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

Human RNA Methyltransferase BCDIN3D Regulates MicroRNA Processing

(2012) Blerta Xhemalce et al.   CELL

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

(2012) Kate D. Meyer et al.   CELL

Going beyond five bases in DNA sequencing

(2012) Jonas Korlach et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Control of ground-state pluripotency by allelic regulation of Nanog

(2012) Yusuke Miyanari et al.   NATURE

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

(2012) Dan Dominissini et al.   NATURE

RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis

(2012) Francesca Tuorto et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The NIH Roadmap Epigenomics Program data resource

(2012) Lisa Helbling Chadwick   Epigenomics

Base-Pair Resolution DNA Methylation Sequencing Reveals Profoundly Divergent Epigenetic Landscapes in Acute Myeloid Leukemia

(2012) Altuna Akalin et al.   PLoS Genetics

An integrated ChIP-seq analysis platform with customizable workflows

(2011) Eugenia G Giannopoulou et al.   BMC BIOINFORMATICS

N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO

(2011) Guifang Jia et al.   Nature Chemical Biology

Widespread RNA and DNA Sequence Differences in the Human Transcriptome

(2011) M. Li et al.   SCIENCE

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

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

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

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

Discrimination of Methylcytosine from Hydroxymethylcytosine in DNA Molecules

(2010) Meni Wanunu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

Yeast targets for mRNA methylation

(2010) Zsuzsanna Bodi et al.   NUCLEIC ACIDS RESEARCH

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs

(2010) Morten Beck Rye et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

(2010) Elizabeth G. Wilbanks et al.   PLoS One

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

Finding the fifth base: Genome-wide sequencing of cytosine methylation

(2009) R. Lister et al.   GENOME RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications

(2008) Paul F Agris   EMBO REPORTS

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE