RNA-Seq Gene Profiling - A Systematic Empirical Comparison

TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference

(2013) Naoki Nariai et al.   BIOINFORMATICS

NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data

(2013) Xinyun Ma et al.   BMC BIOINFORMATICS

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

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

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

(2013) Daehwan Kim 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

Tools for mapping high-throughput sequencing data

(2012) Nuno A. Fonseca et al.   BIOINFORMATICS

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Cole Trapnell et al.   Nature Protocols

Modelling and simulating generic RNA-Seq experiments with the flux simulator

(2012) Thasso Griebel et al.   NUCLEIC ACIDS RESEARCH

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

(2012) Intawat Nookaew et al.   NUCLEIC ACIDS RESEARCH

IQSeq: Integrated Isoform Quantification Analysis Based on Next-Generation Sequencing

(2012) Jiang Du et al.   PLoS One

IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data

(2011) Hyunsoo Kim et al.   BMC BIOINFORMATICS

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

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

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

Sorting nexin 6 interacts with breast cancer metastasis suppressor-1 and promotes transcriptional repression

(2010) José Rivera et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Caveolin 1 and Caveolin 2 are associated with breast cancer basal-like and triple-negative immunophenotype

(2008) S E Elsheikh et al.   BRITISH JOURNAL OF CANCER

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