A new view of transcriptome complexity and regulation through the lens of local splicing variations

Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators

(2015) Qinghong Yan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

hnRNP U protein is required for normal pre-mRNA splicing and postnatal heart development and function

(2015) Junqiang Ye et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global analysis of physical and functional RNA targets of hnRNP L reveals distinct sequence and epigenetic features of repressed and enhanced exons

(2015) Brian S. Cole et al.   RNA

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

Transcriptome analysis of distinct mouse strains reveals kinesin light chain-1 splicing as an amyloid-  accumulation modifier

(2014) T. Morihara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A circadian gene expression atlas in mammals: Implications for biology and medicine

(2014) Ray Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The human splicing code reveals new insights into the genetic determinants of disease

(2014) H. Y. Xiong et al.   SCIENCE

Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development

(2014) Jimena Giudice et al.   Nature Communications

The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation

(2014) Qin Li et al.   eLife

Transcriptome-Wide RNA Interaction Profiling Reveals Physical and Functional Targets of hnRNP L in Human T Cells

(2013) G. Shankarling et al.   MOLECULAR AND CELLULAR BIOLOGY

Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges

(2013) Michael T Lovci et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

U1 small nuclear ribonucleoprotein complex and RNA splicing alterations in Alzheimer's disease

(2013) B. Bai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

AVISPA: a web tool for the prediction and analysis of alternative splicing

(2013) Yoseph Barash et al.   GENOME BIOLOGY

Intron-centric estimation of alternative splicing from RNA-seq data

(2012) D. D. Pervouchine et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Neuronal regulation of pre-mRNA splicing by polypyrimidine tract binding proteins, PTBP1 and PTBP2

(2012) Niroshika Keppetipola et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain

(2012) D. D. Licatalosi et al.   GENES & DEVELOPMENT

Tissue-Specific Alternative Splicing Remodels Protein-Protein Interaction Networks

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

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

PSD-95 is post-transcriptionally repressed during early neural development by PTBP1 and PTBP2

(2012) Sika Zheng et al.   NATURE NEUROSCIENCE

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq

(2012) Yin Hu et al.   NUCLEIC ACIDS RESEARCH

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data

(2012) Shihao Shen et al.   NUCLEIC ACIDS RESEARCH

Alternative splicing networks regulated by signaling in human T cells

(2012) N. M. Martinez et al.   RNA

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

SpliceTrap: a method to quantify alternative splicing under single cellular conditions

(2011) Jie Wu et al.   BIOINFORMATICS

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

Deciphering the splicing code

(2010) Yoseph Barash 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

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

RNA and Disease

(2009) Thomas A. Cooper et al.   CELL

Calcium signaling in neurodegeneration

(2009) Philippe Marambaud et al.   Molecular Neurodegeneration

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

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

(2008) Qun Pan et al.   NATURE GENETICS

A General Definition and Nomenclature for Alternative Splicing Events

(2008) Michael Sammeth et al.   PLoS Computational Biology