A comparison of per sample global scaling and per gene normalization methods for differential expression analysis of RNA-seq data

Goodness-of-Fit Tests and Model Diagnostics for Negative Binomial Regression of RNA Sequencing Data

(2015) Gu Mi et al.   PLoS One

New gene models and alternative splicing in the maize pathogen Colletotrichum graminicola revealed by RNA-Seq analysis

(2014) Ivo Schliebner et al.   BMC GENOMICS

Discovery of Novel Genes and Gene Isoforms by Integrating Transcriptomic and Proteomic Profiling from Mouse Liver

(2014) Peng Wu et al.   JOURNAL OF PROTEOME RESEARCH

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

A Comparative Study of Techniques for Differential Expression Analysis on RNA-Seq Data

(2014) Zong Hong Zhang et al.   PLoS One

A shared transcriptional program in early breast neoplasias despite genetic and clinical distinctions

(2014) Alayne L Brunner et al.   GENOME BIOLOGY

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

(2014) Charity W Law et al.   GENOME BIOLOGY

Reliable Identification of Genomic Variants from RNA-Seq Data

(2013) Robert Piskol et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

Gene-based single nucleotide polymorphism discovery in bovine muscle using next-generation transcriptomic sequencing

(2013) Anis Djari et al.   BMC GENOMICS

Comparison of software packages for detecting differential expression in RNA-seq studies

(2013) F. Seyednasrollah et al.   BRIEFINGS IN BIOINFORMATICS

Whole Genome Sequencing as a Diagnostic Test: Challenges and Opportunities

(2013) C. C. Chrystoja et al.   CLINICAL CHEMISTRY

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

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

(2013) Franck Rapaport et al.   GENOME BIOLOGY

A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data

(2012) Vanessa M. Kvam et al.   AMERICAN JOURNAL OF BOTANY

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

(2012) Marcel H. Schulz 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

CEDER: Accurate Detection of Differentially Expressed Genes by Combining Significance of Exons Using RNA-Seq

(2012) Lin Wan et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Technical considerations for functional sequencing assays

(2012) Weihua Zeng et al.   NATURE IMMUNOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

Sequencing technology does not eliminate biological variability

(2011) Kasper D Hansen et al.   NATURE BIOTECHNOLOGY

TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays

(2010) Henrik Bengtsson et al.   BMC BIOINFORMATICS

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

(2010) James H Bullard et al.   BMC BIOINFORMATICS

SNP discovery in the bovine milk transcriptome using RNA-Seq technology

(2010) Angela Cánovas et al.   MAMMALIAN GENOME

mRNA and microRNA quality control for RT-qPCR analysis

(2010) C. Becker et al.   METHODS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

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

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

RNA-seq: from technology to biology

(2009) Samuel Marguerat et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Next-Generation Sequencing: From Basic Research to Diagnostics

(2009) K. V. Voelkerding et al.   CLINICAL CHEMISTRY

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