A nested parallel experiment demonstrates differences in intensity-dependence between RNA-seq and microarrays

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance

(2014) Charles Wang et al.   NATURE BIOTECHNOLOGY

Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

(2014) Shanrong Zhao et al.   PLoS One

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

(2014) Charity W Law et al.   GENOME BIOLOGY

Iron sensing and regulation in Saccharomyces cerevisiae: Ironing out the mechanistic details

(2013) Caryn E Outten et al.   CURRENT OPINION IN MICROBIOLOGY

Design and Analysis of Bar-seq Experiments

(2013) David G. Robinson et al.   G3-Genes Genomes Genetics

Length bias correction for RNA-seq data in gene set analyses

(2011) Liyan Gao et al.   BIOINFORMATICS

Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling

(2011) Paweł P. Łabaj et al.   BIOINFORMATICS

Impact of the spotted microarray preprocessing method on fold-change compression and variance stability

(2011) Jérôme Ambroise et al.   BMC BIOINFORMATICS

RNA-seq: technical variability and sampling

(2011) Lauren M McIntyre et al.   BMC GENOMICS

Gene set enrichment analysis: performance evaluation and usage guidelines

(2011) J.-H. Hung et al.   BRIEFINGS IN BIOINFORMATICS

The Response to Heat Shock and Oxidative Stress in Saccharomyces cerevisiae

(2011) K. A. Morano et al.   GENETICS

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim

(2010) Shaohua Zeng et al.   BMC GENOMICS

System-Level Analysis of Genes and Functions Affecting Survival During Nutrient Starvation in Saccharomyces cerevisiae

(2010) D. Gresham et al.   GENETICS

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

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

A general modular framework for gene set enrichment analysis

(2009) Marit Ackermann et al.   BMC BIOINFORMATICS

Quantitative miRNA expression analysis: Comparing microarrays with next-generation sequencing

(2009) H. Willenbrock et al.   RNA

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

(2008) Peter A. C. 't Hoen et al.   NUCLEIC ACIDS RESEARCH