Genome-wide identification of mRNA 5-methylcytosine in mammals

Tet2 promotes pathogen infection-induced myelopoiesis through mRNA oxidation

(2018) Qicong Shen et al.   NATURE

Distinguishing RNA modifications from noise in epitranscriptome maps

(2018) Anya V Grozhik et al.   Nature Chemical Biology

RNA-dependent chromatin targeting of TET2 for endogenous retrovirus control in pluripotent stem cells

(2018) Diana Guallar et al.   NATURE GENETICS

RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia

(2018) Jason X. Cheng et al.   Nature Communications

Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs

(2017) Carine Legrand et al.   GENOME RESEARCH

NSUN2-Mediated m5C Methylation and METTL3/METTL14-Mediated m6A Methylation Cooperatively Enhance p21 Translation

(2017) Qiu Li et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Dynamic landscape and regulation of RNA editing in mammals

(2017) Meng How Tan et al.   NATURE

Transcriptome-Wide Mapping of RNA 5-Methylcytosine in Arabidopsis mRNAs and Noncoding RNAs

(2017) Rakesh David et al.   PLANT CELL

NSun2 Deficiency Protects Endothelium From Inflammation via mRNA Methylation of ICAM-1Novelty and Significance

(2016) Yuhong Luo et al.   CIRCULATION RESEARCH

Regulation of Poly(A) Tail and Translation during the Somatic Cell Cycle

(2016) Jong-Eun Park et al.   MOLECULAR CELL

Stem cell function and stress response are controlled by protein synthesis

(2016) Sandra Blanco et al.   NATURE

Accessory subunits are integral for assembly and function of human mitochondrial complex I

(2016) David A. Stroud et al.   NATURE

Messenger RNA modifications: Form, distribution, and function

(2016) W. V. Gilbert et al.   SCIENCE

Polyester: simulating RNA-seq datasets with differential transcript expression

(2015) Alyssa C. Frazee et al.   BIOINFORMATICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

A giant molecular proton pump: structure and mechanism of respiratory complex I

(2015) Leonid A. Sazanov   NATURE REVIEWS MOLECULAR CELL BIOLOGY

GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes

(2015) Patricia P. Chan et al.   NUCLEIC ACIDS RESEARCH

Nucleotide modifications within bacterial messenger RNAs regulate their translation and are able to rewire the genetic code

(2015) Thomas Philipp Hoernes et al.   NUCLEIC ACIDS RESEARCH

Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating organismal lifespan

(2015) Markus Schosserer et al.   Nature Communications

The Pivotal Regulatory Landscape of RNA Modifications

(2014) Sheng Li et al.   Annual Review of Genomics and Human Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

m6A RNA Modification Controls Cell Fate Transition in Mammalian Embryonic Stem Cells

(2014) Pedro J. Batista et al.   Cell Stem Cell

Role of RNA methyltransferases in tissue renewal and pathology

(2014) Sandra Blanco et al.   CURRENT OPINION IN CELL BIOLOGY

Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders

(2014) S. Blanco et al.   EMBO JOURNAL

Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation

(2014) Carlo G. Artieri et al.   GENOME RESEARCH

The Translational Landscape of the Mammalian Cell Cycle

(2013) Craig R. Stumpf et al.   MOLECULAR CELL

Identification of direct targets and modified bases of RNA cytosine methyltransferases

(2013) Vahid Khoddami et al.   NATURE BIOTECHNOLOGY

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

Yeast Nop2 and Rcm1 methylate C2870 and C2278 of the 25S rRNA, respectively

(2013) Sunny Sharma et al.   NUCLEIC ACIDS RESEARCH

NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs

(2013) Shobbir Hussain et al.   Cell Reports

Transcriptome-Wide Mapping of 5-methylcytidine RNA Modifications in Bacteria, Archaea, and Yeast Reveals m5C within Archaeal mRNAs

(2013) Sarit Edelheit et al.   PLoS Genetics

Characterizing 5-methylcytosine in the mammalian epitranscriptome

(2013) Shobbir Hussain et al.   GENOME BIOLOGY

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

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

(2012) Zhiyu Peng et al.   NATURE BIOTECHNOLOGY

The difficult calls in RNA editing

(2012) Brenda Bass 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

Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA

(2012) Jeffrey E. Squires et al.   NUCLEIC ACIDS RESEARCH

MODOMICS: a database of RNA modification pathways—2013 update

(2012) Magdalena A. Machnicka et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast 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

ViennaRNA Package 2.0

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

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

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

RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage

(2010) M. Schaefer et al.   GENES & DEVELOPMENT

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Analyzing real-time PCR data by the comparative CT method

(2008) Thomas D Schmittgen et al.   Nature Protocols