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2025 Journal Article Testing the potential of zebularine to induce heritable changes in crop growth and developmentFinnegan, E. Jean, Crisp, Peter A., Zhang, Peng, Eglitis-Sexton, Judith, Greenwood, Julian, Hintzsche, Jessica, Li, Jianbo, Taylor, Jen, Wallace, Xiaomei and Swain, Stephen (2025). Testing the potential of zebularine to induce heritable changes in crop growth and development. Theoretical and Applied Genetics, 138 (1) 26, 26-1. doi: 10.1007/s00122-024-04799-3 |
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2024 Journal Article Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translationSmith, Aaron B., Ganguly, Diep R., Moore, Marten, Bowerman, Andrew F., Janapala, Yoshika, Shirokikh, Nikolay E., Pogson, Barry J. and Crisp, Peter A. (2024). Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation. The Plant Journal, 117 (3), 818-839. doi: 10.1111/tpj.16531 |
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2024 Journal Article Utilisation of Methylome Data to Identify Stably Unmethylated Regions in Plant GenomesEglitis-Sexton, Judith, Mangila, Leroy, Andrews, Haylie, Hickey, Lee and Crisp, Peter (2024). Utilisation of Methylome Data to Identify Stably Unmethylated Regions in Plant Genomes. Bio-Protocol, 14 (4), 1-16. doi: 10.21769/bioprotoc.4944 |
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2023 Journal Article Genetic mapping, candidate gene identification and marker validation for host plant resistance to the race 4 of Fusarium oxysporum f. sp. cubense using Musa acuminata ssp. malaccensisChen, Andrew, Sun, Jiaman, Viljoen, Altus, Mostert, Diane, Xie, Yucong, Mangila, Leroy, Bothma, Sheryl, Lyons, Rebecca, Hřibová, Eva, Christelová, Pavla, Uwimana, Brigitte, Amah, Delphine, Pearce, Stephen, Chen, Ning, Batley, Jacqueline, Edwards, David, Doležel, Jaroslav, Crisp, Peter, Brown, Allan F., Martin, Guillaume, Yahiaoui, Nabila, D’Hont, Angelique, Coin, Lachlan, Swennen, Rony and Aitken, Elizabeth A. B. (2023). Genetic mapping, candidate gene identification and marker validation for host plant resistance to the race 4 of Fusarium oxysporum f. sp. cubense using Musa acuminata ssp. malaccensis. Pathogens, 12 (6) 820, 820. doi: 10.3390/pathogens12060820 |
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2022 Journal Article Epigenetic features drastically impact CRISPR–Cas9 efficacy in plantsWeiss, Trevor, Crisp, Peter A., Rai, Krishan M., Song, Meredith, Springer, Nathan M. and Zhang, Feng (2022). Epigenetic features drastically impact CRISPR–Cas9 efficacy in plants. Plant Physiology, 190 (2), 1153-1164. doi: 10.1093/plphys/kiac285 |
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2022 Journal Article Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networksWrightsman, Travis, Marand, Alexandre P., Crisp, Peter A., Springer, Nathan M. and Buckler, Edward S. (2022). Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks. The Plant Genome, 15 (3) e20249, 1-13. doi: 10.1002/tpg2.20249 |
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2022 Journal Article Identifying transcription factor-DNA interactions using machine learningBang, Sohyun, Galli, Mary, Crisp, Peter A., Gallavotti, Andrea and Schmitz, Robert J. (2022). Identifying transcription factor-DNA interactions using machine learning. In Silico Plants, 4 (2) diac014, 1-15. doi: 10.1093/insilicoplants/diac014 |
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2022 Journal Article Enzymes degraded under high light maintain proteostasis by transcriptional regulation in ArabidopsisLi, Lei, Duncan, Owen, Ganguly, Diep R., Lee, Chun Pong, Crisp, Peter A., Wijerathna-Yapa, Akila, Salih, Karzan, Trösch, Josua, Pogson, Barry J. and Millar, A. Harvey (2022). Enzymes degraded under high light maintain proteostasis by transcriptional regulation in Arabidopsis. Proceedings of the National Academy of Sciences, 119 (20) e2121362119, 1-11. doi: 10.1073/pnas.2121362119 |
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2022 Journal Article Genome‐wide loss of CHH methylation with limited transcriptome changes in Setaria viridis DOMAINS REARRANGED METHYLTRANSFERASE (DRM) mutantsRead, Andrew, Weiss, Trevor, Crisp, Peter A, Liang, Zhikai, Noshay, Jaclyn, Menard, Claire C, Wang, Chunfang, Song, Meredith, Hirsch, Candice N, Springer, Nathan M and Zhang, Feng (2022). Genome‐wide loss of CHH methylation with limited transcriptome changes in Setaria viridis DOMAINS REARRANGED METHYLTRANSFERASE (DRM) mutants. The Plant Journal, 111 (1), 103-116. doi: 10.1111/tpj.15781 |
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2022 Journal Article Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traitsVafadarshamasbi, Ulduz, Mace, Emma, Jordan, David and Crisp, Peter A. (2022). Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits. Biochemical Society Transactions, 50 (1), 583-596. doi: 10.1042/bst20210908 |
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2022 Journal Article Harnessing genetic variation at regulatory regions to fine-tune traits for climate resilient cropsGanguly, Diep R., Hickey, Lee T. and Crisp, Peter A. (2022). Harnessing genetic variation at regulatory regions to fine-tune traits for climate resilient crops. Molecular Plant, 15 (2), 222-224. doi: 10.1016/j.molp.2021.12.011 |
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2022 Journal Article Beyond the gene: epigenetic and cis-regulatory targets offer new breeding potential for the futureCrisp, Peter A., Bhatnagar-Mathur, Pooja, Hundleby, Penny, Godwin, Ian D., Waterhouse, Peter M. and Hickey, Lee T. (2022). Beyond the gene: epigenetic and cis-regulatory targets offer new breeding potential for the future. Current Opinion in Biotechnology, 73, 88-94. doi: 10.1016/j.copbio.2021.07.008 |
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2022 Journal Article Epigenome guided crop improvement: current progress and future opportunitiesZhang, Yan, Andrews, Haylie, Eglitis-Sexton, Judith, Godwin, Ian, Tanurdžić, Miloš and Crisp, Peter A. (2022). Epigenome guided crop improvement: current progress and future opportunities. Emerging Topics in Life Sciences, 6 (2), 141-151. doi: 10.1042/etls20210258 |
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2022 Journal Article Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory informationZhou, Peng, Enders, Tara A., Myers, Zachary A., Magnusson, Erika, Crisp, Peter A., Noshay, Jaclyn M., Gomez-Cano, Fabio, Liang, Zhikai, Grotewold, Erich, Greenham, Kathleen and Springer, Nathan M. (2022). Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory information. The Plant Cell, 34 (1), 514-534. doi: 10.1093/plcell/koab267 |
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2021 Journal Article Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomesNoshay, Jaclyn M., Liang, Zhikai, Zhou, Peng, Crisp, Peter A., Marand, Alexandre P., Hirsch, Candice N., Schmitz, Robert J. and Springer, Nathan M. (2021). Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes. G3: Genes, Genomes, Genetics, 11 (8) jkab190. doi: 10.1093/g3journal/jkab190 |
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2021 Journal Article Science forum: a community-led initiative for training in reproducible researchAuer, Susann, Haelterman, Nele A., Weissgerber, Tracey L., Erlich, Jeffrey C., Susilaradeya, Damar, Julkowska, Magdalena, Gazda, Małgorzata Anna, Schwessinger, Benjamin, Jadavji, Nafisa M., Abitua, Angela, Niraulu, Anzela, Shahb, Aparna, Clyburne-Sherinb, April, Guiquel, Benoit, Alicea, Bradly, Lamanna, Caroline, Ganguly, Diep, Perkins, Eric, Jambor, Helena, Li, Ian Man Ho, Tsang, Jennifer, Kamens, Joanne, Teytelman, Lenny, Paul, Mariella, Cronin, Michelle, Schmelling, Nicolas, Crisp, Peter, Kutum, Rintu, Phuyal, Santosh ... Bachle, Susanna (2021). Science forum: a community-led initiative for training in reproducible research. eLife, 10 e64719. doi: 10.7554/eLife.64719 |
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2021 Journal Article Current status and prospects of plant genome editing in AustraliaZhang, Yan, Restall, Jemma, Crisp, Peter, Godwin, Ian and Liu, Guoquan (2021). Current status and prospects of plant genome editing in Australia. In Vitro Cellular & Developmental Biology - Plant, 57 (4), 1-10. doi: 10.1007/s11627-021-10188-y |
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2021 Journal Article Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maizeLiang, Zhikai, Anderson, Sarah N., Noshay, Jaclyn M., Crisp, Peter A., Enders, Tara A. and Springer, Nathan M. (2021). Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize. Plant Physiology, 186 (1), 1-14. doi: 10.1093/plphys/kiab073 |
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2021 Journal Article Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposonsNoshay, Jaclyn M., Marand, Alexandre P., Anderson, Sarah N., Zhou, Peng, Mejia Guerra, Maria Katherine, Lu, Zefu, O’Connor, Christine H., Crisp, Peter A., Hirsch, Candice N., Schmitz, Robert J. and Springer, Nathan M. (2021). Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons. Genetics, 217 (1) iyaa003, 1-13. doi: 10.1093/genetics/iyaa003 |
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2020 Journal Article Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomesCrisp, Peter A., Marand, Alexandre P., Noshay, Jaclyn M., Zhou, Peng, Lu, Zefu, Schmitz, Robert J. and Springer, Nathan M. (2020). Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes. Proceedings of the National Academy of Sciences, 117 (38), 202010250-24000. doi: 10.1073/pnas.2010250117 |
