Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap

A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification

(2015) Shanrong Zhao et al.   BMC GENOMICS

Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential

(2015) Joshua D Welch et al.   BMC GENOMICS

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling

(2014) Wei Zhao et al.   BMC GENOMICS

Analysis of stranded information using an automated procedure for strand specific RNA sequencing

(2014) Benjamín Sigurgeirsson et al.   BMC GENOMICS

Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

(2014) Shanrong Zhao et al.   PLoS One

Assessment of the Impact of Using a Reference Transcriptome in Mapping Short RNA-Seq Reads

(2014) Shanrong Zhao   PLoS One

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Assessing the impact of human genome annotation choice on RNA-seq expression estimates

(2013) Po-Yen Wu et al.   BMC BIOINFORMATICS

Strand-Specific RNA-Seq Provides Greater Resolution of Transcriptome Profiling

(2013) James Dominic Mills et al.   CURRENT GENOMICS

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers

(2012) Shanker Kalyana-Sundaram et al.   CELL

Transcriptome analysis using next-generation sequencing

(2012) Kai-Oliver Mutz et al.   CURRENT OPINION IN BIOTECHNOLOGY

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

The GENCODE pseudogene resource

(2012) Baikang Pei et al.   GENOME BIOLOGY

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Microarrays, deep sequencing and the true measure of the transcriptome

(2011) John H Malone et al.   BMC BIOLOGY

Sequencing Illustrates the Transcriptional Response of Legionella pneumophila during Infection and Identifies Seventy Novel Small Non-Coding RNAs

(2011) Barbara A. Weissenmayer et al.   PLoS One

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Independent filtering increases detection power for high-throughput experiments

(2010) R. Bourgon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Expression of IL-24, an Activator of the JAK1/STAT3/SOCS3 Cascade, Is Enhanced in Inflammatory Bowel Disease

(2009) A. Andoh et al.   JOURNAL OF IMMUNOLOGY

Regulatory roles of natural antisense transcripts

(2009) Mohammad Ali Faghihi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Overlapping genes in the human and mouse genomes

(2008) Chaitanya R Sanna et al.   BMC GENOMICS

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