EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

(2014) Rob Patro et al.   NATURE BIOTECHNOLOGY

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

(2014) Charity W Law et al.   GENOME BIOLOGY

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

Modelling and simulating generic RNA-Seq experiments with the flux simulator

(2012) Thasso Griebel et al.   NUCLEIC ACIDS RESEARCH

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

Accurate Estimation of Expression Levels of Homologous Genes in RNA-seq Experiments

(2011) Bogdan Paşaniuc et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Accurate quantification of transcriptome from RNA-Seq data by effective length normalization

(2010) Soohyun Lee et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Statistical inferences for isoform expression in RNA-Seq

(2009) Hui Jiang et al.   BIOINFORMATICS

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

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

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

(2008) M. Sultan et al.   SCIENCE