RNA-seq: impact of RNA degradation on transcript quantification

Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals

(2012) H. Tani et al.   GENOME RESEARCH

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

RNA degradation compromises the reliability of microRNA expression profiling

(2009) David Ibberson et al.   BMC BIOTECHNOLOGY

Reverse transcription-quantitative polymerase chain reaction: description of a RIN-based algorithm for accurate data normalization

(2009) Alexandre Ho-Pun-Cheung et al.   BMC MOLECULAR BIOLOGY

Gene expression in colorectal neoplasia: modifications induced by tissue ischaemic time and tissue handling protocol

(2009) Susan E Bray et al.   HISTOPATHOLOGY

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

Mapping accessible chromatin regions using Sono-Seq

(2009) R. K. Auerbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

lumi: a pipeline for processing Illumina microarray

(2008) P. Du et al.   BIOINFORMATICS

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS