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List of works by Ben Hayes

A catalogue of novel bovine long noncoding RNA across 18 tissues

scientific article

A computationally efficient algorithm for genomic prediction using a Bayesian model

scientific article published on 30 April 2015

A genome map of divergent artificial selection between Bos taurus dairy cattle and Bos taurus beef cattle.

scientific article published on 5 December 2008

A genome wide association study for QTL affecting direct and maternal effects of stillbirth and dystocia in cattle.

scientific article

A hybrid expectation maximisation and MCMC sampling algorithm to implement Bayesian mixture model based genomic prediction and QTL mapping

scientific article

A linkage disequilibrium-based approach to position unmapped SNPs in crop species

scientific article published on 29 October 2021

A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers

scientific article published on 15 May 2008

A multi-trait Bayesian method for mapping QTL and genomic prediction

scientific article published on 24 March 2018

A multi-trait, meta-analysis for detecting pleiotropic polymorphisms for stature, fatness and reproduction in beef cattle.

scientific article

A novel predictor of multilocus haplotype homozygosity: comparison with existing predictors.

scientific article

A single nucleotide polymorphism on chromosome 10 is highly predictive for the polled phenotype in Australian Merino sheep.

scientific article published on 18 October 2011

A validated genome wide association study to breed cattle adapted to an environment altered by climate change.

scientific article

A validated genome-wide association study in 2 dairy cattle breeds for milk production and fertility traits using variable length haplotypes

article

Accelerating crop genetic gains with genomic selection

scientific article published on 19 December 2018

Accelerating improvement of livestock with genomic selection

scientific article

Accelerating wheat breeding for end-use quality with multi-trait genomic predictions incorporating near infrared and nuclear magnetic resonance-derived phenotypes.

scientific article published on 24 August 2017

Accounting for dominance to improve genomic evaluations of dairy cows for fertility and milk production traits

scientific article published on February 2016

Accuracy of direct genomic values in Holstein bulls and cows using subsets of SNP markers.

scientific article

Accuracy of genomic breeding values in multi-breed dairy cattle populations

scientific article

Accuracy of genomic prediction of complex traits in sugarcane

scientific article published in 2021

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

scientific article published on April 1, 2012

Accuracy of genomic selection using stochastic search variable selection in Australian Holstein Friesian dairy cattle

scientific article published in October 2009

Accuracy of genotype imputation based on random and selected reference sets in purebred and crossbred sheep populations and its effect on accuracy of genomic prediction.

scientific article

Accuracy of genotype imputation in sheep breeds.

scientific article published on 27 May 2011

Accuracy of imputation to whole-genome sequence data in Holstein Friesian cattle

scientific article

Accuracy of marker-assisted selection with single markers and marker haplotypes in cattle

scientific article published on 01 August 2007

Accuracy of pedigree and genomic predictions of carcass and novel meat quality traits in multi-breed sheep data assessed by cross-validation

scientific article

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 cattle.

scientific article published on 8 May 2013

Across-breed validation study confirms and identifies new loci associated with sexual precocity in Brahman and Nellore cattle

scientific article published on 14 August 2019

An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in [...]

scientific article (publication date: 24 April 2009)

An extensive resource of single nucleotide polymorphism markers associated with Atlantic salmon (Salmo salar) expressed sequences

article by Ben Hayes et al published May 2007 in Aquaculture

An independent validation association study of carcass quality, shear force, intramuscular fat percentage and omega-3 polyunsaturated fatty acid content with gene markers in Australian lamb.

scientific article

An initiator codon mutation in SDE2 causes recessive embryonic lethality in Holstein cattle.

scientific article published on 18 April 2018

Analysis of Polycerate Mutants Reveals the Evolutionary Co-option of HOXD1 for Horn Patterning in Bovidae

scientific article published on 01 May 2021

Animal board invited review: genetic possibilities to reduce enteric methane emissions from ruminants

scientific article

Application of a Bayesian non-linear model hybrid scheme to sequence data for genomic prediction and QTL mapping

scientific article published on 15 August 2017

Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle.

scientific article

Author Correction: A chickpea genetic variation map based on the sequencing of 3,366 genomes

scientific article published in 2022

Author reply to A commentary on Pitfalls of predicting complex traits from SNPs

scientific article published on December 2013

Break-even cost of genotyping genetic mutations affecting economic traits in Australian pig enterprises

article

Breeding crops to feed 10 billion

scientific article published on 17 June 2019

Breeding improves wheat productivity under contrasting agrochemical input levels

scientific article published on 17 June 2019

Casein haplotypes and their association with milk production traits in Norwegian Red cattle

scientific article published on 20 February 2009

Characterizing homozygosity across United States, New Zealand and Australian Jersey cow and bull populations

scientific article published on 15 March 2015

Comparison of casein haplotypes between two geographically distant European dairy goat breeds

scientific article published on 01 February 2008

Comparison of heritabilities of dairy traits in Australian Holstein-Friesian cattle from genomic and pedigree data and implications for genomic evaluations.

scientific article

Components of the accuracy of genomic prediction in a multi-breed sheep population.

scientific article published on October 2012

Construction of a dense SNP map for bovine chromosome 6 to assist the assembly of the bovine genome sequence

scientific article published on 26 February 2008

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

scientific article

Design of a bovine low-density SNP array optimized for imputation

scientific article (publication date: 2012)

Design of a low-density SNP chip for the main Australian sheep breeds and its effect on imputation and genomic prediction accuracy

scientific article published on 11 September 2015

Detailed phenotyping identifies genes with pleiotropic effects on body composition.

scientific article

Detection and validation of structural variations in bovine whole-genome sequence data

scientific article

Detection of chromosome segments of zebu and taurine origin and their effect on beef production and growth.

scientific article published on 4 February 2011

Detection of quantitative trait loci in Bos indicus and Bos taurus cattle using genome-wide association studies

scientific article

Deterministic models of breeding scheme designs that incorporate genomic selection.

scientific article published in November 2010

Differentially Expressed Genes in Endometrium and Corpus Luteum of Holstein Cows Selected for High and Low Fertility Are Enriched for Sequence Variants Associated with Fertility

scientific article published on 25 November 2015

Efficient parentage assignment and pedigree reconstruction with dense single nucleotide polymorphism data.

scientific article

Estimated allele substitution effects underlying genomic evaluation models depend on the scaling of allele counts.

scientific article published on 30 October 2017

Evaluation of marker assisted selection in pig enterprises

Exome sequence genotype imputation in globally diverse hexaploid wheat accessions.

scientific article published on 4 April 2017

Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome

scientific article published on 01 May 2019

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

scientific article published on 23 November 2015

Gene by environment interactions for production traits in Australian dairy cattle

article

Genetic Gain and Inbreeding from Genomic Selection in a Simulated Commercial Breeding Program for Perennial Ryegrass.

scientific article published in March 2016

Genetic architecture of complex traits and accuracy of genomic prediction: coat colour, milk-fat percentage, and type in Holstein cattle as contrasting model traits

scientific article

Genetic support for a quantitative trait nucleotide in the ABCG2 gene affecting milk composition of dairy cattle

scientific article

Genetic variants in mammary development, prolactin signalling and involution pathways explain considerable variation in bovine milk production and milk composition.

scientific article

Genetics of complex traits: prediction of phenotype, identification of causal polymorphisms and genetic architecture

scientific article

Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection

scientific article (publication date: February 2012)

Genome-wide association and genomic selection in animal breeding

scientific article

Genome-wide association studies for feedlot and growth traits in cattle.

scientific article

Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds

scientific article

Genomewide association study of methane emissions in Angus beef cattle with validation in dairy cattle.

scientific article published in October 2016

Genomic Selection Improves Heat Tolerance in Dairy Cattle.

scientific article published on 29 September 2016

Genomic prediction for rust resistance in diverse wheat landraces.

scientific article

Genomic prediction of reproduction traits for Merino sheep.

scientific article published on 17 February 2017

Genomic prediction using low-coverage portable Nanopore sequencing

scientific article published on 15 December 2021

Genomic selection for feed efficiency in dairy cattle.

scientific article published on 16 October 2013

Genomic selection for recovery of original genetic background from hybrids of endangered and common breeds.

scientific article published on 14 October 2013

Genomic selection for tolerance to heat stress in Australian dairy cattle

scientific article published on April 2016

Genomic selection in livestock populations

scientific article published on December 2010

Genomic selection.

scientific article

Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array.

scientific article

Harnessing genomic information for livestock improvement

scientific article published on 01 March 2019

High throughput whole rumen metagenome profiling using untargeted massively parallel sequencing

scientific article

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

scientific article published on 28 December 2013

Hot topic: Definition and implementation of a breeding value for feed efficiency in dairy cows.

scientific article published on 5 August 2015

How old are quantitative trait loci and how widely do they segregate?

scientific article published on 01 April 2015

Identification and characterisation of novel SNP markers in Atlantic cod: evidence for directional selection

scientific article

Identification of genomic regions associated with inbreeding depression in Holstein and Jersey dairy cattle

scientific article

Impact of QTL properties on the accuracy of multi-breed genomic prediction.

scientific article

Improved accuracy of genomic prediction for dry matter intake of dairy cattle from combined European and Australian data sets.

scientific article

Improved precision of QTL mapping using a nonlinear Bayesian method in a multi-breed population leads to greater accuracy of across-breed genomic predictions

scientific article

Improving Genetic Gain with Genomic Selection in Autotetraploid Potato.

scientific article published on November 2016

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

scientific article published on 01 July 2012

Improving breeding efficiency in potato using molecular and quantitative genetics

scientific article published on 04 September 2014

Improving the analysis of low heritability complex traits for enhanced genetic gain in potato

scientific article published on 29 December 2013

Imputation of genotypes from low density (50,000 markers) to high density (700,000 markers) of cows from research herds in Europe, North America, and Australasia using 2 reference populations

scientific article published on 25 January 2014

Imputation of missing genotypes from sparse to high density using long-range phasing.

scientific article

Including nonadditive genetic effects in mating programs to maximize dairy farm profitability.

scientific article published on 8 December 2016

Including overseas performance information in genomic evaluations of Australian dairy cattle

scientific article published on 12 March 2015

Incorporating heifer feed efficiency in the Australian selection index using genomic selection

scientific article published on 27 March 2014

Increased accuracy of artificial selection by using the realized relationship matrix.

scientific article published in February 2009

Inferring demography from runs of homozygosity in whole-genome sequence, with correction for sequence errors

scientific article (publication date: September 2013)

Insights into population genetics and evolution of polyploids and their ancestors.

scientific article

Investigating the effect of two methane-mitigating diets on the rumen microbiome using massively parallel sequencing.

scientific article

LASSO with cross-validation for genomic selection

scientific article published in December 2009

Latent Biochemical Relationships in the Blood–Milk Metabolic Axis of Dairy Cows Revealed by Statistical Integration of 1H NMR Spectroscopic Data ⬇️

scientific article published on February 21, 2013

Leveraging genetically simple traits to identify small-effect variants for complex phenotypes.

scientific article

Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle

scientific article published on 13 July 2008

Linkage disequilibrium over short physical distances measured in sheep using a high-density SNP chip

scientific article published on 17 July 2014

Long-term selection strategies for complex traits using high-density genetic markers

scientific article published on 01 August 2012

Mapping genes for complex traits in domestic animals and their use in breeding programmes

scientific article

Mapping of a quantitative trait locus for resistance against infectious salmon anaemia in Atlantic salmon (Salmo salar): comparing survival analysis with analysis on affected/resistant data.

scientific article

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

scientific article published on 19 February 2018

Metagenomic predictions: from microbiome to complex health and environmental phenotypes in humans and cattle

scientific article

Metagenomics of rumen bacteriophage from thirteen lactating dairy cattle

scientific article

Mitigation of inbreeding while preserving genetic gain in genomic breeding programs for outbred plants.

scientific article published on 31 March 2017

Molecular characterization of a long range haplotype affecting protein yield and mastitis susceptibility in Norwegian Red cattle.

scientific article

Multi-breed genomic prediction using Bayes R with sequence data and dropping variants with a small effect.

scientific article published on 21 September 2017

Multibreed genome wide association can improve precision of mapping causative variants underlying milk production in dairy cattle.

scientific article published on 24 January 2014

Multibreed genomic prediction using multitrait genomic residual maximum likelihood and multitask Bayesian variable selection.

scientific article published on 14 March 2018

Multivariate analysis of a genome-wide association study in dairy cattle.

scientific article

Non-additive genetic variation in growth, carcass and fertility traits of beef cattle

scientific article

Nonlinear regulation enhances the phenotypic expression of trans-acting genetic polymorphisms

scientific article

Novel multilocus measure of linkage disequilibrium to estimate past effective population size.

scientific article

Novel strategies to minimize progeny inbreeding while maximizing genetic gain using genomic information.

scientific article published on January 2012

Optimisation of marker assisted selection for abalone breeding programs

Optimized Genetic Testing for Polledness in Multiple Breeds of Cattle

scientific article published on 06 February 2020

Pitfalls of predicting complex traits from SNPs

scientific article

Polyceraty (multi-horns) in Damara sheep maps to ovine chromosome 2

scientific article published on 14 January 2016

Polymorphic regions affecting human height also control stature in cattle.

scientific article

Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males

scientific article published on 10 May 2006

Power of a genome scan to detect and locate quantitative trait loci in cattle using dense single nucleotide polymorphisms

scientific article published on 01 April 2010

Predicting unobserved phenotypes for complex traits from whole-genome SNP data

scientific article

Publisher Correction: Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome

scientific article published on 01 July 2019

Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits.

scientific article

Putative enhancer sites in the bovine genome are enriched with variants affecting complex traits.

scientific article

Quantitative trait loci for clinical mastitis on chromosomes 2, 6, 14 and 20 in Norwegian Red cattle.

scientific article published on 15 February 2011

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

scientific article published on 13 September 2017

Rare Variants in Transcript and Potential Regulatory Regions Explain a Small Percentage of the Missing Heritability of Complex Traits in Cattle.

scientific article published on 7 December 2015

Recent and historical recombination in the admixed Norwegian Red cattle breed ⬇️

scientific article published on January 14, 2011

Recent human effective population size estimated from linkage disequilibrium

scientific article published on 9 March 2007

Regulatory and coding genome regions are enriched for trait associated variants in dairy and beef cattle

scientific article

Reliability of genomic predictions across multiple populations.

scientific article published on 12 October 2009

Responses of dairy cows with divergent residual feed intake as calves to metabolic challenges during midlactation and the nonlactating period

scientific article published on 28 March 2018

SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates.

scientific article published on 26 April 2007

Selection for complex traits leaves little or no classic signatures of selection.

scientific article

Selection on Optimal Haploid Value Increases Genetic Gain and Preserves More Genetic Diversity Relative to Genomic Selection

scientific article published on 19 June 2015

Sequencing the mosaic genome of Brahman cattle identifies historic and recent introgression including polled

scientific article published in Scientific Reports

Short communication: Genomic selection using a multi-breed, across-country reference population.

scientific article published in May 2011

Short communication: Implementation of a breeding value for heat tolerance in Australian dairy cattle.

scientific article published on 12 July 2017

Short communication: Validation of genomic breeding value predictions for feed intake and feed efficiency traits.

scientific article

Simultaneous discovery, estimation and prediction analysis of complex traits using a bayesian mixture model

scientific article published on 7 April 2015

Strategies and considerations for implementing genomic selection to improve traits with additive and non-additive genetic architectures in sugarcane breeding

scientific article published in 2021

Strategies and utility of imputed SNP genotypes for genomic analysis in dairy cattle

scientific article

Targeted imputation of sequence variants and gene expression profiling identifies twelve candidate genes associated with lactation volume, composition and calving interval in dairy cattle.

scientific article published on 27 November 2015

Technical note: Equivalent genomic models with a residual polygenic effect

scientific article published on 24 December 2015

Technical note: Prediction of breeding values using marker-derived relationship matrices

scientific article published on 11 April 2008

The cost-benefit of genomic testing of heifers and using sexed semen in pasture-based dairy herds

scientific article published on 26 April 2018

The distribution of SNP marker effects for faecal worm egg count in sheep, and the feasibility of using these markers to predict genetic merit for resistance to worm infections

article

The effects of demography and long-term selection on the accuracy of genomic prediction with sequence data

scientific article

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

scientific article

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

scientific article

Two-Variance-Component Model Improves Genetic Prediction in Family Datasets.

scientific article

Use of a microsatellite-based pedigree in estimation of heritabilities for economic traits in Australian blue mussel, Mytilus galloprovincialis.

scientific article published on 8 August 2011

Use of gene expression data for predicting continuous phenotypes for animal production and breeding.

scientific article

Using prior information from humans to prioritize genes and gene-associated variants for complex traits in livestock

scientific article published on 14 September 2020

Using the genomic relationship matrix to predict the accuracy of genomic selection

scientific article published on 01 December 2011

Validation of markers with non-additive effects on milk yield and fertility in Holstein and Jersey cows

scientific article published on 22 July 2015

Validation of single nucleotide polymorphisms associated with milk production traits in dairy cattle

article

Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits

scientific article published on 5 April 2018

Variants at the ASIP locus contribute to coat color darkening in Nellore cattle

scientific article published on 28 April 2021

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

scientific article

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

scientific article published on 13 July 2014

genomicSimulation: fast R functions for stochastic simulation of breeding programs

scientific article published in 2022

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