Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle

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

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

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

The role of regulatory variation in complex traits and disease

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

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

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

(2015) et al.   SCIENCE

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

(2014) S. Anders et al.   BIOINFORMATICS

Allele-specific expression and eQTL analysis in mouse adipose tissue

(2014) Yehudit Hasin-Brumshtein et al.   BMC GENOMICS

A new approach for efficient genotype imputation using information from relatives

(2014) Mehdi Sargolzaei et al.   BMC GENOMICS

µ-Calpain, calpastatin, and growth hormone receptor genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in Angus cattle selected to increase minor haplotype and allele frequencies1,2,3

(2014) R. G. Tait et al.   JOURNAL OF ANIMAL SCIENCE

Estimation of genomic breeding values for residual feed intake in a multibreed cattle population1

(2014) M. Khansefid et al.   JOURNAL OF ANIMAL SCIENCE

Holstein-Friesian calves selected for divergence in residual feed intake during growth exhibited significant but reduced residual feed intake divergence in their first lactation

(2014) K.A. Macdonald et al.   JOURNAL OF DAIRY SCIENCE

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

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

Accuracy of prediction of genomic breeding values for residual feed intake and carcass and meat quality traits in Bos taurus, Bos indicus, and composite beef cattle1

(2013) S. Bolormaa et al.   JOURNAL OF ANIMAL SCIENCE

A new single nucleotide polymorphism in the calpastatin (CAST) gene associated with beef tenderness

(2013) J.H. Calvo et al.   MEAT SCIENCE

Genomic imprinting and parent-of-origin effects on complex traits

(2013) Heather A. Lawson et al.   NATURE REVIEWS GENETICS

Adipose and Muscle Tissue Gene Expression of Two Genes (NCAPG and LCORL) Located in a Chromosomal Region Associated with Cattle Feed Intake and Gain

(2013) Amanda K. Lindholm-Perry et al.   PLoS One

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

High throughput whole rumen metagenome profiling using untargeted massively parallel sequencing

(2012) Elizabeth M Ross et al.   BMC GENETICS

Accuracy of genomic predictions of residual feed intake and 250-day body weight in growing heifers using 625,000 single nucleotide polymorphism markers

(2012) J.E. Pryce et al.   JOURNAL OF DAIRY SCIENCE

A survey of tissue-specific genomic imprinting in mammals

(2012) Adam R. Prickett et al.   MOLECULAR GENETICS AND GENOMICS

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

(2011) Y. Chen et al.   ANIMAL GENETICS

Association, effects and validation of polymorphisms within the NCAPG - LCORL locus located on BTA6 with feed intake, gain, meat and carcass traits in beef cattle

(2011) Amanda K Lindholm-Perry et al.   BMC GENETICS

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

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

(2010) Tomi Pastinen   NATURE REVIEWS GENETICS

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals

(2009) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

LEPROT and LEPROTL1 cooperatively decrease hepatic growth hormone action in mice

(2009) Thierry Touvier et al.   JOURNAL OF CLINICAL INVESTIGATION

Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing

(2008) Ryan D. Morin et al.   BIOTECHNIQUES