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

A normalization strategy for comparing tag count data

(2012) Koji Kadota et al.   Algorithms for Molecular Biology

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Removing technical variability in RNA-seq data using conditional quantile normalization

(2012) K. D. Hansen et al.   BIOSTATISTICS

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Essential role of microphthalmia transcription factor for DNA replication, mitosis and genomic stability in melanoma

(2011) T Strub et al.   ONCOGENE

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell 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

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species

(2010) Song Liu et al.   NUCLEIC ACIDS RESEARCH

Should We Abandon the t-Test in the Analysis of Gene Expression Microarray Data: A Comparison of Variance Modeling Strategies

(2010) Marine Jeanmougin et al.   PLoS One

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

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

Consolidated strategy for the analysis of microarray spike-in data

(2008) Matthew N. McCall et al.   NUCLEIC ACIDS RESEARCH