Dr David Kainer
Dr

David Kainer

Email: 

Background

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.

Availability

Dr David Kainer is:
Available for supervision
Media expert

Fields of research

Agricultural, Veterinary and Food Sciences Bioinformatics and computational biology Biological Sciences Biological network analysis Forestry sciences Genetics Genomics Genomics and transcriptomics Information and Computing Sciences Machine learning Neural networks Tree improvement (incl. selection and breeding)

Qualifications

  • Doctoral (Research) of Population, Ecological and Evolutionary Genetics, Australian National University
  • Member, Australian Bioinformatics and Computational Biology Society, Australian Bioinformatics and Computational Biology Society
  • Journal Editorial Board Member, Forestry Research, Forestry Research
  • Board Member, IUFRO Tree Biotech, IUFRO Tree Biotech

Research interests

  • Graph Neural Networks applied to biological data

    Biological interaction data is often best formatted as networks. These can get large and complex, with multiple types of node entities (genes, metabolites etc) and edge relationships. Graph Neural Networks (GNNs) are currently the most powerful way to make predictions on such networks and gain insights that would be hidden from traditional linear models.

  • Network perturbation and phenotype prediction

    What is the effect of editing a gene, or multiple genes? I am applying AI on biological networks to predict the outcomes of gene knockouts or expression tweaks.

  • Tree genomics

    All aspects of tree multi-omics, especially genomics. I have worked with data from diverse tree species: Eucalypts, Poplars, Oak as well as tree crops such as Mango.

Search Professor David Kainer’s works on UQ eSpace

42 works between 2014 and 2025
All (42) Journal Article (38) Conference Publication (2) Other Outputs (2)

21 - 40 of 42 works

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

The genetic architecture of nitrogen use efficiency in switchgrass (Panicum virgatum L.)

2021

Journal Article

Characterization of terpene biosynthesis in Melaleuca quinquenervia and ecological consequences of terpene accumulation during myrtle rust infection

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

Characterization of terpene biosynthesis in Melaleuca quinquenervia and ecological consequences of terpene accumulation during myrtle rust infection

2020

Journal Article

Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models

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

Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models

2020

Journal Article

Modeled economic potential for Eucalyptus spp. production for jet fuel additives in the United States

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

Modeled economic potential for Eucalyptus spp. production for jet fuel additives in the United States

2020

Journal Article

Genome-wide association study of wood anatomical and morphological traits in Populus trichocarpa

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

Genome-wide association study of wood anatomical and morphological traits in Populus trichocarpa

2020

Journal Article

A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant

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

A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant

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

Can exascale computing and explainable artificial intelligence applied to plant biology deliver on the United Nations sustainable development goals?

2020

Journal Article

The draft nuclear genome assembly of Eucalyptus pauciflora: a pipeline for comparing de novo assemblies

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

The draft nuclear genome assembly of Eucalyptus pauciflora: a pipeline for comparing de novo assemblies

2019

Journal Article

A high-performance computing implementation of iterative random forest for the creation of predictive expression networks

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

A high-performance computing implementation of iterative random forest for the creation of predictive expression networks

2019

Journal Article

Accelerating climate resilient plant breeding by applying next-generation artificial intelligence

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

Accelerating climate resilient plant breeding by applying next-generation artificial intelligence

2019

Journal Article

Finding new cell wall regulatory genes in populus trichocarpa using multiple lines of evidence

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

Finding new cell wall regulatory genes in populus trichocarpa using multiple lines of evidence

2019

Journal Article

Multitrait genome-wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits

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

Multitrait genome-wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits

2019

Conference Publication

Attacking the opioid epidemic: Determining the epistatic and pleiotropic genetic architectures for chronic pain and opioid addiction

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

Attacking the opioid epidemic: Determining the epistatic and pleiotropic genetic architectures for chronic pain and opioid addiction

2019

Journal Article

MinIONQC: fast and simple quality control for MinION sequencing data

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

MinIONQC: fast and simple quality control for MinION sequencing data

2019

Journal Article

Harnessing the MinION: An example of how to establish long-read sequencing in a laboratory using challenging plant tissue from Eucalyptus pauciflora

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

Harnessing the MinION: An example of how to establish long-read sequencing in a laboratory using challenging plant tissue from Eucalyptus pauciflora

2018

Journal Article

Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

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

Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

2018

Journal Article

High Throughput Screening Technologies in Biomass Characterization

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

High Throughput Screening Technologies in Biomass Characterization

2017

Journal Article

Transcriptome analysis of terpene chemotypes of Melaleuca alternifolia across different tissues

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

Transcriptome analysis of terpene chemotypes of Melaleuca alternifolia across different tissues

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

Assessment of a non-destructive method to predict oil yield in Eucalyptus polybractea (blue mallee)

2015

Journal Article

Genomic approaches to selection in outcrossing perennials: focus on essential oil crops

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

Genomic approaches to selection in outcrossing perennials: focus on essential oil crops

Availability

Dr David Kainer is:
Available for supervision

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Enquiries

Contact Dr David Kainer directly for media enquiries about:

  • biofuel
  • bioinformatics
  • computational biology
  • genomics
  • GWAS
  • network biology
  • Tree Genetics

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