mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

RNA-seq: impact of RNA degradation on transcript quantification

(2014) Irene Gallego Romero et al.   BMC BIOLOGY

Detecting and correcting systematic variation in large-scale RNA sequencing data

(2014) Sheng Li et al.   NATURE BIOTECHNOLOGY

Sequencing Degraded RNA Addressed by 3' Tag Counting

(2014) Benjamín Sigurgeirsson et al.   PLoS One

NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data

(2013) Xinyun Ma et al.   BMC BIOINFORMATICS

Comparative analysis of RNA sequencing methods for degraded or low-input samples

(2013) Xian Adiconis et al.   NATURE METHODS

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Spatio-temporal transcriptome of the human brain

(2011) Hyo Jung Kang et al.   NATURE

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries

(2010) Lukas Habegger et al.   BIOINFORMATICS

Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq

(2010) Zhengpeng Wu et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome

(2010) T. R. Mercer et al.   GENOME RESEARCH

Diverse Endonucleolytic Cleavage Sites in the Mammalian Transcriptome Depend upon MicroRNAs, Drosha, and Additional Nucleases

(2010) Fedor V. Karginov et al.   MOLECULAR CELL

Expanding the MicroRNA Targeting Code: Functional Sites with Centered Pairing

(2010) Chanseok Shin et al.   MOLECULAR CELL

AREsite: a database for the comprehensive investigation of AU-rich elements

(2010) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

(2010) Oliver Stegle et al.   PLoS Computational Biology

Modeling non-uniformity in short-read rates in RNA-Seq data

(2010) Jun Li et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Many Pathways of RNA Degradation

(2009) Jonathan Houseley et al.   CELL

Effects of Antemortem and Postmortem Variables on Human Brain mRNA Quality: A BrainNet Europe Study

(2009) Pascal F. Durrenberger et al.   JOURNAL OF NEUROPATHOLOGY AND EXPERIMENTAL NEUROLOGY

Conserved principles of mammalian transcriptional regulation revealed by RNA half-life

(2009) Caroline C. Friedel et al.   NUCLEIC ACIDS RESEARCH

Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells

(2008) L. V. Sharova et al.   DNA RESEARCH

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS