Thiol-linked alkylation of RNA to assess expression dynamics

m 6 A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover

(2017) Shengdong Ke et al.   GENES & DEVELOPMENT

Epitranscriptome sequencing technologies: decoding RNA modifications

(2017) Xiaoyu Li et al.   NATURE METHODS

Structural basis of N6-adenosine methylation by the METTL3–METTL14 complex

(2016) Xiang Wang et al.   NATURE

Editorial:Nucleic Acids Researchannual Web Server Issue in 2016

(2016)   NUCLEIC ACIDS RESEARCH

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

WGE: a CRISPR database for genome engineering: Fig. 1.

(2015) Alex Hodgkins et al.   BIOINFORMATICS

RNAN6-methyladenosine methylation in post-transcriptional gene expression regulation

(2015) Yanan Yue et al.   GENES & DEVELOPMENT

Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry

(2015) Erin E. Duffy et al.   MOLECULAR CELL

Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila

(2015) Madalena M. Reimão-Pinto et al.   MOLECULAR CELL

What are super-enhancers?

(2015) Sebastian Pott et al.   NATURE GENETICS

m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation

(2015) Shay Geula et al.   SCIENCE

The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila

(2014) Fabio Mohn et al.   CELL

High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies

(2014) Michal Rabani et al.   CELL

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

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

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

Gene expression regulation mediated through reversible m6A RNA methylation

(2014) Ye Fu et al.   NATURE REVIEWS GENETICS

The dynamic epitranscriptome: N6-methyladenosine and gene expression control

(2014) Kate D. Meyer et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

NextGenMap: fast and accurate read mapping in highly polymorphic genomes

(2013) Fritz J. Sedlazeck et al.   BIOINFORMATICS

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Mouse TU tagging: a chemical/genetic intersectional method for purifying cell type-specific nascent RNA

(2013) L. Gay et al.   GENES & DEVELOPMENT

Diversifying microRNA sequence and function

(2013) Stefan L. Ameres et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response

(2013) Kaspar Burger et al.   RNA Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation

(2012) M. Sun et al.   GENOME RESEARCH

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

High-throughput assessment of microRNA activity and function using microRNA sensor and decoy libraries

(2012) Gavriel Mullokandov et al.   NATURE METHODS

Genome-wide technology for determining RNA stability in mammalian cells

(2012) Hidenori Tani et al.   RNA Biology

Control of the Embryonic Stem Cell State

(2011) Richard A. Young   CELL

Forward and Reverse Genetics through Derivation of Haploid Mouse Embryonic Stem Cells

(2011) Ulrich Elling et al.   Cell Stem Cell

The 3′-to-5′ Exoribonuclease Nibbler Shapes the 3′ Ends of MicroRNAs Bound to Drosophila Argonaute1

(2011) Bo W. Han et al.   CURRENT BIOLOGY

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

(2011) I. M. Min et al.   GENES & DEVELOPMENT

Nucleobase Transport by Human Equilibrative Nucleoside Transporter 1 (hENT1)

(2011) Sylvia Y. M. Yao et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

(2011) C. Miller et al.   Molecular Systems Biology

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Gene silencing by microRNAs: contributions of translational repression and mRNA decay

(2011) Eric Huntzinger et al.   NATURE REVIEWS GENETICS

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

TU-tagging: cell type–specific RNA isolation from intact complex tissues

(2009) Michael R Miller et al.   NATURE METHODS

AmiGO: online access to ontology and annotation data

(2008) Seth Carbon et al.   BIOINFORMATICS

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

(2008) L. Dolken et al.   RNA