List of works - John B Cole

A genome-wide association study for clinical mastitis in first parity US Holstein cows using single-step approach and genomic matrix re-weighting procedure

scientific article

A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits.

scientific article

A simple strategy for managing many recessive disorders in a dairy cattle breeding program

scientific article

Accuracy of genomic predictions in Bos indicus (Nellore) cattle

scientific article

Application of the a posteriori granddaughter design to the Holstein genome.

scientific article published in April 2014

Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes.

scientific article

Association of single nucleotide polymorphisms in candidate genes previously related to genetic variation in fertility with phenotypic measurements of reproductive function in Holstein cows.

scientific article

BREEDING AND GENETICS SYMPOSIUM: Systems biology in animal breeding: Identifying relationships among markers, genes, and phenotypes1

article

Benchmarking dairy herd health status using routinely recorded herd summary data

scientific article

Best prediction of yields for long lactations.

scientific article published in April 2009

Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects BH1, HH2, and HH3 reveal a putative causative mutation in SMC2 for HH3

scientific article (publication date: 2014)

Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis

scientific article

Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection

scientific article published on 27 June 2016

Comparative analyses of sperm DNA methylomes among human, mouse and cattle provide insights into epigenomic evolution and complex traits

scientific article published on 24 March 2019

Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle

scientific article published on 18 May 2020

Construction of PRDM9 allele-specific recombination maps in cattle using large-scale pedigree analysis and genome-wide single sperm genomics.

scientific article

Convergent Evolution of Slick Coat in Cattle through Truncation Mutations in the Prolactin Receptor.

scientific article published on 23 February 2018

Development of a Lifetime Merit-based selection index for US dairy grazing systems

scientific article published on 02 May 2014

Discovering ancestors and connecting relatives in large genomic databases

scientific article published on 16 December 2019

Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle.

scientific article

Dissection of additive, dominance, and imprinting effects for production and reproduction traits in Holstein cattle.

scientific article

Dissection of genomic correlation matrices of US Holsteins using multivariate factor analysis

scientific article published on 06 August 2014

Distribution and location of genetic effects for dairy traits.

scientific article published in June 2009

Diversity and population-genetic properties of copy number variations and multicopy genes in cattle

scientific article published on 15 April 2016

Economic considerations of breeding for polled dairy cows versus dehorning in the United States

scientific article published on 22 March 2017

Effect of artificial selection on runs of homozygosity in u.s. Holstein cattle

scientific article (publication date: 2013)

Effect of sample stratification on dairy GWAS results

scientific article

Evaluation of genetic components in traits related to superovulation, in vitro fertilization, and embryo transfer in Holstein cattle.

scientific article published on 25 January 2017

Explorations in genome-wide association studies and network analyses with dairy cattle fertility traits

scientific article published on 18 May 2016

Fine mapping for Weaver syndrome in Brown Swiss cattle and the identification of 41 concordant mutations across NRCAM, PNPLA8 and CTTNBP2

scientific article

Functional annotation and Bayesian fine-mapping reveals candidate genes for important agronomic traits in Holstein bulls.

scientific article published on 18 June 2019

Genetic and epigenetic architecture of paternal origin contribute to gestation length in cattle

scientific article published on 14 March 2019

Genetic evaluation of lactation persistency for five breeds of dairy cattle.

scientific article published in May 2009

Genetic evaluation of stillbirth in United States Holsteins using a sire-maternal grandsire threshold model.

scientific article published in May 2007

Genetic evaluations for mixed-breed populations

scientific article published on 01 May 2007

Genetic parameters of milk ELISA scores for Johne's disease

scientific article published on 01 April 2010

Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins.

scientific article

Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows

scientific article

Genome-wide association mapping for identification of quantitative trait loci for rectal temperature during heat stress in Holstein cattle.

scientific article

Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height

scientific article (publication date: 13 June 2013)

Genome-wide mapping of loci explaining variance in scrotal circumference in Nellore cattle

scientific article

Genomewide Association Study of African Children Identifies Association of SCHIP1 and PDE8A with Facial Size and Shape.

scientific article

Genomewide association study of reproductive efficiency in female cattle.

scientific article published in May 2014

Genomic Selection in Dairy Cattle: The USDA Experience

scientific article published on 16 November 2016

Genomic evaluation of age at first calving.

scientific article

Genomic evaluation, breed identification, and discovery of a haplotype affecting fertility for Ayrshire dairy cattle

scientific article published on 27 March 2014

Genomic imputation and evaluation using high-density Holstein genotypes ⬇️

scientific article published on October 11, 2012

Genomic inbreeding and relationships among Holsteins, Jerseys, and Brown Swiss.

scientific article published on November 2011

Genomic prediction of disease occurrence using producer-recorded health data: a comparison of methods

scientific article

Genomic prediction of residual feed intake in US Holstein dairy cattle

scientific article published on 15 January 2020

Genomic selection for producer-recorded health event data in US dairy cattle.

scientific article

Genomic signatures reveal new evidences for selection of important traits in domestic cattle.

scientific article published on 26 November 2014

Genomic study and Medical Subject Headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers.

scientific article published in November 2017

Heritability of rectal temperature and genetic correlations with production and reproduction traits in dairy cattle

scientific article published on 01 June 2012

High-density genome-wide association study for residual feed intake in Holstein dairy cattle

scientific article published on 25 September 2019

Identification of a nonsense mutation in CWC15 associated with decreased reproductive efficiency in Jersey cattle

scientific article

Impact of genetic merit for milk somatic cell score of sires and maternal grandsires on herd life of their daughters

scientific article published on 01 May 2009

Improvement of prediction ability for genomic selection of dairy cattle by including dominance effects

scientific article

Invited review: Opportunities for genetic improvement of metabolic diseases

scientific article

Invited review: overview of new traits and phenotyping strategies in dairy cattle with a focus on functional traits

scientific article

Multiparity evaluation of calving ease and stillbirth with separate genetic effects by parity.

scientific article published in August 2008

Phenotypic and genetic effects of recessive haplotypes on yield, longevity, and fertility

scientific article published on 6 July 2016

Phenotypic and genetic relationships of common health disorders with milk and fat yield persistencies from producer-recorded health data and test-day yields.

scientific article

Possibilities in an age of genomics: The future of selection indices

scientific article

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

scientific article published on 13 April 2016

Selecting sequence variants to improve genomic predictions for dairy cattle

scientific article published on 07 March 2017

Short communication: Projecting milk yield using best prediction and the MilkBot lactation model.

scientific article published in July 2012

Short communication: Use of young bulls in the United States

scientific article published on 05 March 2014

Short communication: best prediction of 305-day lactation yields with regional and seasonal effects

scientific article published on 01 March 2011

Short communication: genetic evaluation of stillbirth in US Brown Swiss and Jersey cattle.

scientific article published on 6 February 2014

Single nucleotide polymorphisms associated with thermoregulation in lactating dairy cows exposed to heat stress.

scientific article published on 21 July 2015

Stochastic dynamic simulation modeling including multitrait genetics to estimate genetic, technical, and financial consequences of dairy farm reproduction and selection strategies.

scientific article published on 3 August 2016

Technical note: Changes to herd cutoff date in conception rate evaluations.

scientific article published on 6 December 2012

Technical note: adjustment of traditional cow evaluations to improve accuracy of genomic predictions.

scientific article

Temperature-humidity indices as indicators of milk production losses due to heat stress

article

Use of haplotypes to estimate Mendelian sampling effects and selection limits

scientific article published on 13 April 2011

Use of single nucleotide polymorphisms in candidate genes associated with daughter pregnancy rate for prediction of genetic merit for reproduction in Holstein cows

scientific article published on 28 February 2016

Visualization of results from genomic evaluations

scientific article published on 01 June 2010

Visualization of the transmission of direct genomic values for paternal and maternal chromosomes for 15 traits in US Brown Swiss, Holstein, and Jersey cattle.

scientific article

List of works by John B Cole

A genome-wide association study for clinical mastitis in first parity US Holstein cows using single-step approach and genomic matrix re-weighting procedure

A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits.

A simple strategy for managing many recessive disorders in a dairy cattle breeding program

Accuracy of genomic predictions in Bos indicus (Nellore) cattle

Application of the a posteriori granddaughter design to the Holstein genome.

Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes.

Association of single nucleotide polymorphisms in candidate genes previously related to genetic variation in fertility with phenotypic measurements of reproductive function in Holstein cows.

BREEDING AND GENETICS SYMPOSIUM: Systems biology in animal breeding: Identifying relationships among markers, genes, and phenotypes1

Benchmarking dairy herd health status using routinely recorded herd summary data

Best prediction of yields for long lactations.

Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects BH1, HH2, and HH3 reveal a putative causative mutation in SMC2 for HH3

Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis

Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection

Comparative analyses of sperm DNA methylomes among human, mouse and cattle provide insights into epigenomic evolution and complex traits

Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle

Construction of PRDM9 allele-specific recombination maps in cattle using large-scale pedigree analysis and genome-wide single sperm genomics.

Convergent Evolution of Slick Coat in Cattle through Truncation Mutations in the Prolactin Receptor.

Development of a Lifetime Merit-based selection index for US dairy grazing systems

Discovering ancestors and connecting relatives in large genomic databases

Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle.

Dissection of additive, dominance, and imprinting effects for production and reproduction traits in Holstein cattle.

Dissection of genomic correlation matrices of US Holsteins using multivariate factor analysis

Distribution and location of genetic effects for dairy traits.

Diversity and population-genetic properties of copy number variations and multicopy genes in cattle

Economic considerations of breeding for polled dairy cows versus dehorning in the United States

Effect of artificial selection on runs of homozygosity in u.s. Holstein cattle

Effect of sample stratification on dairy GWAS results

Evaluation of genetic components in traits related to superovulation, in vitro fertilization, and embryo transfer in Holstein cattle.

Explorations in genome-wide association studies and network analyses with dairy cattle fertility traits

Fine mapping for Weaver syndrome in Brown Swiss cattle and the identification of 41 concordant mutations across NRCAM, PNPLA8 and CTTNBP2

Functional annotation and Bayesian fine-mapping reveals candidate genes for important agronomic traits in Holstein bulls.

Genetic and epigenetic architecture of paternal origin contribute to gestation length in cattle

Genetic evaluation of lactation persistency for five breeds of dairy cattle.

Genetic evaluation of stillbirth in United States Holsteins using a sire-maternal grandsire threshold model.

Genetic evaluations for mixed-breed populations

Genetic parameters of milk ELISA scores for Johne's disease

Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins.

Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows

Genome-wide association mapping for identification of quantitative trait loci for rectal temperature during heat stress in Holstein cattle.

Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height

Genome-wide mapping of loci explaining variance in scrotal circumference in Nellore cattle

Genomewide Association Study of African Children Identifies Association of SCHIP1 and PDE8A with Facial Size and Shape.

Genomewide association study of reproductive efficiency in female cattle.

Genomic Selection in Dairy Cattle: The USDA Experience

Genomic evaluation of age at first calving.

Genomic evaluation, breed identification, and discovery of a haplotype affecting fertility for Ayrshire dairy cattle

Genomic imputation and evaluation using high-density Holstein genotypes ⬇️

Genomic inbreeding and relationships among Holsteins, Jerseys, and Brown Swiss.

Genomic prediction of disease occurrence using producer-recorded health data: a comparison of methods

Genomic prediction of residual feed intake in US Holstein dairy cattle

Genomic selection for producer-recorded health event data in US dairy cattle.

Genomic signatures reveal new evidences for selection of important traits in domestic cattle.

Genomic study and Medical Subject Headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers.

Heritability of rectal temperature and genetic correlations with production and reproduction traits in dairy cattle

High-density genome-wide association study for residual feed intake in Holstein dairy cattle

Identification of a nonsense mutation in CWC15 associated with decreased reproductive efficiency in Jersey cattle

Impact of genetic merit for milk somatic cell score of sires and maternal grandsires on herd life of their daughters

Improvement of prediction ability for genomic selection of dairy cattle by including dominance effects

Invited review: Opportunities for genetic improvement of metabolic diseases

Invited review: overview of new traits and phenotyping strategies in dairy cattle with a focus on functional traits

Multiparity evaluation of calving ease and stillbirth with separate genetic effects by parity.

Phenotypic and genetic effects of recessive haplotypes on yield, longevity, and fertility

Phenotypic and genetic relationships of common health disorders with milk and fat yield persistencies from producer-recorded health data and test-day yields.

Possibilities in an age of genomics: The future of selection indices

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

Selecting sequence variants to improve genomic predictions for dairy cattle

Short communication: Projecting milk yield using best prediction and the MilkBot lactation model.

Short communication: Use of young bulls in the United States

Short communication: best prediction of 305-day lactation yields with regional and seasonal effects

Short communication: genetic evaluation of stillbirth in US Brown Swiss and Jersey cattle.

Single nucleotide polymorphisms associated with thermoregulation in lactating dairy cows exposed to heat stress.

Stochastic dynamic simulation modeling including multitrait genetics to estimate genetic, technical, and financial consequences of dairy farm reproduction and selection strategies.

Technical note: Changes to herd cutoff date in conception rate evaluations.

Technical note: adjustment of traditional cow evaluations to improve accuracy of genomic predictions.

Temperature-humidity indices as indicators of milk production losses due to heat stress

Use of haplotypes to estimate Mendelian sampling effects and selection limits

Use of single nucleotide polymorphisms in candidate genes associated with daughter pregnancy rate for prediction of genetic merit for reproduction in Holstein cows

Visualization of results from genomic evaluations

Visualization of the transmission of direct genomic values for paternal and maternal chromosomes for 15 traits in US Brown Swiss, Holstein, and Jersey cattle.