Assessment of the Impact of Using a Reference Transcriptome in Mapping Short RNA-Seq Reads

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

(2014) Shanrong Zhao et al.   PLoS One

Grape RNA-Seq analysis pipeline environment

(2013) D. G. Knowles et al.   BIOINFORMATICS

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

Evaluation of Alignment Algorithms for Discovery and Identification of Pathogens Using RNA-Seq

(2013) Ivan Borozan et al.   PLoS One

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

OSA: a fast and accurate alignment tool for RNA-Seq

(2012) Jun Hu et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Transcriptome analysis using next-generation sequencing

(2012) Kai-Oliver Mutz et al.   CURRENT OPINION IN BIOTECHNOLOGY

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensivein silicoassessment of RNA-seq experiments

(2012) Nagarjun Vijay et al.   MOLECULAR ECOLOGY

Knowledge-Based Reconstruction of mRNA Transcripts with Short Sequencing Reads for Transcriptome Research

(2012) Junhee Seok et al.   PLoS One

Microarrays, deep sequencing and the true measure of the transcriptome

(2011) John H Malone et al.   BMC BIOLOGY

RNA-seq: technical variability and sampling

(2011) Lauren M McIntyre et al.   BMC GENOMICS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Whole Transcriptome Sequencing Reveals Gene Expression and Splicing Differences in Brain Regions Affected by Alzheimer's Disease

(2011) Natalie A. Twine et al.   PLoS One

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

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