DAFS: a data-adaptive flag method for RNA-sequencing data to differentiate genes with low and high expression

Quantitative assessment of single-cell RNA-sequencing methods

(2013) Angela R Wu et al.   NATURE METHODS

Transcriptome-wide Regulation of Pre-mRNA Splicing and mRNA Localization by Muscleblind Proteins

(2012) Eric T. Wang et al.   CELL

RNA-sequence analysis of human B-cells

(2011) J. M. Toung et al.   GENOME RESEARCH

mRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain

(2010) P. Hammer et al.   GENOME RESEARCH

The transcriptional diversity of 25 Drosophila cell lines

(2010) L. Cherbas et al.   GENOME RESEARCH

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Changes in Transcript Abundance in Chlamydomonas reinhardtii following Nitrogen Deprivation Predict Diversion of Metabolism

(2010) R. Miller et al.   PLANT PHYSIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

An investigation into the population abundance distribution of mRNAs, proteins, and metabolites in biological systems

(2009) Chuan Lu et al.   BIOINFORMATICS

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

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

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE