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2026 Journal Article The hidden geometry of breeding constraintsOrtiz-Barrientos, Daniel, Jordan, David and Cooper, Mark (2026). The hidden geometry of breeding constraints. Nature Plants, 12 (7), 1316-1324. doi: 10.1038/s41477-026-02332-6 |
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2026 Journal Article Clustering compresses attractors in Watts–Strogatz threshold Boolean networksAlqarni, Maram, Cooper, Mark, Donovan, Diane and Lefevre, James (2026). Clustering compresses attractors in Watts–Strogatz threshold Boolean networks. Journal of Complex Networks, 14 (4) cnag027, 4. doi: 10.1093/comnet/cnag027 |
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2026 Journal Article Ensembles of Graph Attention Networks Supervised by Genotype-to-Phenotype Structures Improved Genomic Prediction PerformanceTomura, Shunichiro, Powell, Owen, Wilkinson, Melanie J and Cooper, Mark (2026). Ensembles of Graph Attention Networks Supervised by Genotype-to-Phenotype Structures Improved Genomic Prediction Performance. in silico Plants, 8 (1) diag014, 1. doi: 10.1093/insilicoplants/diag014 |
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2026 Journal Article Better breeding leveraging more biologyPowell, Owen M., Hickey, Lee, Tomura, Shunichiro and Cooper, Mark (2026). Better breeding leveraging more biology. Trends in Plant Science. doi: 10.1016/j.tplants.2026.05.004 |
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2026 Journal Article Biology-driven genebank pangenetics meet AI-powered predictions to transform crop breedingAbbai, Ragavendran, Schnurbusch, Thorsten, Cooper, Mark and Pandey, Manish K. (2026). Biology-driven genebank pangenetics meet AI-powered predictions to transform crop breeding. Molecular Plant, 19 (6), 1140-1143. doi: 10.1016/j.molp.2026.03.017 |
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2026 Journal Article Optimisation of weighted ensembles of genomic prediction models in maizeTomura, Shunichiro, Powell, Owen, Wilkinson, Melanie J., Lefevre, James and Cooper, Mark (2026). Optimisation of weighted ensembles of genomic prediction models in maize. In Silico Plants, 8 (1) diag010, 1-19. doi: 10.1093/insilicoplants/diag010 |
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2026 Journal Article Ensemble-based genomic prediction for maize flowering-time improves prediction accuracy and reveals novel insights into trait genetic variationTomura, Shunichiro, Powell, Owen, Wilkinson, Melanie J and Cooper, Mark (2026). Ensemble-based genomic prediction for maize flowering-time improves prediction accuracy and reveals novel insights into trait genetic variation. G3: Genes, Genomes, Genetics, 16 (6) jkag090. doi: 10.1093/g3journal/jkag090 |
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2026 Journal Article Back to the future 2: the implications of germplasm structure on the balance between short and long-term genetic gain in a changing target population of environmentsTechnow, Frank, Podlich, Dean and Cooper, Mark (2026). Back to the future 2: the implications of germplasm structure on the balance between short and long-term genetic gain in a changing target population of environments. G3: Genes, Genomes, Genetics, 16 (4) jkag044, 1-21. doi: 10.1093/g3journal/jkag044 |
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2026 Journal Article Root system growth and function respond to soil temperature in maize (Zea mays L.)Clark, Randy, Chamberlain, Dan, Diepenbrock, Christine, Perugini, Leandro, Hisse, Ignacio R., Cooper, Mark and Messina, Carlos D. (2026). Root system growth and function respond to soil temperature in maize (Zea mays L.). Plant Physiology, 200 (3) kiag120, 1-11. doi: 10.1093/plphys/kiag120 |
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2025 Journal Article The Big BIT maize experiment: A large multi-location, multi-year, multi-tester, multi-population predictive breeding validation studyJines, Michael, Chandler, Michael, Podlich, Dean, Baumgarten, Andrew, Wright, Deanne, Jacobson, Amy, Zhao, Honghua, Gogerty, Jared, Regennitter, Matthew, Hung, Hsiao-Yi, McDowell, Riley, Tang, Tom, Diepenbrock, Christine, Helmi, Hoda, Messina, Carlos, Ross, Andrew, Henke, Gary, Spangler, Lindsay, Caldwell, Matthew, Stirling, Leah, Reyes, Andres, Gho, Carla, Cooper, Mark, Arbuckle, John, Smalley, Matthew, Milach, Sandra, Graham, Geoff and Totir, Liviu Radu (2025). The Big BIT maize experiment: A large multi-location, multi-year, multi-tester, multi-population predictive breeding validation study. The Plant Genome, 18 (4) e70117, 1-17. doi: 10.1002/tpg2.70117 |
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2025 Journal Article Ensemble AnalySis with Interpretable Genomic Prediction (EasiGP): Computational tool for interpreting ensembles of genomic prediction modelsTomura, Shunichiro, Wilkinson, Melanie J., Powell, Owen and Cooper, Mark (2025). Ensemble AnalySis with Interpretable Genomic Prediction (EasiGP): Computational tool for interpreting ensembles of genomic prediction models. The Plant Genome, 18 (4) e70138, 1-16. doi: 10.1002/tpg2.70138 |
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2025 Conference Publication Improving yield predictions in drought-prone environments through trait phenotyping and advanced modellingSeverini, Alan, Cooper, Mark, Hammer, Graeme, Hickey, Lee, Christopher, Jack and Chenu, Karine (2025). Improving yield predictions in drought-prone environments through trait phenotyping and advanced modelling. InterDrought VIII, La Serena, Chile, 17-21 November 2025. |
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2025 Conference Publication Phenotyping foundation traits to enhance genomic prediction for wheat yield stability using advanced crop modellingSeverini, Alan, Cooper, Mark, Hammer, Graeme, Hickey, Lee, Christopher, Jack and Chenu, Karine (2025). Phenotyping foundation traits to enhance genomic prediction for wheat yield stability using advanced crop modelling. TropAg, Brisbane, QLD, Australia, 11-13 November 2025. |
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2025 Journal Article Future-ready crops: biology-driven pangenetics meet AI-powered predictionsAbbai, Ragavendran, Schnurbusch, Thorsten, Cooper, Mark and Pandey, Manish (2025). Future-ready crops: biology-driven pangenetics meet AI-powered predictions. doi: 10.20944/preprints202511.0224.v1 |
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2025 Journal Article Understanding rates of genetic gain in sorghum [Sorghum bicolor (L.) Moench] in the United StatesSingh, J., Merchant, A., Mayor, L., Mbaye, M., Gho, C., Cooper, M. and Messina, C. D. (2025). Understanding rates of genetic gain in sorghum [Sorghum bicolor (L.) Moench] in the United States. The Plant Genome, 18 (3) e70122, e70122. doi: 10.1002/tpg2.70122 |
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2025 Journal Article Back to the future 2: the implications of germplasm structure on the balance between short and long-term genetic gain in a changing target population of environmentsTechnow, Frank, Podlich, Dean and Cooper, Mark (2025). Back to the future 2: the implications of germplasm structure on the balance between short and long-term genetic gain in a changing target population of environments. doi: 10.1101/2025.09.01.673542 |
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2025 Journal Article Envirotyping facilitates understanding of genotype × environment interactions and highlights the potential of stay-green traits in wheatAmin, Asad, Christopher, Jack, Cooper, Mark, Collins, Brian, Voss-Fels, Kai, Hickey, Lee and Chenu, Karine (2025). Envirotyping facilitates understanding of genotype × environment interactions and highlights the potential of stay-green traits in wheat. Field Crops Research, 331 109940, 1-16. doi: 10.1016/j.fcr.2025.109940 |
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2025 Journal Article Breeding perspectives on tackling trait genome-to-phenome (G2P) dimensionality using ensemble-based genomic predictionCooper, Mark, Tomura, Shunichiro, Wilkinson, Melanie J., Powell, Owen and Messina, Carlos D. (2025). Breeding perspectives on tackling trait genome-to-phenome (G2P) dimensionality using ensemble-based genomic prediction. Theoretical and Applied Genetics, 138 (7) 172, 1-24. doi: 10.1007/s00122-025-04960-6 |
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2025 Journal Article Toward a general framework for AI-enabled prediction in crop improvementMessina, Carlos, Garcia-Abadillo, Julian, Powell, Owen, Tomura, Shunichiro, Zare, Alina, Ganapathysubramanian, Baskar and Cooper, Mark (2025). Toward a general framework for AI-enabled prediction in crop improvement. Theoretical and Applied Genetics, 138 (7) 151, 151-7. doi: 10.1007/s00122-025-04928-6 |
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2025 Journal Article Integrating yield gap analysis to capture genotype by environment by management interactions for Australian broadacre sorghum cropping systemsGarba, Ismail I., Fernandez, Javier A., Chen, Qiaomin, Gho, Carla, deVoil, Peter, Cooper, Mark and Chapman, Scott C. (2025). Integrating yield gap analysis to capture genotype by environment by management interactions for Australian broadacre sorghum cropping systems. Field Crops Research, 326 109858, 109858. doi: 10.1016/j.fcr.2025.109858 |
