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

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

Genome-Wide Characterization of RNA Editing in Chicken Embryos Reveals Common Features among Vertebrates

(2015) Laure Frésard et al.   PLoS One

RNA rewriting, recoding, and rewiring in human disease

(2015) Maria Anna Zipeto et al.   TRENDS IN MOLECULAR MEDICINE

Principles Governing A-to-I RNA Editing in the Breast Cancer Transcriptome

(2015) Debora Fumagalli et al.   Cell Reports

Profiling the RNA editomes of wild-typeC. elegansand ADAR mutants

(2014) Han-Qing Zhao et al.   GENOME RESEARCH

Caste-specific RNA editomes in the leaf-cutting ant Acromyrmex echinatior

(2014) Qiye Li et al.   Nature Communications

REDItools: high-throughput RNA editing detection made easy

(2013) Ernesto Picardi et al.   BIOINFORMATICS

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

Consistent Errors in First Strand cDNA Due to Random Hexamer Mispriming

(2013) Thomas P. van Gurp et al.   PLoS One

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

RNA editing in the human ENCODE RNA-seq data

(2012) E. Park 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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) J. K. Pickrell et al.   SCIENCE

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) W. Lin et al.   SCIENCE

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) C. L. Kleinman et al.   SCIENCE

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

(2012) Petr Daneck et al.   GENOME BIOLOGY

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

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

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Very Few RNA and DNA Sequence Differences in the Human Transcriptome

(2011) Daniel R. Schrider et al.   PLoS One

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

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

(2010) T. D. Wu 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

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

RNA editing in regulating gene expression in the brain

(2007) James E.C. Jepson et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms