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2022 Journal Article Structural variants identified using non-Mendelian inheritance patterns advance the mechanistic understanding of autism spectrum disorderKainer, David, Templeton, Alan R., Prates, Erica T., Jacboson, Daniel, Allan, Euan R.O., Climer, Sharlee and Garvin, Michael R. (2022). Structural variants identified using non-Mendelian inheritance patterns advance the mechanistic understanding of autism spectrum disorder. Human Genetics and Genomics Advances, 4 (1) 100150, 1-21. doi: 10.1016/j.xhgg.2022.100150 |
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2022 Journal Article Evaluating the performance of random forest and iterative random forest based methods when applied to gene expression dataWalker, Angelica M., Cliff, Ashley, Romero, Jonathon, Shah, Manesh B., Jones, Piet, Felipe Machado Gazolla, Joao Gabriel, Jacobson, Daniel A and Kainer, David (2022). Evaluating the performance of random forest and iterative random forest based methods when applied to gene expression data. Computational and Structural Biotechnology Journal, 20, 3372-3386. doi: 10.1016/j.csbj.2022.06.037 |
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2019 Journal Article High marker density GWAS provides novel insights into the genomic architecture of terpene oil yield in EucalyptusKainer, David, Padovan, Amanda, Degenhardt, Joerg, Krause, Sandra, Mondal, Prodyut, Foley, William J. and Külheim, Carsten (2019). High marker density GWAS provides novel insights into the genomic architecture of terpene oil yield in Eucalyptus. New Phytologist, 223 (3), 1489-1504. doi: 10.1111/nph.15887 |
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2018 Journal Article Accuracy of Genomic Prediction for Foliar Terpene Traits in Eucalyptus polybracteaKainer, David, Stone, Eric A., Padovan, Amanda, Foley, William J. and Külheim, Carsten (2018). Accuracy of Genomic Prediction for Foliar Terpene Traits in Eucalyptus polybractea. G3: Genes, Genomes, Genetics, 8 (8), 2573-2583. doi: 10.1534/g3.118.200443 |
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2017 Journal Article Plant-Derived Terpenes: A Feedstock for Specialty BiofuelsMewalal, Ritesh, Rai, Durgesh K., Kainer, David, Chen, Feng, Külheim, Carsten, Peter, Gary F. and Tuskan, Gerald A. (2017). Plant-Derived Terpenes: A Feedstock for Specialty Biofuels. Trends in Biotechnology, 35 (3), 227-240. doi: 10.1016/j.tibtech.2016.08.003 |
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2024 Journal Article Centromeres are hotspots for chromosomal inversions and breeding traits in mangoWilkinson, Melanie J., McLay, Kathleen, Kainer, David, Elphinstone, Cassandra, Dillon, Natalie L., Webb, Matthew, Wijesundara, Upendra K., Ali, Asjad, Bally, Ian S. E., Munyengwa, Norman, Furtado, Agnelo, Henry, Robert J., Hardner, Craig M. and Ortiz‐Barrientos, Daniel (2024). Centromeres are hotspots for chromosomal inversions and breeding traits in mango. New Phytologist, 245 (2), 899-913. doi: 10.1111/nph.20252 |
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2024 Journal Article Multi-omic network analysis identifies dysregulated neurobiological pathways in opioid addictionSullivan, Kyle A., Kainer, David, Lane, Matthew, Cashman, Mikaela, Miller, J. Izaak, Garvin, Michael R., Townsend, Alice, Quach, Bryan C., Willis, Caryn, Kruse, Peter, Gaddis, Nathan C., Mathur, Ravi, Corradin, Olivia, Maher, Brion S., Scacheri, Peter C., Sanchez-Roige, Sandra, Palmer, Abraham A., Troiani, Vanessa, Chesler, Elissa J., Kember, Rachel L., Kranzler, Henry R., Justice, Amy C., Xu, Ke, Aouizerat, Bradley E., Hancock, Dana B., Johnson, Eric O. and Jacobson, Daniel A. (2024). Multi-omic network analysis identifies dysregulated neurobiological pathways in opioid addiction. Biological Psychiatry. doi: 10.1016/j.biopsych.2024.11.013 |
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2024 Journal Article Analyses of GWAS signal using GRIN identify additional genes contributing to suicidal behaviorSullivan, Kyle A., Lane, Matthew, Cashman, Mikaela, Miller, J. Izaak, Pavicic, Mirko, Walker, Angelica M., Cliff, Ashley, Romero, Jonathon, Qin, Xuejun, Mullins, Niamh, Docherty, Anna, Coon, Hilary, Ruderfer, Douglas M., International Suicide Genetics Consortium, VA Million Veteran Program, MVP Suicide Exemplar Workgroup, Garvin, Michael R., Pestian, John P., Ashley-Koch, Allison E., Beckham, Jean C., McMahon, Benjamin, Oslin, David W., Kimbrel, Nathan A., Jacobson, Daniel A. and Kainer, David (2024). Analyses of GWAS signal using GRIN identify additional genes contributing to suicidal behavior. Communications Biology, 7 (1) 1360, 1360. doi: 10.1038/s42003-024-06943-7 |
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2024 Journal Article High dimensional predictions of suicide risk in 4.2 million US Veterans using ensemble transfer learningDhaubhadel, Sayera, Ganguly, Kumkum, Ribeiro, Ruy M., Cohn, Judith D., Hyman, James M., Hengartner, Nicolas W., Kolade, Beauty, Singley, Anna, Bhattacharya, Tanmoy, Finley, Patrick, Levin, Drew, Thelen, Haedi, Cho, Kelly, Costa, Lauren, Ho, Yuk-Lam, Justice, Amy C., Pestian, John, Santel, Daniel, Zamora-Resendiz, Rafael, Crivelli, Silvia, Tamang, Suzanne, Martins, Susana, Trafton, Jodie, Oslin, David W., Beckham, Jean C., Kimbrel, Nathan A., Agarwal, Khushbu, Ashley-Koch, Allison E., Aslan, Mihaela ... McMahon, Benjamin H. (2024). High dimensional predictions of suicide risk in 4.2 million US Veterans using ensemble transfer learning. Scientific Reports, 14 (1) 1793, 1-19. doi: 10.1038/s41598-024-51762-9 |
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2023 Journal Article A glimpse into the fungal metabolomic abyss: Novel network analysis reveals relationships between exogenous compounds and their outputsGopalakrishnan Meena, Muralikrishnan, Lane, Matthew J., Tannous, Joanna, Carrell, Alyssa A., Abraham, Paul E., Giannone, Richard J., Ané, Jean-Michel, Keller, Nancy P., Labbé, Jesse L., Kainer, David, Jacobson, Daniel A. and Rush, Tomás A. (2023). A glimpse into the fungal metabolomic abyss: Novel network analysis reveals relationships between exogenous compounds and their outputs. PNAS Nexus, 2 (10) pgad322, 1-15. doi: 10.1093/pnasnexus/pgad322 |
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2023 Journal Article Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineeringNoshay, Jaclyn M., Walker, Tyler, Alexander, William G., Klingeman, Dawn M., Romero, Jonathon, Walker, Angelica M., Prates, Erica, Eckert, Carrie, Irle, Stephan, Kainer, David and Jacobson, Daniel A. (2023). Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering. Nucleic Acids Research, 51 (19), 10147-10161. doi: 10.1093/nar/gkad736 |
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2023 Journal Article Validation of a metabolite–GWAS network for Populus trichocarpa family 1 UDP-glycosyltransferasesSaint-Vincent, Patricia M. B., Furches, Anna, Galanie, Stephanie, Teixeira Prates, Erica, Aldridge, Jessa L., Labbe, Audrey, Zhao, Nan, Martin, Madhavi Z., Ranjan, Priya, Jones, Piet, Kainer, David, Kalluri, Udaya C., Chen, Jin-Gui, Muchero, Wellington, Jacobson, Daniel A. and Tschaplinski, Timothy J. (2023). Validation of a metabolite–GWAS network for Populus trichocarpa family 1 UDP-glycosyltransferases. Frontiers in Plant Science, 14 1210146. doi: 10.3389/fpls.2023.1210146 |
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2023 Journal Article Few-shot learning enables population-scale analysis of leaf traits in Populus trichocarpaLagergren, John Heikki, Pavicic, Mirko, Chhetri, Hari B., York, Larry M., Hyatt, Doug, Kainer, David, Rutter, Erica M., Flores, Kevin, Bailey-Bale, Jack, Klein, Marie, Taylor, Gail, Jacobson, Daniel and Streich, Jared (2023). Few-shot learning enables population-scale analysis of leaf traits in Populus trichocarpa. Plant Phenomics, 5 0072, 1-18. doi: 10.34133/plantphenomics.0072 |
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2023 Journal Article Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop PopulusCope, Kevin R., Prates, Erica T., Miller, John I., Demerdash, Omar N.A., Shah, Manesh, Kainer, David, Cliff, Ashley, Sullivan, Kyle A., Cashman, Mikaela, Lane, Matthew, Matthiadis, Anna, Labbé, Jesse, Tschaplinski, Timothy J., Jacobson, Daniel A. and Kalluri, Udaya C. (2023). Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop Populus. Computational and Structural Biotechnology Journal, 21, 1122-1139. doi: 10.1016/j.csbj.2022.12.052 |
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2023 Journal Article Genetics of varicose veins reveals polygenic architecture and genetic overlap with arterial and venous diseaseLevin, Michael G., Huffman, Jennifer E., Verma, Anurag, Sullivan, Kyle A., Rodriguez, Alexis A., Kainer, David, Garvin, Michael R., Lane, Matthew, Cashman, Mikaela, Miller, J. Izaak, Won, Hyejung, Li, Binglan, Luo, Yuan, Jarvik, Gail P., Hakonarson, Hakon, Jasper, Elizabeth A., Bick, Alexander G., Tsao, Philip S., Ritchie, Marylyn D., Jacobson, Daniel A., Madduri, Ravi K. and Damrauer, Scott M. (2023). Genetics of varicose veins reveals polygenic architecture and genetic overlap with arterial and venous disease. Nature Cardiovascular Research, 2 (1), 44-57. doi: 10.1038/s44161-022-00196-5 |
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2022 Journal Article Lipo-chitooligosaccharides induce specialized fungal metabolite profiles that modulate bacterial growthRush, Tomás A., Tannous, Joanna, Lane, Matthew J., Meena, Muralikrishnan Gopalakrishnan, Carrell, Alyssa A., Golan, Jacob J., Drott, Milton T., Cottaz, Sylvain, Fort, Sébastien, Ané, Jean-Michel, Keller, Nancy P., Pelletier, Dale A., Jacobson, Daniel A., Kainer, David, Abraham, Paul E., Giannone, Richard J. and Labbé, Jesse L. (2022). Lipo-chitooligosaccharides induce specialized fungal metabolite profiles that modulate bacterial growth. mSystems, 7 (6) e01052-22. doi: 10.1128/msystems.01052-22 |
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2022 Journal Article The genetic architecture of nitrogen use efficiency in switchgrass (Panicum virgatum L.)Shrestha, Vivek, Chhetri, Hari B., Kainer, David, Xu, Yaping, Hamilton, Lance, Piasecki, Cristiano, Wolfe, Ben, Wang, Xueyan, Saha, Malay, Jacobson, Daniel, Millwood, Reginald J., Mazarei, Mitra and Stewart, C. Neal (2022). The genetic architecture of nitrogen use efficiency in switchgrass (Panicum virgatum L.). Frontiers in Plant Science, 13 893610. doi: 10.3389/fpls.2022.893610 |
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2021 Journal Article Characterization of terpene biosynthesis in Melaleuca quinquenervia and ecological consequences of terpene accumulation during myrtle rust infectionHsieh, Ji-Fan, Krause, Sandra T., Kainer, David, Degenhardt, Jörg, Foley, William J. and Külheim, Carsten (2021). Characterization of terpene biosynthesis in Melaleuca quinquenervia and ecological consequences of terpene accumulation during myrtle rust infection. Plant-Environment Interactions, 2 (4), 177-193. doi: 10.1002/pei3.10056 |
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2020 Journal Article Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI modelsGarvin, Michael R., Prates, Erica T., Pavicic, Mirko, Jones, Piet, Amos, B. Kirtley, Geiger, Armin, Shah, Manesh B., Streich, Jared, Gazolla, Joao Gabriel Felipe Machado, Kainer, David, Cliff, Ashley, Romero, Jonathon, Keith, Nathan, Brown, James B. and Jacobson, Daniel (2020). Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Genome Biology, 21 (1) 304, 1-26. doi: 10.1186/s13059-020-02191-0 |
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2020 Journal Article Modeled economic potential for Eucalyptus spp. production for jet fuel additives in the United StatesDavis, Maggie R., Kainer, David, Tuskan, Gerald A., Langholtz, Matthew H., Hellwinckel, Chad M., Shedden, Magen and Eaton, Laurence (2020). Modeled economic potential for Eucalyptus spp. production for jet fuel additives in the United States. Biomass and Bioenergy, 143 105807, 1-10. doi: 10.1016/j.biombioe.2020.105807 |
