Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

Tumor-Specific Isoform Switch of the Fibroblast Growth Factor Receptor 2 Underlies the Mesenchymal and Malignant Phenotypes of Clear Cell Renal Cell Carcinomas

(2013) Q. Zhao et al.   CLINICAL CANCER RESEARCH

Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention

(2012) K. Yap et al.   GENES & DEVELOPMENT

A quantitative atlas of polyadenylation in five mammals

(2012) Adnan Derti et al.   GENOME RESEARCH

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Contribution of Antibody-based Protein Profiling to the Human Chromosome-centric Proteome Project (C-HPP)

(2012) Linn Fagerberg et al.   JOURNAL OF PROTEOME RESEARCH

Comparative Proteomics Reveals a Significant Bias Toward Alternative Protein Isoforms with Conserved Structure and Function

(2012) I. Ezkurdia et al.   MOLECULAR BIOLOGY AND EVOLUTION

Tissue-Specific Alternative Splicing Remodels Protein-Protein Interaction Networks

(2012) Jonathan D. Ellis et al.   MOLECULAR CELL

Tissue-Specific Splicing of Disordered Segments that Embed Binding Motifs Rewires Protein Interaction Networks

(2012) Marija Buljan et al.   MOLECULAR CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2012) Thasso Griebel et al.   NUCLEIC ACIDS RESEARCH

APPRIS: annotation of principal and alternative splice isoforms

(2012) Jose Manuel Rodriguez et al.   NUCLEIC ACIDS RESEARCH

Perturbation of Myelin basic protein (Mbp) splice variant expression in developing rat cerebellum following perinatal exposure to methylmercury

(2012) Bhaja K. Padhi et al.   TOXICOLOGY LETTERS

Introns within Ribosomal Protein Genes Regulate the Production and Function of Yeast Ribosomes

(2011) Julie Parenteau et al.   CELL

Estimation of alternative splicing variability in human populations

(2011) M. Gonzalez-Porta et al.   GENOME RESEARCH

Cytoplasmic Intron Sequence-Retaining Transcripts Can Be Dendritically Targeted via ID Element Retrotransposons

(2011) Peter T. Buckley et al.   NEURON

Proofreading and spellchecking: A two-tier strategy for pre-mRNA splicing quality control

(2011) D. E. Egecioglu et al.   RNA

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

(2011) Ernest Turro et al.   GENOME BIOLOGY

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

A global map of human gene expression

(2010) Margus Lukk et al.   NATURE BIOTECHNOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

The European Nucleotide Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Global regulation of alternative splicing during myogenic differentiation

(2010) Christopher S. Bland et al.   NUCLEIC ACIDS RESEARCH

The adaptive significance of unproductive alternative splicing in primates

(2010) A. Skandalis et al.   RNA

Noisy Splicing Drives mRNA Isoform Diversity in Human Cells

(2010) Joseph K. Pickrell et al.   PLoS Genetics

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Estimating accuracy of RNA-Seq and microarrays with proteomics

(2009) Xing Fu et al.   BMC GENOMICS

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Computational analysis of splicing errors and mutations in human transcripts

(2008) Yerbol Z Kurmangaliyev et al.   BMC GENOMICS

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

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Cytoplasmic BKCa channel intron-containing mRNAs contribute to the intrinsic excitability of hippocampal neurons

(2008) T. J. Bell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA