Estimation of alternative splicing isoform frequencies from RNA-Seq data

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Optimization of de novo transcriptome assembly from next-generation sequencing data

(2010) Y. Surget-Groba et al.   GENOME RESEARCH

Transcribed dark matter: meaning or myth?

(2010) C. P. Ponting et al.   HUMAN MOLECULAR GENETICS

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

Alternative expression analysis by RNA sequencing

(2010) Malachi Griffith et al.   NATURE METHODS

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

Identifiability of isoform deconvolution from junction arrays and RNA-Seq

(2009) David Hiller et al.   BIOINFORMATICS

De novo transcriptome assembly with ABySS

(2009) I. Birol et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

Resolving deconvolution ambiguity in gene alternative splicing

(2009) Yiyuan She et al.   BMC BIOINFORMATICS

Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays

(2009) Joshua S Bloom et al.   BMC GENOMICS

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

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

(2009) Ben Langmead et al.   GENOME 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

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

(2008) M. Sultan et al.   SCIENCE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays

(2008) Miguel A Anton et al.   GENOME BIOLOGY