Salmon provides fast and bias-aware quantification of transcript expression

RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes

(2016) Avi Srivastava et al.   BIOINFORMATICS

Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation

(2016) Michael I Love et al.   NATURE BIOTECHNOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Polyester: simulating RNA-seq datasets with differential transcript expression

(2015) Alyssa C. Frazee et al.   BIOINFORMATICS

TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads

(2014) Naoki Nariai et al.   BMC GENOMICS

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

(2014) Katherine A. Hoadley et al.   CELL

Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data

(2014) J. J. Li et al.   GENOME RESEARCH

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

(2014) Rob Patro et al.   NATURE BIOTECHNOLOGY

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

(2013) Peter A C 't Hoen et al.   NATURE BIOTECHNOLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Human β Cell Transcriptome Analysis Uncovers lncRNAs That Are Tissue-Specific, Dynamically Regulated, and Abnormally Expressed in Type 2 Diabetes

(2012) Ignasi Morán et al.   Cell Metabolism

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Estimation of alternative splicing isoform frequencies from RNA-Seq data

(2011) Marius Nicolae et al.   Algorithms for Molecular Biology

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

Statistical Modeling of RNA-Seq Data

(2011) Julia Salzman et al.   STATISTICAL SCIENCE

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads

(2011) Ernest Turro et al.   GENOME BIOLOGY

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS