Dr David Kainer
Senior Research Fellow
School of Agriculture and Food Sustainability
Researcher biography
I am a computational biologist with a centre-wide research role in the ARC Centre of Excellence for Plant Success in Nature and Agriculture, based here at UQ. I spend my time researching new computational techniques for predicting complex quantitative traits by integrating multiple layers of 'omics data (amongst dozens of other things!).
Areas of interest:
- Machine Learning, AI and high performance computing to learn and exploit functional connectivity in biological data
- Gene Expressions networks
- Multiplex networks, information propagation and perturbation
- Genomic Prediction
My goal is to aid crop and forestry breeders in selecting parental lines more accurately, which gives us a pathway to improving certain plant species. I also spend time developing new data analysis techniques that are being applied to human disease and conditions such as Autism and substance addiction.
David completed his PhD at Australian National University in 2017, focusing on the genome-wide basis of foliar terpene variation in Eucalyptus. He then undertook a postdoc at Oak Ridge National Laboratory, a US Dept of Energy lab with a focus on big data. After a stint as a staff scientist at Oak Ridge, David arrived at the Centre of Excellence in 2023 in the role of a Senior Research Fellow.
Journal Articles
Wilkinson, 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. doi: 10.1111/nph.20252
Sullivan, 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. doi: 10.1038/s42003-024-06943-7
Dhaubhadel, 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
Gopalakrishnan 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
Noshay, 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
Saint-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
Lagergren, 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
Levin, 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
Cope, 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
Rush, 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) ARTN e01052-22. doi: 10.1128/msystems.01052-22
Kainer, 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
Walker, 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
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
Hsieh, 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
Garvin, 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
Davis, 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
Chhetri, 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
Orr, 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
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
Wang, 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
Cliff, 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
Harfouche, 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
Furches, 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
Chhetri, 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
Kainer, 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
Lanfear, 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
Schalamun, 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
Wang, 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
Decker, 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
Kainer, 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
Bustos‐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
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
Mewalal, 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
Kainer, 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
Kainer, 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
Lanfear, 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
Conference Papers
Sullivan, Kyle, Miller, J. Izaak, Kainer, David, Lane, Matthew, Cashman, Mikaela, Garvin, Michael R., Townsend, Alice, Kruse, Peter, Quach, Bryan C., Willis, Caryn, Xu, Ke, Aouzierat, Bradley E., Johnson, Eric O., Hancock, Dana B. and Jacobson, Daniel (2023). Network Biology Algorithms Identify Biological Pathways Underlying Cigarette Smoking Behaviors. World Congress of Psychiatric Genetics (WCPG), Montreal, Canada, 10-14 October 2023. Amsterdam, Netherlands: Elsevier. doi: 10.1016/j.euroneuro.2023.08.183
Joubert, Wayne, Weighill, Deborah, Kainer, David, Climer, Sharlee, Justice, Amy, Fagnan, Kjiersten and Jacobson, Daniel (2019). Attacking the opioid epidemic: Determining the epistatic and pleiotropic genetic architectures for chronic pain and opioid addiction. International Conference on High Performance Computing, Networking, Storage, and Analysis (SC), Dallas, TX United States, 11-16 November 2018. Piscataway, NJ United States: Institute of Electrical and Electronics Engineers. doi: 10.1109/SC.2018.00060
Patent
Creative Work
Kainer, David, Lane, Matthew, Sullivan, Kyle A., Cashman, Michaela and Miller, John Izaak (2022). RWRtoolkit: a set of command-line and R tools for performing Random-walk with Restart analyses on multiplex networks in any species. Oak Ridge, TN, United States: Oak Ridge National Laboratory.