Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

A Study ofTP53RNA Splicing Illustrates Pitfalls of RNA-seq Methodology

(2016) Sunali Mehta et al.   CANCER RESEARCH

Molecular pathological classification of colorectal cancer

(2016) Mike F. Müller et al.   VIRCHOWS ARCHIV

Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data

(2015) Peipei Li et al.   BMC BIOINFORMATICS

The consensus molecular subtypes of colorectal cancer

(2015) Justin Guinney et al.   NATURE MEDICINE

Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype

(2014) Eric R. Paquet et al.   JNCI-Journal of the National Cancer Institute

Evaluation of the ability of adjuvant tamoxifen-benefit gene signatures to predict outcome of hormone-naive estrogen receptor-positive breast cancer patients treated with tamoxifen in the advanced setting

(2014) Anieta M. Sieuwerts et al.   Molecular Oncology

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

(2014)   NATURE BIOTECHNOLOGY

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

(2013) Y. Liao et al.   BIOINFORMATICS

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

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

(2013) Franck Rapaport et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

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

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

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

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Translating tumor biology into personalized treatment planning: analytical performance characteristics of the Oncotype DX®Colon Cancer Assay

(2011) Kim M Clark-Langone et al.   BMC CANCER

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

(2010) James H Bullard et al.   BMC BIOINFORMATICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

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