Union Exon Based Approach for RNA-Seq Gene Quantification: To Be or Not to Be?

IRcall and IRclassifier: two methods for flexible detection of intron retention events from RNA-Seq data

(2015) Yang Bai et al.   BMC GENOMICS

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

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

(2015) Shanrong Zhao et al.   BMC GENOMICS

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

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

(2015) et al.   SCIENCE

Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data

(2015) Alexander Kanitz et al.   GENOME BIOLOGY

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

(2014) S. Anders et al.   BIOINFORMATICS

Computational approaches for isoform detection and estimation: good and bad news

(2014) Claudia Angelini et al.   BMC BIOINFORMATICS

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

(2014) Benjamín Sigurgeirsson et al.   BMC GENOMICS

Combined analysis of exon splicing and genome wide polymorphism data predict schizophrenia risk loci

(2014) Christopher Oldmeadow et al.   JOURNAL OF PSYCHIATRIC RESEARCH

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

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

The emerging era of genomic data integration for analyzing splice isoform function

(2014) Hong-Dong Li et al.   TRENDS IN GENETICS

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

A comparison of methods for differential expression analysis of RNA-seq data

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

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

(2013) James Dominic Mills et al.   CURRENT GENOMICS

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Alignment Algorithms for Discovery and Identification of Pathogens Using RNA-Seq

(2013) Ivan Borozan et al.   PLoS One

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

Estimation of alternative splicing isoform frequencies from RNA-Seq data

(2011) Marius Nicolae et al.   Algorithms for Molecular Biology

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu 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

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

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

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

Differential Clathrin Binding and Subcellular Localization of OCRL1 Splice Isoforms

(2009) Rawshan Choudhury et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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