U1 snRNP telescripting regulates a size–function-stratified human genome

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

(2016) N. J. Proudfoot   SCIENCE

XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits

(2016) Hai Fang et al.   Genome Medicine

The end of the message: multiple protein–RNA interactions define the mRNA polyadenylation site

(2015) Yongsheng Shi et al.   GENES & DEVELOPMENT

Effects of Transcription Elongation Rate and Xrn2 Exonuclease Activity on RNA Polymerase II Termination Suggest Widespread Kinetic Competition

(2015) Nova Fong et al.   MOLECULAR CELL

Disruption of DNA-methylation-dependent long gene repression in Rett syndrome

(2015) Harrison W. Gabel et al.   NATURE

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

CGAT: computational genomics analysis toolkit

(2014) D. Sims et al.   BIOINFORMATICS

RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites

(2014) Jesse M. Engreitz et al.   CELL

Competition between Pre-mRNAs for the Splicing Machinery Drives Global Regulation of Splicing

(2013) Elizabeth M. Munding et al.   MOLECULAR CELL

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

Alternative cleavage and polyadenylation: extent, regulation and function

(2013) Ran Elkon et al.   NATURE REVIEWS GENETICS

Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality

(2013) Evgenia Ntini et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

SVD Identifies Transcript Length Distribution Functions from DNA Microarray Data and Reveals Evolutionary Forces Globally Affecting GBM Metabolism

(2013) Nicolas M. Bertagnolli et al.   PLoS One

Minor introns are embedded molecular switches regulated by highly unstable U6atac snRNA

(2013) Ihab Younis et al.   eLife

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data

(2012) Jianxing Feng et al.   BIOINFORMATICS

Origin and evolution of spliceosomal introns

(2012) Igor B Rogozin et al.   Biology Direct

U1 snRNP Determines mRNA Length and Regulates Isoform Expression

(2012) Michael G. Berg et al.   CELL

A quantitative atlas of polyadenylation in five mammals

(2012) Adnan Derti et al.   GENOME RESEARCH

Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation

(2012) C. Yao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons

(2011) S. Gelfman et al.   GENOME RESEARCH

Induction of Antagonistic Soluble Decoy Receptor Tyrosine Kinases by Intronic PolyA Activation

(2011) Sandra Vorlová et al.   MOLECULAR CELL

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

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation

(2010) Daisuke Kaida et al.   NATURE

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

RNA and Disease

(2009) Thomas A. Cooper et al.   CELL

U1-independent pre-mRNA splicing contributes to the regulation of alternative splicing

(2009) Kazuhiro Fukumura et al.   NUCLEIC ACIDS RESEARCH

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Longer First Introns Are a General Property of Eukaryotic Gene Structure

(2008) Keith R. Bradnam et al.   PLoS One

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

(2008) L. Dolken et al.   RNA

Where Do Introns Come From?

(2008) Francesco Catania et al.   PLOS BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY