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

Analysis of HIV-1 Expression Level and Sense of Transcription by High-Throughput Sequencing of the Infected Cell

(2011) G. Lefebvre et al.   JOURNAL OF VIROLOGY

Sequencing technology does not eliminate biological variability

(2011) Kasper D Hansen et al.   NATURE BIOTECHNOLOGY

Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarrays

(2011) Daniel Bottomly et al.   PLoS One

A Genome-Wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues

(2011) Athma A. Pai et al.   PLoS Genetics

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Gene expression profiling of human breast tissue samples using SAGE-Seq

(2010) Z. J. Wu et al.   GENOME RESEARCH

Subset Quantile Normalization Using Negative Control Features

(2010) Zhijin Wu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

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

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

Digital Gene Expression Signatures for Maize Development

(2010) A. L. Eveland et al.   PLANT PHYSIOLOGY

Polymorphic Cis- and Trans-Regulation of Human Gene Expression

(2010) Vivian G. Cheung et al.   PLOS BIOLOGY

Modeling non-uniformity in short-read rates in RNA-Seq data

(2010) Jun Li et al.   GENOME BIOLOGY

Cloud-scale RNA-sequencing differential expression analysis with Myrna

(2010) Ben Langmead et al.   GENOME BIOLOGY

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

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

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

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH