Analysis and design of RNA sequencing experiments for identifying isoform regulation

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

(2010) T. D. Wu et al.   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

Alternative expression analysis by RNA sequencing

(2010) Malachi Griffith et al.   NATURE METHODS

Molecular mechanisms of eukaryotic pre-mRNA 3′ end processing regulation

(2010) Stefania Millevoi et al.   NUCLEIC ACIDS RESEARCH

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

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

A Statistical Method for the Detection of Alternative Splicing Using RNA-Seq

(2010) Liguo Wang et al.   PLoS One

Global and unbiased detection of splice junctions from RNA-seq data

(2010) Adam Ameur et al.   GENOME BIOLOGY

Modeling non-uniformity in short-read rates in RNA-Seq data

(2010) Jun Li et al.   GENOME BIOLOGY

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

RNA and Disease

(2009) Thomas A. Cooper et al.   CELL

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

(2009) Christine Mayr et al.   CELL

Cancer-associated regulation of alternative splicing

(2009) Julian P Venables et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Splice site strength–dependent activity and genetic buffering by poly-G runs

(2009) Xinshu Xiao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A physical and functional link between splicing factors promotes pre-mRNA 3′ end processing

(2009) Stefania Millevoi et al.   NUCLEIC ACIDS RESEARCH

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing

(2009) M. Yassour et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Identification of Alternative Splicing Markers for Breast Cancer

(2008) J. P. Venables et al.   CANCER RESEARCH

The RNA-binding Protein CUGBP1 Regulates Stability of Tumor Necrosis Factor mRNA in Muscle Cells

(2008) Libin Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

The M2 splice isoform of pyruvate kinase is important for cancer metabolism and tumour growth

(2008) Heather R. Christofk et al.   NATURE

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites

(2008) R. Sandberg et al.   SCIENCE

Annotating genomes with massive-scale RNA sequencing

(2008) France Denoeud et al.   GENOME BIOLOGY