Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries

SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export

(2016) Michaela Müller-McNicoll et al.   GENES & DEVELOPMENT

3’UTR Shortening Potentiates MicroRNA-Based Repression of Pro-differentiation Genes in Proliferating Human Cells

(2016) Yonit Hoffman et al.   PLoS Genetics

3USS: a web server for detecting alternative 3′UTRs from RNA-seq experiments

(2015) Loredana Le Pera et al.   BIOINFORMATICS

Global estimation of the 3′ untranslated region landscape using RNA sequencing

(2015) MinHyeok Kim et al.   METHODS

A change-point model for identifying 3′UTR switching by next-generation RNA sequencing

(2014) Wei Wang et al.   BIOINFORMATICS

IsoSCM: improved and alternative 3′ UTR annotation using multiple change-point inference

(2014) Sol Shenker et al.   RNA

Dynamic expression of 3′ UTRs revealed by Poisson hidden Markov modeling of RNA-Seq: Implications in gene expression profiling

(2013) Jun Lu et al.   GENE

Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression

(2013) S. Lianoglou et al.   GENES & DEVELOPMENT

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Alternative cleavage and polyadenylation: extent, regulation and function

(2013) Ran Elkon et al.   NATURE REVIEWS GENETICS

Genome-wide maps of polyadenylation reveal dynamic mRNA 3'-end formation in mammalian cell lineages

(2013) L. Wang et al.   RNA

Alternative cleavage and polyadenylation: the long and short of it

(2013) Bin Tian et al.   TRENDS IN BIOCHEMICAL SCIENCES

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Shortening of 3′UTRs Correlates with Poor Prognosis in Breast and Lung Cancer

(2012) Antonio Lembo et al.   PLoS One

Ending the message: poly(A) signals then and now

(2011) N. J. Proudfoot   GENES & DEVELOPMENT

Differential genome-wide profiling of tandem 3' UTRs among human breast cancer and normal cells by high-throughput sequencing

(2011) Y. Fu et al.   GENOME RESEARCH

Transcriptional activity regulates alternative cleavage and polyadenylation

(2011) Z. Ji et al.   Molecular Systems Biology

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

(2009) Christine Mayr et al.   CELL

Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development

(2009) Z. Ji et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites

(2008) R. Sandberg et al.   SCIENCE