Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals

(2018) Aniek C. Bouwman et al.   NATURE GENETICS

Gene expression analysis of blood, liver, and muscle in cattle divergently selected for high and low residual feed intake1

(2017) M. Khansefid et al.   JOURNAL OF ANIMAL SCIENCE

lmerTest Package: Tests in Linear Mixed Effects Models

(2017) Alexandra Kuznetsova et al.   Journal of Statistical Software

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Annotation-free quantification of RNA splicing using LeafCutter

(2017) Yang I. Li et al.   NATURE GENETICS

Genome-wide identification of splicing QTLs in the human brain and their enrichment among schizophrenia-associated loci

(2017) Atsushi Takata et al.   Nature Communications

Genome-wide comparative analyses of correlated and uncorrelated phenotypes identify major pleiotropic variants in dairy cattle

(2017) Ruidong Xiang et al.   Scientific Reports

Rapid Discovery of De Novo Deleterious Mutations in Cattle Enhances the Value of Livestock as Model Species

(2017) E. Bourneuf et al.   Scientific Reports

Exploiting biological priors and sequence variants enhances QTL discovery and genomic prediction of complex traits

(2016) I. M. MacLeod et al.   BMC GENOMICS

Detailed phenotyping identifies genes with pleiotropic effects on body composition

(2016) Sunduimijid Bolormaa et al.   BMC GENOMICS

Identification of context-dependent expression quantitative trait loci in whole blood

(2016) Daria V Zhernakova et al.   NATURE GENETICS

RNA splicing is a primary link between genetic variation and disease

(2016) Yang I. Li et al.   SCIENCE

Cross-platform normalization of microarray and RNA-seq data for machine learning applications

(2016) Jeffrey A. Thompson et al.   PeerJ

Sequence-based Association Analysis Reveals an MGST1 eQTL with Pleiotropic Effects on Bovine Milk Composition

(2016) Mathew D. Littlejohn et al.   Scientific Reports

Alternative Splicing QTLs in European and African Populations

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

Extensive variation between tissues in allele specific expression in an outbred mammal

(2015) Amanda J. Chamberlain et al.   BMC GENOMICS

Bovine chromosomal regions affecting rheological traits in acid-induced skim milk gels

(2015) M. Glantz et al.   JOURNAL OF DAIRY SCIENCE

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

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Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

(2015) Leif Andersson et al.   GENOME BIOLOGY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

A new approach for efficient genotype imputation using information from relatives

(2014) Mehdi Sargolzaei et al.   BMC GENOMICS

Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle

(2014) Hans D Daetwyler et al.   NATURE GENETICS

A Multi-Trait, Meta-analysis for Detecting Pleiotropic Polymorphisms for Stature, Fatness and Reproduction in Beef Cattle

(2014) Sunduimijid Bolormaa et al.   PLoS Genetics

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

A Statistical Framework for Joint eQTL Analysis in Multiple Tissues

(2013) Timothée Flutre et al.   PLoS Genetics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Genome-wide association analysis for quantitative trait loci influencing Warner-Bratzler shear force in five taurine cattle breeds

(2012) M. C. McClure et al.   ANIMAL GENETICS

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

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

Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels

(2012) M. Erbe et al.   JOURNAL OF DAIRY SCIENCE

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

The future of livestock breeding: genomic selection for efficiency, reduced emissions intensity, and adaptation

(2012) Ben J. Hayes et al.   TRENDS IN GENETICS

Global gene expression profiling reveals genes expressed differentially in cattle with high and low residual feed intake

(2011) Y. Chen et al.   ANIMAL GENETICS

In-depth annotation of SNPs arising from resequencing projects using NGS-SNP

(2011) J. R. Grant et al.   BIOINFORMATICS

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS