Annotation-free quantification of RNA splicing using LeafCutter

Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins

(2016) Yun-Hua Esther Hsiao et al.   GENOME RESEARCH

RNA splicing is a primary link between genetic variation and disease

(2016) Yang I. Li et al.   SCIENCE

Survey of the Heritability and Sparse Architecture of Gene Expression Traits across Human Tissues

(2016) Heather E. Wheeler et al.   PLoS Genetics

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

(2016) Jorge Vaquero-Garcia et al.   eLife

Alternative Splicing QTLs in European and African Populations

(2015) Halit Ongen et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Fast and efficient QTL mapper for thousands of molecular phenotypes

(2015) Halit Ongen et al.   BIOINFORMATICS

WASP: allele-specific software for robust molecular quantitative trait locus discovery

(2015) Bryce van de Geijn et al.   NATURE METHODS

Discover hidden splicing variations by mapping personal transcriptomes to personal genomes

(2015) Shayna Stein et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Rob Patro et al.   NATURE BIOTECHNOLOGY

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

Identification of genetic variants associated with alternative splicing using sQTLseekeR

(2014) Jean Monlong et al.   Nature Communications

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

(2013) Ning Leng et al.   BIOINFORMATICS

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming

(2013) Hong Han et al.   NATURE

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds

(2013) Jie Wu et al.   NUCLEIC ACIDS RESEARCH

Drift and conservation of differential exon usage across tissues in primate species

(2013) A. Reyes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

(2013) Magali Soumillon et al.   Cell Reports

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

(2012) H. Tilgner et al.   GENOME RESEARCH

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

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

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Association of CD40 with rheumatoid arthritis confirmed in a large UK case-control study

(2009) G. Orozco et al.   ANNALS OF THE RHEUMATIC DISEASES

Regulation of Vertebrate Nervous System Alternative Splicing and Development by an SR-Related Protein

(2009) John A. Calarco et al.   CELL