Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms

Snakemake—a scalable bioinformatics workflow engine

(2018) Johannes Köster et al.   BIOINFORMATICS

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing

(2017) Julien Lagarde et al.   NATURE GENETICS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Highly accessible AU-rich regions in 3’ untranslated regions are hotspots for binding of regulatory factors

(2017) Mireya Plass et al.   PLoS Computational Biology

A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation

(2016) Andreas J. Gruber et al.   GENOME RESEARCH

The Ensembl gene annotation system

(2016) Bronwen L. Aken et al.   Database-The Journal of Biological Databases and Curation

Quantitative visualization of alternative exon expression from RNA-seq data

(2015) Yarden Katz et al.   BIOINFORMATICS

N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

(2015) Nian Liu et al.   NATURE

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

Ensembl Genomes 2016: more genomes, more complexity

(2015) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

RNA-seq: impact of RNA degradation on transcript quantification

(2014) Irene Gallego Romero et al.   BMC BIOLOGY

Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal

(2014) B. Lackford et al.   EMBO JOURNAL

Identification and consequences of miRNA–target interactions — beyond repression of gene expression

(2014) Jean Hausser et al.   NATURE REVIEWS GENETICS

APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals

(2014) Leiming You et al.   NUCLEIC ACIDS RESEARCH

Global 3′ UTR shortening has a limited effect on protein abundance in proliferating T cells

(2014) Andreas R. Gruber et al.   Nature Communications

IVT-seq reveals extreme bias in RNA sequencing

(2014) Nicholas F Lahens et al.   GENOME BIOLOGY

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

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

3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts

(2013) N. Spies et al.   GENOME RESEARCH

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

A quantitative atlas of polyadenylation in five mammals

(2012) Adnan Derti et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An in-depth map of polyadenylation sites in cancer

(2012) Yuefeng Lin et al.   NUCLEIC ACIDS RESEARCH

Genome-wide Analysis of Pre-mRNA 3′ End Processing Reveals a Decisive Role of Human Cleavage Factor I in the Regulation of 3′ UTR Length

(2012) Georges Martin et al.   Cell Reports

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

(2011) Ryan K. Dale et al.   BIOINFORMATICS

Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression

(2011) S. Kishore et al.   Briefings in Functional Genomics

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

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

(2009) Christine Mayr et al.   CELL

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

(2008) R. Sandberg et al.   SCIENCE