Discover hidden splicing variations by mapping personal transcriptomes to personal genomes

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

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

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

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

Tissue-Specific Effects of Genetic and Epigenetic Variation on Gene Regulation and Splicing

(2015) Maria Gutierrez-Arcelus et al.   PLoS Genetics

RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations

(2014) Steven C. Munger et al.   GENETICS

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

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

(2013) A. Battle et al.   GENOME RESEARCH

Functional implications of splicing polymorphisms in the human genome

(2013) Yerbol Z. Kurmangaliyev et al.   HUMAN MOLECULAR GENETICS

A systemic sclerosis and systemic lupus erythematosus pan-meta-GWAS reveals new shared susceptibility loci

(2013) Jose-Ezequiel Martin et al.   HUMAN MOLECULAR GENETICS

Molecular Effects of Autoimmune-Risk Promoter Polymorphisms on Expression, Exon Choice, and Translational Efficiency of Interferon Regulatory Factor 5

(2013) Daniel N. Clark et al.   JOURNAL OF INTERFERON AND CYTOKINE RESEARCH

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Analysis and design of RNA sequencing experiments for identifying RNA editing and other single-nucleotide variants

(2013) J.-H. Lee et al.   RNA

GLiMMPS: Robust statistical model for regulatory variation of alternative splicing using RNA-seq data

(2013) Keyan Zhao et al.   GENOME BIOLOGY

Four Promoters of IRF5 Respond Distinctly to Stimuli and are Affected by Autoimmune-Risk Polymorphisms

(2013) Daniel N. Clark et al.   Frontiers in Immunology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes

(2012) Darren A. Cusanovich et al.   HUMAN MOLECULAR GENETICS

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

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

(2012) Shihao Shen et al.   NUCLEIC ACIDS RESEARCH

First Exon Length Controls Active Chromatin Signatures and Transcription

(2012) Nicole I. Bieberstein et al.   Cell Reports

Context-dependent robustness to 5′ splice site polymorphisms in human populations

(2011) Zhi-xiang Lu et al.   HUMAN MOLECULAR GENETICS

Genome-wide association and linkage identify modifier loci of lung disease severity in cystic fibrosis at 11p13 and 20q13.2

(2011) Fred A Wright et al.   NATURE GENETICS

Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure

(2011) Louise V Wain et al.   NATURE GENETICS

GWASdb: a database for human genetic variants identified by genome-wide association studies

(2011) Mulin Jun Li et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Association of Familial Late-Onset Alzheimer's Disease Replicates BIN1 and CLU and Nominates CUGBP2 in Interaction with APOE

(2011) Ellen M. Wijsman et al.   PLoS Genetics

Genetic variation of pre-mRNA alternative splicing in human populations

(2011) Zhi-Xiang Lu et al.   Wiley Interdisciplinary Reviews-RNA

Genome-wide association study identifies novel loci for plasma levels of protein C: the ARIC study

(2010) W. Tang et al.   BLOOD

RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression

(2010) E. Lalonde et al.   GENOME RESEARCH

The novel and independent association between single-point SNP of NPHP4 gene and renal function in non-diabetic Japanese population: the Takahata study

(2010) Tsuneo Konta et al.   JOURNAL OF HUMAN GENETICS

New Insights into the Role of RNase L in Innate Immunity

(2010) Arindam Chakrabarti et al.   JOURNAL OF INTERFERON AND CYTOKINE RESEARCH

A BRCA1 promoter variant (rs11655505) and breast cancer risk

(2010) P. Verderio et al.   JOURNAL OF MEDICAL GENETICS

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

Genome-wide association study identifies a locus at 7p15.2 associated with endometriosis

(2010) Jodie N Painter et al.   NATURE GENETICS

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

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

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

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

(2009) Jacob F. Degner et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The pathobiology of splicing

(2009) Amanda J Ward et al.   JOURNAL OF PATHOLOGY

Validating, augmenting and refining genome-wide association signals

(2009) John P. A. Ioannidis et al.   NATURE REVIEWS GENETICS

Fine-Scale Variation and Genetic Determinants of Alternative Splicing across Individuals

(2009) Jasmin Coulombe-Huntington et al.   PLoS Genetics

Association of interferon regulatory factor 5 haplotypes, similar to that found in systemic lupus erythematosus, in a large subgroup of patients with rheumatoid arthritis

(2008) Rebeca Dieguez-Gonzalez et al.   ARTHRITIS AND RHEUMATISM

ICA69 is a novel Rab2 effector regulating ER–Golgi trafficking in insulinoma cells

(2008) Laura Buffa et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

A 5′ Splice Site Enhances the Recruitment of Basal Transcription Initiation Factors In Vivo

(2008) Christian Kroun Damgaard et al.   MOLECULAR CELL

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Genome-wide analysis of transcript isoform variation in humans

(2008) Tony Kwan et al.   NATURE GENETICS

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

Splicing regulation: From a parts list of regulatory elements to an integrated splicing code

(2008) Z. Wang et al.   RNA