A survey of polymorphisms detected from sequences of popular beef breeds1,2,3

Estimation of breed-specific heterosis effects for birth, weaning, and yearling weight in cattle1

(2015) L. N. Schiermiester et al.   JOURNAL OF ANIMAL SCIENCE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Large-effect pleiotropic or closely linked QTL segregate within and across ten US cattle breeds

(2014) Mahdi Saatchi et al.   BMC GENOMICS

Balancing Selection Is the Main Force Shaping the Evolution of Innate Immunity Genes

(2014) A. Ferrer-Admetlla et al.   JOURNAL OF IMMUNOLOGY

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

(2014) Hans D Daetwyler et al.   NATURE GENETICS

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Multi-Tissue Omics Analyses Reveal Molecular Regulatory Networks for Puberty in Composite Beef Cattle

(2014) Angela Cánovas et al.   PLoS One

Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity

(2013) Kyung-Tai Lee et al.   BMC GENOMICS

Whole genome sequencing of Gir cattle for identifying polymorphisms and loci under selection

(2013) Xiaoping Liao et al.   GENOME

Prediction of heterosis using genome-wide SNP-marker data: application to egg production traits in white Leghorn crosses

(2013) E N Amuzu-Aweh et al.   HEREDITY

Massively parallel sequencing of Chikso (Korean brindle cattle) to discover genome-wide SNPs and InDels

(2013) Jung-Woo Choi et al.   MOLECULES AND CELLS

Large-scale gene function analysis with the PANTHER classification system

(2013) Huaiyu Mi et al.   Nature Protocols

Genotyping-by-Sequencing (GBS): A Novel, Efficient and Cost-Effective Genotyping Method for Cattle Using Next-Generation Sequencing

(2013) Marcos De Donato et al.   PLoS One

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

(2012) Pablo Cingolani et al.   FLY

Accuracy of genomic breeding values in multibreed beef cattle populations derived from deregressed breeding values and phenotypes1,2

(2012) K. L. Weber et al.   JOURNAL OF ANIMAL SCIENCE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle

(2012) D. M. Larkin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genetic prehistory of southern Africa

(2012) Joseph K. Pickrell et al.   Nature Communications

Population Genomic Scan for Candidate Signatures of Balancing Selection to Guide Antigen Characterization in Malaria Parasites

(2012) Alfred Amambua-Ngwa et al.   PLoS Genetics

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery

(2011) Paul Stothard et al.   BMC GENOMICS

Partial-genome evaluation of postweaning feed intake and efficiency of crossbred beef cattle1,2

(2011) W. M. Snelling et al.   JOURNAL OF ANIMAL SCIENCE

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

(2011) Mark A DePristo et al.   NATURE GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Characterization of biological types of cattle (Cycle VIII): Carcass, yield, and longissimus palatability traits12

(2010) T. L. Wheeler et al.   JOURNAL OF ANIMAL SCIENCE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Genetic evaluation of Angus cattle for carcass marbling using ultrasound and genomic indicators1

(2009) M. D. MacNeil et al.   JOURNAL OF ANIMAL SCIENCE

Targets of Balancing Selection in the Human Genome

(2009) A. M. Andres et al.   MOLECULAR BIOLOGY AND EVOLUTION

Development and Characterization of a High Density SNP Genotyping Assay for Cattle

(2009) Lakshmi K. Matukumalli et al.   PLoS One

Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery

(2009) Sebastian H Eck et al.   GENOME BIOLOGY

A whole-genome assembly of the domestic cow, Bos taurus

(2009) Aleksey V Zimin et al.   GENOME BIOLOGY

Invited Review: Reliability of genomic predictions for North American Holstein bulls

(2008) P.M. VanRaden et al.   JOURNAL OF DAIRY SCIENCE

Natural selection has driven population differentiation in modern humans

(2008) Luis B Barreiro et al.   NATURE GENETICS