Optimizing Selection of the Reference Population for Genotype Imputation From Array to Sequence Variants

Identification of polymorphisms in the bovine collagenous lectins and their association with infectious diseases in cattle

(2018) R. S. Fraser et al.   IMMUNOGENETICS

Identification of key contributors in complex population structures

(2017) Markus Neuditschko et al.   PLoS One

GHap: an R package for genome-wide haplotyping

(2016) Yuri T. Utsunomiya et al.   BIOINFORMATICS

A combined coalescence gene-dropping tool for evaluating genomic selection in complex scenarios (ms2gs)

(2016) M. Pérez-Enciso et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

Reducing animal sequencing redundancy by preferentially selecting animals with low-frequency haplotypes

(2016) D.M. Bickhart et al.   JOURNAL OF DAIRY SCIENCE

Reference-based phasing using the Haplotype Reference Consortium panel

(2016) Po-Ru Loh et al.   NATURE GENETICS

Next-generation genotype imputation service and methods

(2016) Sayantan Das et al.   NATURE GENETICS

AlphaSim: Software for Breeding Program Simulation

(2016) Anne-Michelle Faux et al.   Plant Genome

Evaluation of measures of correctness of genotype imputation in the context of genomic prediction: a review of livestock applications

(2014) M. P. L. Calus et al.   Animal

Evaluation of variant identification methods for whole genome sequencing data in dairy cattle

(2014) Christine F Baes 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

Fast Principal Component Analysis of Large-Scale Genome-Wide Data

(2014) Gad Abraham et al.   PLoS One

Toward genomic prediction from whole-genome sequence data: impact of sequencing design on genotype imputation and accuracy of predictions

(2013) T Druet et al.   HEREDITY

Comparison of different methods for imputing genome-wide marker genotypes in Swedish and Finnish Red Cattle

(2013) P. Ma et al.   JOURNAL OF DAIRY SCIENCE

Detection of Haplotypes Associated with Prenatal Death in Dairy Cattle and Identification of Deleterious Mutations in GART, SHBG and SLC37A2

(2013) Sébastien Fritz et al.   PLoS One

Design of a Bovine Low-Density SNP Array Optimized for Imputation

(2012) Didier Boichard et al.   PLoS One

Performance of Genotype Imputation for Rare Variants Identified in Exons and Flanking Regions of Genes

(2011) Li Li et al.   PLoS One

Characteristics of linkage disequilibrium in North American Holsteins

(2010) Jarmila Bohmanova et al.   BMC GENOMICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Genotype imputation for genome-wide association studies

(2010) Jonathan Marchini et al.   NATURE REVIEWS GENETICS

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

QMSim: a large-scale genome simulator for livestock

(2009) M. Sargolzaei et al.   BIOINFORMATICS

Arachnomelia in Brown Swiss cattle maps to chromosome 5

(2009) Cord Drögemüller et al.   MAMMALIAN GENOME

Extent of Linkage Disequilibrium in Holstein Cattle in North America

(2008) M. Sargolzaei et al.   JOURNAL OF DAIRY SCIENCE