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2020 Journal Article Genome-wide association study of wood anatomical and morphological traits in Populus trichocarpaChhetri, Hari B., Furches, Anna, Macaya-Sanz, David, Walker, Alejandro R., Kainer, David, Jones, Piet, Harman-Ware, Anne E., Tschaplinski, Timothy J., Jacobson, Daniel, Tuskan, Gerald A. and DiFazio, Stephen P. (2020). Genome-wide association study of wood anatomical and morphological traits in Populus trichocarpa. Frontiers in Plant Science, 11 545748. doi: 10.3389/fpls.2020.545748 |
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2020 Journal Article A phylogenomic approach reveals a low somatic mutation rate in a long-lived plantOrr, Adam J., Padovan, Amanda, Kainer, David, Kulheim, Carsten, Bromham, Lindell, Bustos-Segura, Carlos, Foley, William, Haff, Tonya, Hsieh, Ji-Fan, Morales-Suarez, Alejandro, Cartwright, Reed A. and Lanfear, Robert (2020). A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant. Royal Society of London. Proceedings B. Biological Sciences, 287 (1922) 20192364, 20192364. doi: 10.1098/rspb.2019.2364 |
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2020 Journal Article Can exascale computing and explainable artificial intelligence applied to plant biology deliver on the United Nations sustainable development goals?Streich, Jared, Romero, Jonathon, Gazolla, João Gabriel Felipe Machado, Kainer, David, Cliff, Ashley, Prates, Erica Teixeira, Brown, James B, Khoury, Sacha, Tuskan, Gerald A, Garvin, Michael, Jacobson, Daniel and Harfouche, Antoine L (2020). Can exascale computing and explainable artificial intelligence applied to plant biology deliver on the United Nations sustainable development goals?. Current Opinion in Biotechnology, 61, 217-225. doi: 10.1016/j.copbio.2020.01.010 |
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2020 Journal Article The draft nuclear genome assembly of Eucalyptus pauciflora: a pipeline for comparing de novo assembliesWang, Weiwen, Das, Ashutosh, Kainer, David, Schalamun, Miriam, Morales-Suarez, Alejandro, Schwessinger, Benjamin and Lanfear, Robert (2020). The draft nuclear genome assembly of Eucalyptus pauciflora: a pipeline for comparing de novo assemblies. GigaScience, 9 (1) giz160, 1-12. doi: 10.1093/gigascience/giz160 |
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2019 Journal Article A high-performance computing implementation of iterative random forest for the creation of predictive expression networksCliff, Ashley, Romero, Jonathon, Kainer, David, Walker, Angelica, Furches, Anna and Jacobson, Daniel (2019). A high-performance computing implementation of iterative random forest for the creation of predictive expression networks. Genes, 10 (12) 996, 1-13. doi: 10.3390/genes10120996 |
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2019 Journal Article Accelerating climate resilient plant breeding by applying next-generation artificial intelligenceHarfouche, Antoine L., Jacobson, Daniel A., Kainer, David, Romero, Jonathon C., Harfouche, Antoine H., Mugnozza, Giuseppe Scarascia, Moshelion, Menachem, Tuskan, Gerald A., Keurentjes, Joost J. B. and Altman, Arie (2019). Accelerating climate resilient plant breeding by applying next-generation artificial intelligence. Trends in Biotechnology, 37 (11), 1217-1235. doi: 10.1016/j.tibtech.2019.05.007 |
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2019 Journal Article Finding new cell wall regulatory genes in populus trichocarpa using multiple lines of evidenceFurches, Anna, Kainer, David, Weighill, Deborah, Large, Annabel, Jones, Piet, Walker, Angelica M., Romero, Jonathon, Gazolla, Joao Gabriel Felipe Machado, Joubert, Wayne, Shah, Manesh, Streich, Jared, Ranjan, Priya, Schmutz, Jeremy, Sreedasyam, Avinash, Macaya-Sanz, David, Zhao, Nan, Martin, Madhavi Z., Rao, Xiaolan, Dixon, Richard A., DiFazio, Stephen, Tschaplinski, Timothy J., Chen, Jin-Gui, Tuskan, Gerald A. and Jacobson, Daniel (2019). Finding new cell wall regulatory genes in populus trichocarpa using multiple lines of evidence. Frontiers in Plant Science, 10 1249. doi: 10.3389/fpls.2019.01249 |
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2019 Journal Article Multitrait genome-wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traitsChhetri, Hari B., Macaya-Sanz, David, Kainer, David, Biswal, Ajaya K., Evans, Luke M., Chen, Jin-Gui, Collins, Cassandra, Hunt, Kimberly, Mohanty, Sushree S., Rosenstiel, Todd, Ryno, David, Winkeler, Kim, Yang, Xiaohan, Jacobson, Daniel, Mohnen, Debra, Muchero, Wellington, Strauss, Steven H., Tschaplinski, Timothy J., Tuskan, Gerald A. and DiFazio, Stephen P. (2019). Multitrait genome-wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits. New Phytologist, 223 (1), 293-309. doi: 10.1111/nph.15777 |
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2019 Journal Article MinIONQC: fast and simple quality control for MinION sequencing dataLanfear, R., Schalamun, M., Kainer, D., Wang, W. and Schwessinger, B. (2019). MinIONQC: fast and simple quality control for MinION sequencing data. Bioinformatics, 35 (3), 523-525. doi: 10.1093/bioinformatics/bty654 |
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2019 Journal Article Harnessing the MinION: An example of how to establish long-read sequencing in a laboratory using challenging plant tissue from Eucalyptus paucifloraSchalamun, Miriam, Nagar, Ramawatar, Kainer, David, Beavan, Eleanor, Eccles, David, Rathjen, John P., Lanfear, Robert and Schwessinger, Benjamin (2019). Harnessing the MinION: An example of how to establish long-read sequencing in a laboratory using challenging plant tissue from Eucalyptus pauciflora. Molecular Ecology Resources, 19 (1), 77-89. doi: 10.1111/1755-0998.12938 |
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2018 Journal Article Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test caseWang, Weiwen, Schalamun, Miriam, Morales-Suarez, Alejandro, Kainer, David, Schwessinger, Benjamin and Lanfear, Robert (2018). Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case. BMC Genomics, 19 (1) 977, 1-15. doi: 10.1186/s12864-018-5348-8 |
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2018 Journal Article High Throughput Screening Technologies in Biomass CharacterizationDecker, Stephen R., Harman-Ware, Anne E., Happs, Renee M., Wolfrum, Edward J., Tuskan, Gerald A., Kainer, David, Oguntimein, Gbekeloluwa B., Rodriguez, Miguel, Weighill, Deborah, Jones, Piet and Jacobson, Daniel (2018). High Throughput Screening Technologies in Biomass Characterization. Frontiers in Energy Research, 6 120, 1-18. doi: 10.3389/fenrg.2018.00120 |
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2017 Journal Article Transcriptome analysis of terpene chemotypes of Melaleuca alternifolia across different tissuesBustos‐Segura, Carlos, Padovan, Amanda, Kainer, David, Foley, William J. and Külheim, Carsten (2017). Transcriptome analysis of terpene chemotypes of Melaleuca alternifolia across different tissues. Plant, Cell & Environment, 40 (10), 2406-2425. doi: 10.1111/pce.13048 |
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2017 Journal Article Assessment of a non-destructive method to predict oil yield in Eucalyptus polybractea (blue mallee)Kainer, David, Bush, David, Foley, William J. and Külheim, Carsten (2017). Assessment of a non-destructive method to predict oil yield in Eucalyptus polybractea (blue mallee). Industrial Crops and Products, 102, 32-44. doi: 10.1016/j.indcrop.2017.03.008 |
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2015 Journal Article Genomic approaches to selection in outcrossing perennials: focus on essential oil cropsKainer, David, Lanfear, Robert, Foley, William J. and Külheim, Carsten (2015). Genomic approaches to selection in outcrossing perennials: focus on essential oil crops. Theoretical and Applied Genetics, 128 (12), 2351-2365. doi: 10.1007/s00122-015-2591-0 |
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2015 Journal Article The effects of partitioning on phylogenetic inferenceKainer, David and Lanfear, Robert (2015). The effects of partitioning on phylogenetic inference. Molecular Biology and Evolution, 32 (6), 1611-1627. doi: 10.1093/molbev/msv026 |
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2014 Journal Article Selecting optimal partitioning schemes for phylogenomic datasetsLanfear, Robert, Calcott, Brett, Kainer, David, Mayer, Christoph and Stamatakis, Alexandros (2014). Selecting optimal partitioning schemes for phylogenomic datasets. BMC Evolutionary Biology, 14 (1) 82, 1-14. doi: 10.1186/1471-2148-14-82 |
