad of miRNA variants in control and Huntington’s disease brain regions detected by massively parallel sequencing

(2010) Eulàlia Martí et al.   NUCLEIC ACIDS RESEARCH

Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing

(2010) Ernesto Picardi et al.   NUCLEIC ACIDS RESEARCH

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

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

ISMB/ECCB 2009 Proceedings papers committee

(2009)   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