Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels

Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands’

(2014) Patrick Deelen et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Guidelines for investigating causality of sequence variants in human disease

(2014) D. G. MacArthur et al.   NATURE

Whole-genome sequence variation, population structure and demographic history of the Dutch population

(2014) Laurent C Francioli et al.   NATURE GENETICS

Heritability and genomics of gene expression in peripheral blood

(2014) Fred A Wright et al.   NATURE GENETICS

Allelic Expression of Deleterious Protein-Coding Variants across Human Tissues

(2014) Kimberly R. Kukurba et al.   PLoS Genetics

Reliable Identification of Genomic Variants from RNA-Seq Data

(2013) Robert Piskol et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Analysis of Allele-Specific Expression in Mouse Liver by RNA-Seq: A Comparison With Cis -eQTL Identified Using Genetic Linkage

(2013) Sandrine Lagarrigue et al.   GENETICS

Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data

(2013) B. L. Browning et al.   GENETICS

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

(2013) A. Battle et al.   GENOME RESEARCH

Genome-wide association studies identify several new loci associated with pigmentation traits and skin cancer risk in European Americans

(2013) Mingfeng Zhang et al.   HUMAN MOLECULAR GENETICS

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Systematic identification of trans eQTLs as putative drivers of known disease associations

(2013) Harm-Jan Westra et al.   NATURE GENETICS

Developments in FINDbase worldwide database for clinically relevant genomic variation allele frequencies

(2013) Petros Papadopoulos et al.   NUCLEIC ACIDS RESEARCH

ClinVar: public archive of relationships among sequence variation and human phenotype

(2013) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

DeepSAGE Reveals Genetic Variants Associated with Alternative Polyadenylation and Expression of Coding and Non-coding Transcripts

(2013) Daria V. Zhernakova et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Extremely low-coverage sequencing and imputation increases power for genome-wide association studies

(2012) Bogdan Pasaniuc et al.   NATURE GENETICS

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

Unraveling the Regulatory Mechanisms Underlying Tissue-Dependent Genetic Variation of Gene Expression

(2012) Jingyuan Fu et al.   PLoS Genetics

Epistatic Selection between Coding and Regulatory Variation in Human Evolution and Disease

(2011) Tuuli Lappalainen et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button

(2011) Morris A Swertz et al.   BMC BIOINFORMATICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Genotype Imputation with Thousands of Genomes

(2011) Bryan Howie et al.   G3-Genes Genomes Genetics

The Architecture of Gene Regulatory Variation across Multiple Human Tissues: The MuTHER Study

(2011) Alexandra C. Nica et al.   PLoS Genetics

Trans-eQTLs Reveal That Independent Genetic Variants Associated with a Complex Phenotype Converge on Intermediate Genes, with a Major Role for the HLA

(2011) Rudolf S. N. Fehrmann et al.   PLoS Genetics

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Multiple common variants for celiac disease influencing immune gene expression

(2010) Patrick C A Dubois et al.   NATURE GENETICS

Genome-wide allele-specific analysis: insights into regulatory variation

(2010) Tomi Pastinen   NATURE REVIEWS GENETICS

Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS

(2010) Dan L. Nicolae et al.   PLoS Genetics

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

(2009) Jacob F. Degner et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing

(2009) Graham A. Heap et al.   HUMAN MOLECULAR GENETICS

Genetic variation in the prostate stem cell antigen gene PSCA confers susceptibility to urinary bladder cancer

(2009) Xifeng Wu et al.   NATURE GENETICS

Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner

(2009) A. S. Dimas et al.   SCIENCE

Genetic variation in PSCA is associated with susceptibility to diffuse-type gastric cancer

(2008) Hiromi Sakamoto et al.   NATURE GENETICS