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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 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. 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, 109940. 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 |
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2025 Other Outputs Envirotyping Facilitates Understanding of Genotype x Environment Interactions and Highlights the Potential of Stay-green Traits in WheatAmin, Asad, Christopher, Jack, Forknall, Clayton, Cooper, Mark, Macdonald, Bethany, Collins, Brian, Voss-Fels, Kai, Hickey, Lee and Chenu, Karine (2025). Envirotyping Facilitates Understanding of Genotype x Environment Interactions and Highlights the Potential of Stay-green Traits in Wheat. doi: 10.1101/2025.03.11.642575 |
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2025 Journal Article Improved Genomic Prediction Performance with Ensembles of Diverse ModelsTomura, Shunichiro, Wilkinson, Melanie J., Cooper, Mark and Powell, Owen (2025). Improved Genomic Prediction Performance with Ensembles of Diverse Models. G3: Genes, Genomes, Genetics, 15 (5) jkaf048, 1-15. doi: 10.1093/g3journal/jkaf048 |
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2025 Book Chapter Pangenomes empower the investigation of biological adaptationsLiu, Yang, Kainer, David, Jannah, Adillatul Lathiifatun and Cooper, Mark (2025). Pangenomes empower the investigation of biological adaptations. Plant pangenomes and pangenomics. (pp. 361-384) edited by Jen-tsung Chen. London, United Kingdom: Elsevier. doi: 10.1016/b978-0-443-26791-8.00018-2 |
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2025 Journal Article Transgene effects vary among maize populations with implications for improving quantitative traitsLinares, Julien F., Coles, Nathan D., Mo, Hua, Habben, Jeffrey E., Humbert, Sabrina, Messina, Carlos, Tang, Tom, Cooper, Mark, Gho, Carla, Carrasco, Ricardo, Carter, Javier, Flounders, Jillian Wicher and Brummer, E. Charles (2025). Transgene effects vary among maize populations with implications for improving quantitative traits. Crop Science, 65 (1) e21408. doi: 10.1002/csc2.21408 |
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2024 Other Outputs Improvements in prediction performance of ensemble approaches for genomic prediction in crop breedingTomura, Shunichiro, Cooper, Mark and Powell, Owen (2024). Improvements in prediction performance of ensemble approaches for genomic prediction in crop breeding. doi: 10.1101/2024.09.06.611589 |
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2024 Conference Publication Prediction of non-additive genetic effects with hierarchical genomic prediction modelsPowell, Owen, McLean, Greg, Brider, Jason, Saddigh, Joe, Technow, Frank, Tang, Tom, Totir, Radu, Messina, Carlos D., Hammer, Graeme and Cooper, Mark (2024). Prediction of non-additive genetic effects with hierarchical genomic prediction models. International Conference of Quantitative Genetics (ICQG) 7, Vienna, Austria, 22-26 July 2024. doi: 10.6084/m9.figshare.26425735.v1 |
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2024 Other Outputs Molecular Breeding MethodsCooper, Mark, Messina, Carlos, Technow, Frank and Totir, Radu (2024). Molecular Breeding Methods. 11985930. |
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2024 Journal Article Contrasting leaf‐scale photosynthetic low‐light response and its temperature dependency are key to differences in crop‐scale radiation use efficiencyWu, Alex, Truong, Sandra Huynh, McCormick, Ryan, van Oosterom, Erik J., Messina, Carlos D., Cooper, Mark and Hammer, Graeme L. (2024). Contrasting leaf‐scale photosynthetic low‐light response and its temperature dependency are key to differences in crop‐scale radiation use efficiency. New Phytologist, 241 (6), 2435-2447. doi: 10.1111/nph.19537 |
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2024 Journal Article Methods for evaluating effects of transgenes for quantitative traitsLinares, Julien F., Coles, Nathan D., Mo, Hua, Habben, Jeffrey E., Humbert, Sabrina, Messina, Carlos, Tang, Tom, Cooper, Mark, Gho, Carla, Carrasco, Ricardo, Carter, Javier, Flounders, Jillian Wicher and Brummer, E. Charles (2024). Methods for evaluating effects of transgenes for quantitative traits. Crop Science, 64 (1), 141-148. doi: 10.1002/csc2.21141 |
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2024 Book Chapter Transforming food production with AICooper, Mark, Hickey, Lee, Jiang, Xianxian, La Fata, Giorgio, Lomas, Harold, Miller, Tim, O’Brien, Susan, Patel, Parth and Tomarchio, Samuel (2024). Transforming food production with AI. Food AI: A game changer for Australia’s food and beverage sector. (pp. 5-13) edited by Janet R. McColl-Kennedy and Damian Hine. Brisbane, QLD, Australia: The University of Queensland, Australia's Food and Beverage Accelerator (FaBA). |
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2023 Conference Publication APSIM-WGP: a software platform to predict crop GxExM interactionsPowell, Owen, McLean, Greg, Brider, Jason, Hammer, Graeme and Cooper, Mark (2023). APSIM-WGP: a software platform to predict crop GxExM interactions. GxExM Symposium II, Gainesville, FL USA, 6-7 November 2023. |
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2023 Journal Article Genetic modification can improve crop yields — but stop overselling itKhaipho-Burch, Merritt, Cooper, Mark, Crossa, Jose, de Leon, Natalia, Holland, James, Lewis, Ramsey, McCouch, Susan, Murray, Seth C., Rabbi, Ismail, Ronald, Pamela, Ross-Ibarra, Jeffrey, Weigel, Detlef and Buckler, Edward S. (2023). Genetic modification can improve crop yields — but stop overselling it. Nature, 621 (7979), 470-473. doi: 10.1038/d41586-023-02895-w |
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2023 Other Outputs Crop improvement can accelerate agriculture adaptation to societal demands and climate changeMessina, Carlos D., Borras, Lucas, Tang, Tom and Cooper, Mark (2023). Crop improvement can accelerate agriculture adaptation to societal demands and climate change. doi: 10.1101/2023.09.19.558447 |
