Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum

Gene Expression Variation Resolves Species and Individual Strains among Coral-Associated Dinoflagellates within the GenusSymbiodinium

(2016) John E. Parkinson et al.   Genome Biology and Evolution

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Ancestral genetic diversity associated with the rapid spread of stress-tolerant coral symbionts in response to Holocene climate change

(2016) Benjamin C. C. Hume et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle

(2016) M. Aranda et al.   Scientific Reports

RNA editing of non-coding RNA and its role in gene regulation

(2015) Chammiran Daniel et al.   BIOCHIMIE

Dynamic response of RNA editing to temperature in Drosophila

(2015) Leila E Rieder et al.   BMC BIOLOGY

Dinoflagellate Gene Structure and Intron Splice Sites in a Genomic Tandem Array

(2015) Gregory S. Mendez et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis

(2015) S. Lin et al.   SCIENCE

The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing

(2015) Shahar Alon et al.   eLife

The DYW Subgroup PPR Protein MEF35 Targets RNA Editing Sites in the Mitochondrial rpl16, nad4 and cob mRNAs in Arabidopsis thaliana

(2015) Nadja Brehme et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Massive Gene Transfer and Extensive RNA Editing of a Symbiotic Dinoflagellate Plastid Genome

(2014) Sutada Mungpakdee et al.   Genome Biology and Evolution

Genome-Wide Transcript Profiling Reveals the Coevolution of Plastid Gene Sequences and Transcript Processing Pathways in the Fucoxanthin Dinoflagellate Karlodinium veneficum

(2014) Elisabeth Richardson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Lineage-Specific Transcriptional Profiles of Symbiodinium spp. Unaltered by Heat Stress in a Coral Host

(2014) Daniel J. Barshis et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2014) Qiye Li et al.   Nature Communications

A genome-wide map of hyper-edited RNA reveals numerous new sites

(2014) Hagit T. Porath et al.   Nature Communications

Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver

(2014) Valerie Blanc et al.   GENOME BIOLOGY

RNA Editing in Plants and Its Evolution

(2013) Mizuki Takenaka et al.   Annual Review of Genetics

REDItools: high-throughput RNA editing detection made easy

(2013) Ernesto Picardi et al.   BIOINFORMATICS

Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals

(2013) Sebastian Baumgarten et al.   BMC GENOMICS

Draft Assembly of the Symbiodinium minutum Nuclear Genome Reveals Dinoflagellate Gene Structure

(2013) Eiichi Shoguchi et al.   CURRENT BIOLOGY

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

(2013) Steven A Roberts et al.   NATURE GENETICS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

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

Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity

(2013) S. A. Shabalina et al.   NUCLEIC ACIDS RESEARCH

ADAR Regulates RNA Editing, Transcript Stability, and Gene Expression

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

DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis

(2013) Benjamin JM Taylor et al.   eLife

Hypoxia-inducible C-to-U coding RNA editing downregulatesSDHBin monocytes

(2013) Bora E. Baysal et al.   PeerJ

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

RNA editing in the human ENCODE RNA-seq data

(2012) E. Park et al.   GENOME RESEARCH

A Tertiary Plastid Gains RNA Editing in Its New Host

(2012) Christopher J. Jackson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

(2012) Zhiyu Peng et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Symbiodinium Transcriptomes: Genome Insights into the Dinoflagellate Symbionts of Reef-Building Corals

(2012) Till Bayer et al.   PLoS One

Functional remodeling of RNA processing in replacement chloroplasts by pathways retained from their predecessors

(2012) R. G. Dorrell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic

(2012) M. Beauchemin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA editing of protein sequences: A rare event in human transcriptomes

(2012) C. L. Kleinman et al.   RNA

RNA Editing Underlies Temperature Adaptation in K+ Channels from Polar Octopuses

(2012) S. Garrett et al.   SCIENCE

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

Comparative Genomic and Transcriptomic Characterization of the Toxigenic Marine Dinoflagellate Alexandrium ostenfeldii

(2011) Nina Jaeckisch et al.   PLoS One

Coral thermal tolerance shaped by local adaptation of photosymbionts

(2011) E. J. Howells et al.   Nature Climate Change

Functions and Regulation of RNA Editing by ADAR Deaminases

(2010) Kazuko Nishikura   Annual Review of Biochemistry

Transcriptome Profiling of a Toxic Dinoflagellate Reveals a Gene-Rich Protist and a Potential Impact on Gene Expression Due to Bacterial Presence

(2010) Ahmed Moustafa et al.   PLoS One

RNA editing: a driving force for adaptive evolution?

(2009) Willemijn M. Gommans et al.   BIOESSAYS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Substitutional editing of Heterocapsa triquetra chloroplast transcripts and a folding model for its divergent chloroplast 16S rRNA

(2009) Yunkun Dang et al.   GENE

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

mRNA EDITING AND SPLICED-LEADER RNATRANS-SPLICING GROUPSOXYRRHIS,NOCTILUCA,HETEROCAPSA, ANDAMPHIDINIUMAS BASAL LINEAGES OF DINOFLAGELLATES

(2008) Huan Zhang et al.   JOURNAL OF PHYCOLOGY