Publications
Pre-print
- Modelling illustrates that genomic selection provides new opportunities for intercrop breeding
Bančič J., C. Werner, C. Gaynor, G. Gorjanc, D. Odeny, H.F. Ojulong, I.K. Dawson, S. Hoad J.M. Hickey
bioRxiv
- Modelling illustrates that genomic selection provides new opportunities for intercrop breeding
- AlphaSimR: An R-package for Breeding Program Simulations
Gaynor C.R., G. Gorjanc, J.M. Hickey
bioRxiv
- AlphaSimR: An R-package for Breeding Program Simulations
- Genomic selection strategies for clonal propagated crops
Werner, C.R., C.R. Gaynor, D.J. Sargent, A. Lillo, G. Gorjanc, J.M. Hickey
bioRxiv
- Genomic selection strategies for clonal propagated crops
- A Two-Part Strategy using Genomic Selection in Hybrid Crop Breeding Programs
Powell, M.O., C.R. Gaynor, G. Gorjanc, C.R. Werner, J.M. Hickey
bioRxiv
- A Two-Part Strategy using Genomic Selection in Hybrid Crop Breeding Programs
- AlphaPart – R implementation of the method for partitioning genetic trends
Obsteter, J., J. Holl, R., J.M. Hickey, G. Gorjanc
bioRxiv
- AlphaPart – R implementation of the method for partitioning genetic trends
- Genetics of recombination rate variation in the pig
Johnsson, M., A. Whalen, R. Ros-Freixedes, G.Gorjanc, C. Chen, W.O. Herring, D. de Konning, J.M. Hickey
bioRxiv
- Genetics of recombination rate variation in the pig
- Using high-throughput phenotypes to enable genomic selection by inferring genotypes
Whalen, A, R. C. Gaynor, J.M. Hickey
bioRxiv
- Using high-throughput phenotypes to enable genomic selection by inferring genotypes
- Phasing and imputation of single nucleotide polymorphism data of missing parents of bi-parental plant populations
Gonen, S, Valentin Wimmer, R. C. Gaynor, Ed Byrne, G. Gorjanc, J.M. Hickey
bioRxiv
- Phasing and imputation of single nucleotide polymorphism data of missing parents of bi-parental plant populations
- AlphaFamImpute: high accuracy imputation in full-sib families from genotype-by-sequencing data
Whalen, A, G. Gorjanc, J.M. Hickey
bioRxiv
- AlphaFamImpute: high accuracy imputation in full-sib families from genotype-by-sequencing data
- Genomic data enables genetic evaluation using data recorded on LMIC smallholder dairy farms
Powell, M. O., R. Mrode, R. C. Gaynor, M. Johnsson, G. Gorjanc, J.M. Hickey
bioRxiv
- Genomic data enables genetic evaluation using data recorded on LMIC smallholder dairy farms
- A family-based phasing algorithm for sequence data
Battagin, M., S. Gonen, R. Ros-Freixedes, A. Whalen, G. Gorjanc, J.M. Hickey
bioRxiv
- A family-based phasing algorithm for sequence data
- Plant breeders should be determining economic weights for a selection index instead of using independent culling for choosing parents in breeding programs with genomic selection
Batista, L., R.C. Gaynor, G.R.A. Margarido, T. Byrne, P. Amer, G. Gorjanc, J.M. Hickey
bioRxiv
- Plant breeders should be determining economic weights for a selection index instead of using independent culling for choosing parents in breeding programs with genomic selection
2020
- Genome-based trait prediction in multi- environment breeding trials in groundnut
Pandey, M.K, S. Chaudhari, D. Jarquin, P. Janila, J. Crossa, S. C. Patil, S. Sundravadana, D. Khare, R. S. Bhat, T. Radhakrishnan, J.M. Hickey, R. K. Varshney
Theoretical and Applied Genetics (2020).
- Genome-based trait prediction in multi- environment breeding trials in groundnut
- Extending long-range phasing and haplotype library imputation algorithms to very large and heterogeneous datasets
Money, D.P, D. Wilson, J. Jenko, G. Gorjanc, J.M. Hickey
Genetics Selection Evolution, 52:38.
- Extending long-range phasing and haplotype library imputation algorithms to very large and heterogeneous datasets
- Evaluation of sequencing strategies for whole-genome imputation with hybrid peeling
Ros-Freixedes, R., A. Whalen, A.J. Mileham, G. Gorjanc, J.M. Hickey
Genetics Selection Evolution, 52:18.
- Evaluation of sequencing strategies for whole-genome imputation with hybrid peeling
- Accuracy of whole-genome sequence imputation using hybrid peeling in large pedigreed livestock populations
Ros-Freixedes, R., A. Whalen, C. Chen, G. Gorjanc, W.O. Herring, A.J. Mileham, J.M. Hickey
Genetics Selection Evolution, 52:17.
- Accuracy of whole-genome sequence imputation using hybrid peeling in large pedigreed livestock populations
- In silico simulation of future hybrid performance to evaluate heterotic pool formation in a self-pollinating crop
Cowling W.A., R. C. Gaynor, R. Antolin, G. Gorjanc, S.M. Edwards, O. Powell, J.M. Hickey
Scientific Reports, 10:4037.
- In silico simulation of future hybrid performance to evaluate heterotic pool formation in a self-pollinating crop
2019
- Modelling spatial variation in agricultural field trials with INLA
M. Lie Selle, I. Steinsland, J.M. Hickey, G. Gorjanc
Theoretical and Applied Genetics, 132:3277-3293.
- Modelling spatial variation in agricultural field trials with INLA
- Efficient use of genomic information for sustainable genetic improvement in small cattle populations
J. Obšteter, J. Jenko, J.M. Hickey, G. Gorjanc
Journal of Dairy Science, 102:9971-9982.
- Efficient use of genomic information for sustainable genetic improvement in small cattle populations
- Students’, colleagues’ and research partners’ experience about work and accomplishments from collaborating with Robin Thompson
Hickey, J.M., W.G. Hill, A. Blasco, N. Cameron, B. Cullis, B. McGuirk, E. Mäntysaari, J. Ruane, G. Simm R. Veerkamp, P.M. Visscher, N.R. Wray
Journal of Animal Breeding and Genetics, 136:301-309.
- Students’, colleagues’ and research partners’ experience about work and accomplishments from collaborating with Robin Thompson
- The Fest Issue on Robin Thompson’s contributions to statistics, genetics and animal/plant genetic improvement schemes
Hickey, J.M., G. Gorjanc, W.G. Hill
Journal of Animal Breeding and Genetics, 136:229-229.
- The Fest Issue on Robin Thompson’s contributions to statistics, genetics and animal/plant genetic improvement schemes
- Family-specific genotype arrays increase the accuracy of pedigree based imputation at very low marker densities
Whalen, A., G. Gorjanc, J.M. Hickey
Genetics Selection Evolution, 51:33.
- Family-specific genotype arrays increase the accuracy of pedigree based imputation at very low marker densities
- The role of genetics in mainstreaming the production of new and orphan crops to diversify food systems and support human nutrition
Dawson, I.K., W. Powell, P. Hendre, J. Bančič, J.M. Hickey, R. Kindt, S. Hoad, I. Hale, R. Jamnadass
New Phytologist, 224:37-54.
- The role of genetics in mainstreaming the production of new and orphan crops to diversify food systems and support human nutrition
- Removal of alleles by genome editing – RAGE against the deleterious load
Johnsson, M., R.C. Gaynor, J. Jenko, G. Gorjanc, D.J. de Koning, J.M. Hickey
Genetics Selection Evolution, 51:14.
- Removal of alleles by genome editing – RAGE against the deleterious load
- The effects of training population design on genomic prediction accuracy in wheat
McKinnon Edwards, S., J.B. Buntjer, R. Jackson, A.R. Bentley, J. Lage, E. Byrne, C. Burt, P. Jack, S. Berry, E. Flatman, B. Poupard, S. Smith, C. Hayes, R.C. Gaynor, G. Gorjanc, P. Howell, E. Ober, I.J. Mackay, J.M. Hickey
Theoretical and Applied Genetics, 132:1943-1952.
- The effects of training population design on genomic prediction accuracy in wheat
- Analysis of a large data set reveals haplotypes carrying putatively recessive lethal alleles with pleiotropic effects on economically important traits in beef cattle
Jenko, J., M.C. McClure, D. Matthews, J. McClure, M. Johnsson, G. Gorjanc, J.M. Hickey
Genetics Selection Evolution, 51:9.
- Analysis of a large data set reveals haplotypes carrying putatively recessive lethal alleles with pleiotropic effects on economically important traits in beef cattle
- A Large-Scale Pedigree Resource of Wheat Reveals Evidence for Adaptation and Selection by Breeders
N. Fradgley , K.A. Gardner, J. Cockram, J. Elderfield, J.M. Hickey, P. Howell, R. Jackson, I.J. Mackay
PLOS Biology, 17(2):e3000071.
- A Large-Scale Pedigree Resource of Wheat Reveals Evidence for Adaptation and Selection by Breeders
2018
- A Strategy To Exploit Surrogate Sire Technology in Livestock Breeding Programs
Gottardo, P., G. Gorjanc, M. Battagin, C.R. Gaynor, J. Jenko, R. Ros-Freixedes, C.B.A. Whitelaw, A. Mileham, W. Herring, J.M. Hickey
G3 – Genes, Genomes, Genetics, 9:203-215.
- A Strategy To Exploit Surrogate Sire Technology in Livestock Breeding Programs
- Sequence variability, constraint and selection in the CD163 gene in pigs
Johnsson, M., R. Ros-Freixedes, G. Gorjanc, M.A. Campbell, S. Naswa, K. Kelly, J. Lightner, S. Rounsley, J.M. Hickey
Genetics Selection Evolution, 50:69.
- Sequence variability, constraint and selection in the CD163 gene in pigs
- Hybrid peeling for fast and accurate calling, phasing and imputation with sequence data of any coverage in pedigrees
Whalen, A., R. Ros-Freixedes, D. L. Wilson, G. Gorjanc, J.M. Hickey
Genetics Selection Evolution, 50:67.
- Hybrid peeling for fast and accurate calling, phasing and imputation with sequence data of any coverage in pedigrees
- Parentage assignment with low density array data and low coverage sequence data
Whalen, A., G. Gorjanc, J.M. Hickey
Journal of Animal Breeding and Genetics, 136:102-112.
- Parentage assignment with low density array data and low coverage sequence data
- Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing
Ros-Freixedes, R., M. Battagin, M. Johnsson, G. Gorjanc, DA.J. Mileham, S.D. Rounsley, J.M. Hickey
Genetics Selection Evolution, 50:64.
- Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing
- Assessment of the performance of hidden Markov models for imputation in animal breeding
Whalen, A., G. Gorjanc, R. Ros-Freixedes, J.M. Hickey
Genetics Selection Evolution, 50:44.
- Assessment of the performance of hidden Markov models for imputation in animal breeding
- A heuristic method for fast and accurate phasing and imputation of single nucleotide polymorphism data in bi-lateral plant populations
Gonen, S., V. Wimmer, R.C. Gaynor, E. Byrne, G. Gorjanc, J.M. Hickey
Theoretical Applied Genetics, 131:2345-2357.
- A heuristic method for fast and accurate phasing and imputation of single nucleotide polymorphism data in bi-lateral plant populations
- Accuracy of genotype imputation in Labrador Retrievers
Friedrich, J., R. Antolin, S. M. Edwards, E. Sánchez-Molano, M. J. Haskell, J.M. Hickey, P. Wiener
Animal Genetics, 49:303-311.
- Accuracy of genotype imputation in Labrador Retrievers
- Optimal cross selection for long-term genetic gain in two-part programs with rapid recurrent genomic selection
Gorjanc, G., R. C. Gaynor, J.M. Hickey
Theoretical and Applied Genetics, 131:1953-1966.
- Optimal cross selection for long-term genetic gain in two-part programs with rapid recurrent genomic selection
- AlphaMate: a program for optimising selection, maintenance of diversity, and mate allocation in breeding programs
Gorjanc, G., J.M. Hickey
Bioinformatics, 19:3408-3411.
- AlphaMate: a program for optimising selection, maintenance of diversity, and mate allocation in breeding programs
- Joint Genomic Prediction of Canine Hip Dysplasia in UK and US Labrador Retrievers
Edwards, S.M., J.A. Woolliams, J.M. Hickey, S.C. Blott, D.N. Clements, E. Sánchez-Molano, R.J. Todhunter, P. Wiener
Frontiers Genetics, 9:101.
- Joint Genomic Prediction of Canine Hip Dysplasia in UK and US Labrador Retrievers
2017
- A method for allocating low-coverage sequencing resources by targeting haplotypes rather than individuals
Ros-Freixedes, R., S. Gonen, G. Gorjanc, J.M. Hickey
Genetics Selection Evolution, 49:78
- A method for allocating low-coverage sequencing resources by targeting haplotypes rather than individuals
- Genomic prediction unifies animal and plant breeding programs to form platforms for biological discovery
Hickey, J.M., T. Chiurugwi, I. Mackay, W. Powell, and Implementing Genomic Selection in CGIAR Breeding Programs Workshop Participants.
Nature Genetics, 49:1297-1303.
- Genomic prediction unifies animal and plant breeding programs to form platforms for biological discovery
- The potential of shifting recombination hotspots to increase genetic gain in livestock breeding
Gonen, S., M. Battagin, S.E. Johnston, G. Gorjanc and J. M. Hickey.
Genetics Selection Evolution, 49:55.
- The potential of shifting recombination hotspots to increase genetic gain in livestock breeding
- A two-part strategy for using genomic selection to develop inbred lines
Gaynor, R.C., G. Gorjanc, A. R. Bentley, E. S. Ober, P. Howell, R. Jackson, I. J. Mackay, J. M. Hickey.
Crop Science, 57:2372-2386.
- A two-part strategy for using genomic selection to develop inbred lines
- A method for the allocation of sequencing resources in genotyped livestock populations
Gonen,S., R. Ros-Freixedes, M. Battagin, G. Gorjanc and J.M. Hickey.
Genetics Selection Evolution, 49:47.
- A method for the allocation of sequencing resources in genotyped livestock populations
- Potential of Low-Coverage Genotyping-by-Sequencing and Imputation for Cost-Effective Genomic Selection in Biparental Segregating Populations
Gorjanc, G., J.F. Dumasy, S. Gonen, R. C. Gaynor, R. Antolin, J. M. Hickey.
Crop Science, 57:1–17.
- Potential of Low-Coverage Genotyping-by-Sequencing and Imputation for Cost-Effective Genomic Selection in Biparental Segregating Populations
- Genotype Imputation to Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon
Tsai, H.Y., O. Matika, S. M. Edwards, R. Antolín-Sánchez, A. Hamilton, D. R. Guy, A. E. Tinch, K. Gharbi, M. J. Stear, J. B. Taggart, J. E. Bron, J. M. Hickey, R. D. Houston.
G3 (Bethesda). 117.040717.
- Genotype Imputation to Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon
- A hybrid method for the imputation of genomic data in livestock population
Antolin R., C. Nettelblad, G. Gorjanc, D. Money, J.M. Hickey.
Genetics Selection Evolution, 49:30.
- A hybrid method for the imputation of genomic data in livestock population
- Prospects for Cost-Effective Genomic Selection via Accurate Within-Family Imputation
Gorjanc, G., M. Battagin, J.F. Dumasy, R. Antolin, R. C. Gaynor, J. M. Hickey.
Crop Science, 57:216–228.
- Prospects for Cost-Effective Genomic Selection via Accurate Within-Family Imputation
- Potential of gene drives with genome editing to increase genetic gain in livestock breeding programs
Gonen, S, J. Jenko, G. Gorjanc, A.J. Mileham, C.B.A. Whitelaw, J.M. Hickey.
Genetics Selection Evolution, 49:3.
- Potential of gene drives with genome editing to increase genetic gain in livestock breeding programs
2016
- Genome-Enabled Prediction Models for Yield Related Traits in Chickpea
Roorkiwal, M., A. Rathore, R. R. Das, M. K. Singh, A. Jain, S. Samineni, P. M. Gaur, B. Chellapilla, S. Tripathi, Y. Li, J. M. Hickey, A. Lorenz, T. Sutton, J. Crossa, J. L. Jannink, R. K. Varshney.
Frontiers in Plant Science, vol.7 no.1666
- Genome-Enabled Prediction Models for Yield Related Traits in Chickpea
- Maximizing the potential of multi-parental crop populations
Olufunmilayo, L., J. Elderfield, K. A. Gardner, R. C. Gaynor, J. M. Hickey, J. M. Hibberd, I. J. Mackay, A. R. Bentley.
Applied & Translational Genomics, 11 (2016) 9–17.
- Maximizing the potential of multi-parental crop populations
- AlphaSim: Software for Breeding Program Simulation
Faux A. M., G. Gorjanc, R. C. Gaynor , M. Battagin, S. M. Edwards, D. L. Wilson, Sarah J. Hearne, S. Gonen, and J. M. Hickey.
The Plant Genome, vol. 9, no.3
- AlphaSim: Software for Breeding Program Simulation
- Effect of manipulating recombination rates on response to selection in livestock breeding programs
Battagin, M., G. Gorjanc, A. M. Faux, S. E. Johnston and J. M. Hickey.
Genetics Selection Evolution, 48:44.
- Effect of manipulating recombination rates on response to selection in livestock breeding programs
- Implementation of Genomic Selection in The Poultry Industry
Wolc, A., A. Kranis, J. Arango, P. Settar, J. E. Fulton, N. P. O’Sullivan, A. Avendano, K. A. Watson, J. M. Hickey, G. de los Campos, R.L. Fernando, D. J. Garrick, J. C. M. Dekkers.
Animal Frontiers, 6: 1.
- Implementation of Genomic Selection in The Poultry Industry
- Promotion of Alleles by Genome Editing in Livestock Breeding Programmes.
Hickey, J. M. , C. Bruce, A. Whitelaw and G. Gorjanc.
Journal of Animal Breeding and Genetics, 133(2):83-4.
- Promotion of Alleles by Genome Editing in Livestock Breeding Programmes.
- Initiating Maize Pre-Breeding Programs Using Genomic Selection to Harness Polygenic Variation from Landrace Populations.
Gorjanc, G., J. Jenko, S. J. Hearne and J. M. Hickey.
BMC Genomics, 17(1):30.
- Initiating Maize Pre-Breeding Programs Using Genomic Selection to Harness Polygenic Variation from Landrace Populations.
2015
- Analytical and Decision Support Tools for Genomics-Assisted Breeding.
Varshney, R. K., V. K. Singh, J. M. Hickey, X. Xun, D. F. Marshall, J. Wang, D. Edwards and J. M. Ribaut.
Trends in Plant Science, 21(4): 354–363.
- Analytical and Decision Support Tools for Genomics-Assisted Breeding.
- Gpluse: Beyond Genomic Selection.
Mackay, I. J., E. S. Ober and J. M. Hickey.
Food and Energy Security, 4(1):25-35.
- Gpluse: Beyond Genomic Selection.
- Potential of Promotion of Alleles by Genome Editing to Improve Quantitative Traits in Livestock Breeding Programs.
Jenko, J., G. Gorjanc, M. A. Cleveland, R. K. Varshney, C. B. Whitelaw, J. A. Woolliams and J. M. Hickey.
Genetics Selection Evolution, 47:55.
- Potential of Promotion of Alleles by Genome Editing to Improve Quantitative Traits in Livestock Breeding Programs.
- Imputation of Single Nucleotide Polymorphism Genotypes in Biparental, Backcross, and Topcross Populations with a Hidden Markov Model.
Hickey, J. M., G. Gorjanc, R. K. Varshney and C. Nettelblad.
Crop Science, 55(5):1934.
- Imputation of Single Nucleotide Polymorphism Genotypes in Biparental, Backcross, and Topcross Populations with a Hidden Markov Model.
- Potential of Genotyping-by-Sequencing for Genomic Selection in Livestock Populations.
Gorjanc, G., M. A. Cleveland, R. D. Houston and J. M. Hickey.
Genetics Selection Evolution, 47:12.
- Potential of Genotyping-by-Sequencing for Genomic Selection in Livestock Populations.
- Reliability of Pedigree-Based and Genomic Evaluations in Selected Populations.
Gorjanc, G., P. Bijma and J. M. Hickey.
Genetics Selection Evolution, 47:65.
- Reliability of Pedigree-Based and Genomic Evaluations in Selected Populations.
2014
- Alphampsim: Flexible Simulation of Multi-Parent Crosses.
Hickey, J. M., G. Gorjanc, S. Hearne and B. E. Huang.
Bioinformatics, 30(18):2686-8.
- Alphampsim: Flexible Simulation of Multi-Parent Crosses.
- Evaluation of Genomic Selection Training Population Designs and Genotyping Strategies in Plant Breeding Programs Using Simulation.
Hickey, J. M., S. Dreisigacker, J. Crossa, S. Hearne, R. Babu, B. M. Prasanna, M. Grondona, A. Zambelli, V. S. Windhausen, K. Mathews and G. Gorjanc.
Crop Science, 54(4):1476.
- Evaluation of Genomic Selection Training Population Designs and Genotyping Strategies in Plant Breeding Programs Using Simulation.
- Evaluation of Measures of Correctness of Genotype Imputation in the Context of Genomic Prediction: A Review of Livestock Applications.
Calus, M. P., A. C. Bouwman, J. M. Hickey, R. F. Veerkamp and H. A. Mulder.
Animal, 8(11):1743-53.
- Evaluation of Measures of Correctness of Genotype Imputation in the Context of Genomic Prediction: A Review of Livestock Applications.
- Imputation of Non-Genotyped Individuals Based on Genotyped Relatives: Assessing the Imputation Accuracy of a Real Case Scenario in Dairy Cattle.
Bouwman, A. C., J. M. Hickey, M. P. Calus and R. F. Veerkamp.
Genetics Selection Evolution, 46:6.
- Imputation of Non-Genotyped Individuals Based on Genotyped Relatives: Assessing the Imputation Accuracy of a Real Case Scenario in Dairy Cattle.
2013
- Extending Long-Range Phasing and Haplotype Library Imputation Methods to Impute Genotypes on Sex Chromosomes.
Hickey, J. M. and A. Kranis.
Genetics Selection Evolution, 45:10.
- Extending Long-Range Phasing and Haplotype Library Imputation Methods to Impute Genotypes on Sex Chromosomes.
- Genomic Evaluations Using Similarity between Haplotypes.
Hickey, J. M., B. P. Kinghorn, B. Tier, S. A. Clark, J. H. van der Werf and G. Gorjanc.
Journal of Animal Breeding and Genetics, 130(4):259-69
- Genomic Evaluations Using Similarity between Haplotypes.
- Genotype Imputation to Increase Sample Size in Pedigreed Populations.
Hickey, J. M., M. A. Cleveland, C. Maltecca, G. Gorjanc, B. Gredler and A. Kranis.
Methods in Molecular Biology, 1019:395-410.
- Genotype Imputation to Increase Sample Size in Pedigreed Populations.
- Sequencing Millions of Animals for Genomic Selection 2.0.
Hickey, J. M.
Journal of Animal Breeding and Genetics, 130(5):331-2
- Sequencing Millions of Animals for Genomic Selection 2.0.
- Genotype Phasing in Populations of Closely Related Individuals.
Hickey, J. M.
Methods in Molecular Biology, 1019:381-94.
- Genotype Phasing in Populations of Closely Related Individuals.
- Whole-Genome Regression and Prediction Methods Applied to Plant and Animal Breeding.
De Los Campos, G., J. M. Hickey, R. Pong-Wong, H. D. Daetwyler and M. P. Calus.
Genetics, 193(2):327-45.
- Whole-Genome Regression and Prediction Methods Applied to Plant and Animal Breeding.
- Genomic Prediction in Animals and Plants: Simulation of Data, Validation, Reporting, and Benchmarking.
Daetwyler, H. D., M. P. Calus, R. Pong-Wong, G. de Los Campos and J. M. Hickey.
Genetics, 193(2):347-65.
- Genomic Prediction in Animals and Plants: Simulation of Data, Validation, Reporting, and Benchmarking.
- Genomic Prediction in CIMMYT Maize and Wheat Breeding Programs.
Crossa, J., P. Pérez, J. Hickey, J. Burgueño, L. Ornella, J. Cerón-Rojas, X. Zhang, S. Dreisigacker, R. Babu, Y. Li, D. Bonnett and K. Mathews.
Heredity, 112(1):48-60.
- Genomic Prediction in CIMMYT Maize and Wheat Breeding Programs.
- Genomic Prediction in Maize Breeding Populations with Genotyping-by-Sequencing.
G. Crossa, J., Y. Beyene, S. Kassa, P. Perez, J. M. Hickey, C. Chen, G. de los Campos, J. Burgueno, V. S. Windhausen, E. Buckler, J. L. Jannink, M. A. Lopez Cruz and R. Babu.
G3 (Bethesda), 3(11):1903-26.
- Genomic Prediction in Maize Breeding Populations with Genotyping-by-Sequencing.
- Practical Implementation of Cost-Effective Genomic Selection in Commercial Pig Breeding Using Imputation.
Cleveland, M. A. and J. M. Hickey.
Journal of Animal Science, 91(8):3583-92.
- Practical Implementation of Cost-Effective Genomic Selection in Commercial Pig Breeding Using Imputation.
- The Effect of Genomic Information on Optimal Contribution Selection in Livestock Breeding Programs.
Clark, S. A., B. P. Kinghorn, J. M. Hickey and J. H. van der Werf.
Genetics Selection Evolution, 45:44.
- The Effect of Genomic Information on Optimal Contribution Selection in Livestock Breeding Programs.
- Genetic Prediction of Complex Traits: Integrating Infinitesimal and Marked Genetic Effects.
Carre, C., F. Gamboa, D. Cros, J. M. Hickey, G. Gorjanc and E. Manfredi.
Genetica, 141(4-6):239-46.
- Genetic Prediction of Complex Traits: Integrating Infinitesimal and Marked Genetic Effects.
2012
- Effectiveness of Genomic Prediction of Maize Hybrid Performance in Different Breeding Populations and Environments.
Windhausen, V. S., G. N. Atlin, J. M. Hickey, J. Crossa, J. L. Jannink, M. E. Sorrells, B. Raman, J. E. Cairns, A. Tarekegne, K. Semagn, Y. Beyene, P. Grudloyma, F. Technow, C. Riedelsheimer and A. E. Melchinger.
G3 (Bethesda), 2(11):1427-36.
- Effectiveness of Genomic Prediction of Maize Hybrid Performance in Different Breeding Populations and Environments.
- Assessment of Alternative Genotyping Strategies to Maximize Imputation Accuracy at Minimal Cost.
Huang, Y., J. M. Hickey, M. A. Cleveland and C. Maltecca.
Genetics Selection Evolution, 44:25.
- Assessment of Alternative Genotyping Strategies to Maximize Imputation Accuracy at Minimal Cost.
- A Phasing and Imputation Method for Pedigreed Populations That Results in a Single-Stage Genomic Evaluation.
Hickey, J. M., B. P. Kinghorn, B. Tier, J. H. van der Werf and M. A. Cleveland.
Genetics Selection Evolution, 44:9.
- A Phasing and Imputation Method for Pedigreed Populations That Results in a Single-Stage Genomic Evaluation.
- Simulated Data for Genomic Selection and Genome-Wide Association Studies Using a Combination of Coalescent and Gene Drop Methods.
Hickey, J. M. and G. Gorjanc.
G3 (Bethesda), 2(4):425-7.
- Simulated Data for Genomic Selection and Genome-Wide Association Studies Using a Combination of Coalescent and Gene Drop Methods.
- Factors Affecting the Accuracy of Genotype Imputation in Populations from Several Maize Breeding Programs.
Hickey, J. M., J. Crossa, R. Babu and G. de los Campos.
Crop Science, 52(2):654.
- Factors Affecting the Accuracy of Genotype Imputation in Populations from Several Maize Breeding Programs.
- A Common Dataset for Genomic Analysis of Livestock Populations.
Cleveland, M. A., J. M. Hickey and S. Forni.
G3 (Bethesda), 2(4):429-35.
- A Common Dataset for Genomic Analysis of Livestock Populations.
- The Importance of Information on Relatives for the Prediction of Genomic Breeding Values and the Implications for the Makeup of Reference Data Sets in Livestock Breeding Schemes.
Clark, S. A., J. M. Hickey, H. D. Daetwyler and J. H. van der Werf.
Genetics Selection Evolution, 44:4.
- The Importance of Information on Relatives for the Prediction of Genomic Breeding Values and the Implications for the Makeup of Reference Data Sets in Livestock Breeding Schemes.
2011
- A Combined Long-Range Phasing and Long Haplotype Imputation Method to Impute Phase for SNP Genotypes.
Hickey, J. M., B. P. Kinghorn, B. Tier, J. F. Wilson, N. Dunstan and J. H. van der Werf.
Genetics Selection Evolution, 43:12.
- A Combined Long-Range Phasing and Long Haplotype Imputation Method to Impute Phase for SNP Genotypes.
- Genotype Imputation for the Prediction of Genomic Breeding Values in Non-Genotyped and Low-Density Genotyped Individuals.
Cleveland, M. A., J. M. Hickey and B. P. Kinghorn.
BMC Proceedings, Volume 5 Supplement 3:S6.
- Genotype Imputation for the Prediction of Genomic Breeding Values in Non-Genotyped and Low-Density Genotyped Individuals.
- Different Models of Genetic Variation and Their Effect on Genomic Evaluation.
Clark, S. A., J. M. Hickey and J. H. van der Werf.
Genetics Selection Evolution, 43:18.
- Different Models of Genetic Variation and Their Effect on Genomic Evaluation.
2010
- Accuracy of Estimated Genomic Breeding Values for Wool and Meat Traits in a Multi-Breed Sheep Population.
Daetwyler, H. D., J. M. Hickey, J. M. Henshall, S. Dominik, B. Gredler, J. H. J. van der Werf and B. J. Hayes.
Animal Production Science, 50(12):1004.
- Accuracy of Estimated Genomic Breeding Values for Wool and Meat Traits in a Multi-Breed Sheep Population.
2009
- Estimation of Prediction Error Variances Via Monte Carlo Sampling Methods Using Different Formulations of the Prediction Error Variance.
Hickey, J. M., R. F. Veerkamp, M. P. Calus, H. A. Mulder and R. Thompson.
Genetics Selection Evolution, 41:23.
- Estimation of Prediction Error Variances Via Monte Carlo Sampling Methods Using Different Formulations of the Prediction Error Variance.
2008
- Estimation of Accuracy and Bias in Genetic Evaluations with Genetic Groups Using Sampling.
Hickey, J. M., M. G. Keane, D. A. Kenny, A. R. Cromie, H. A. Mulder and R. F. Veerkamp.
Journal of Animal Science, 86(5):1047-56.
- Estimation of Accuracy and Bias in Genetic Evaluations with Genetic Groups Using Sampling.
2007
- Genetic Parameters for EUROP Carcass Traits within Different Groups of Cattle in Ireland.
Hickey, J. M., M. G. Keane, D. A. Kenny, A. R. Cromie and R. F. Veerkamp.
Journal of Animal Science, 85(2):314-21.
- Genetic Parameters for EUROP Carcass Traits within Different Groups of Cattle in Ireland.
- Heterogeneity of Genetic Parameters for Calving Difficulty in Holstein Heifers in Ireland.
Hickey, J. M., M. G. Keane, D. A. Kenny, A. R. Cromie, P. R. Amer and R. F. Veerkamp.
Journal of Dairy Science, 90(8):3900-8.
- Heterogeneity of Genetic Parameters for Calving Difficulty in Holstein Heifers in Ireland.
2006
- Genetic Aspects of Growth of Holstein-Friesian Dairy Cows from Birth to Maturity.
Coffey, M. P., J. M. Hickey and S. Brotherstone.
Journal of Dairy Science, 89(1):322-9.
- Genetic Aspects of Growth of Holstein-Friesian Dairy Cows from Birth to Maturity.