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

Accurate Estimation of Expression Levels of Homologous Genes in RNA-seq Experiments

(2011) Bogdan Paşaniuc et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Inference of Isoforms from Short Sequence Reads

(2011) Jianxing Feng et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq

(2010) Zhengpeng Wu et al.   BIOINFORMATICS

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

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Detection of splice junctions from paired-end RNA-seq data by SpliceMap

(2010) K. F. Au et al.   NUCLEIC ACIDS RESEARCH

Statistical inferences for isoform expression in RNA-Seq

(2009) Hui Jiang et al.   BIOINFORMATICS

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

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

Why the need for qPCR publication guidelines?—The case for MIQE

(2009) Stephen A. Bustin   METHODS

Optimal spliced alignments of short sequence reads

(2008) F. De Bona et al.   BIOINFORMATICS

Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing

(2008) Ryan D. Morin et al.   BIOTECHNIQUES

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

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

A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE

(2008) Geoffrey J. Faulkner et al.   GENOMICS

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

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE