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

40 works between 2014 and 2024
All (40) Journal Article (36) Conference Publication (2) Other Outputs (2)

1 - 20 of 40 works

Featured

2022

Journal Article

Structural variants identified using non-Mendelian inheritance patterns advance the mechanistic understanding of autism spectrum disorder

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

Structural variants identified using non-Mendelian inheritance patterns advance the mechanistic understanding of autism spectrum disorder

Featured

2022

Journal Article

Evaluating the performance of random forest and iterative random forest based methods when applied to gene expression data

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

Evaluating the performance of random forest and iterative random forest based methods when applied to gene expression data

Featured

2019

Journal Article

High marker density GWAS provides novel insights into the genomic architecture of terpene oil yield in Eucalyptus

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

High marker density GWAS provides novel insights into the genomic architecture of terpene oil yield in Eucalyptus

Featured

2018

Journal Article

Accuracy of Genomic Prediction for Foliar Terpene Traits in Eucalyptus polybractea

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

Accuracy of Genomic Prediction for Foliar Terpene Traits in Eucalyptus polybractea

Featured

2017

Journal Article

Plant-Derived Terpenes: A Feedstock for Specialty Biofuels

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

Plant-Derived Terpenes: A Feedstock for Specialty Biofuels

2024

Journal Article

Centromeres are hotspots for chromosomal inversions and breeding traits in mango

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, 245 (2), 899-913. doi: 10.1111/nph.20252

Centromeres are hotspots for chromosomal inversions and breeding traits in mango

2024

Journal Article

Analyses of GWAS signal using GRIN identify additional genes contributing to suicidal behavior

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, 1360. doi: 10.1038/s42003-024-06943-7

Analyses of GWAS signal using GRIN identify additional genes contributing to suicidal behavior

2024

Journal Article

High dimensional predictions of suicide risk in 4.2 million US Veterans using ensemble transfer learning

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

High dimensional predictions of suicide risk in 4.2 million US Veterans using ensemble transfer learning

2023

Conference Publication

Network Biology Algorithms Identify Biological Pathways Underlying Cigarette Smoking Behaviors

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

Network Biology Algorithms Identify Biological Pathways Underlying Cigarette Smoking Behaviors

2023

Journal Article

A glimpse into the fungal metabolomic abyss: Novel network analysis reveals relationships between exogenous compounds and their outputs

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

A glimpse into the fungal metabolomic abyss: Novel network analysis reveals relationships between exogenous compounds and their outputs

2023

Journal Article

Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering

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

Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering

2023

Other Outputs

Methods for controlling cell wall biosynthesis and genetically modified plants

Jacobson, Daniel, Tschaplinski, Timothy J., Kainer, David, Weighill, Deborah A. and Furches, Anna K. (2023). Methods for controlling cell wall biosynthesis and genetically modified plants. 11725215.

Methods for controlling cell wall biosynthesis and genetically modified plants

2023

Journal Article

Validation of a metabolite–GWAS network for Populus trichocarpa family 1 UDP-glycosyltransferases

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

Validation of a metabolite–GWAS network for Populus trichocarpa family 1 UDP-glycosyltransferases

2023

Journal Article

Few-shot learning enables population-scale analysis of leaf traits in Populus trichocarpa

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

Few-shot learning enables population-scale analysis of leaf traits in Populus trichocarpa

2023

Journal Article

Genetics of varicose veins reveals polygenic architecture and genetic overlap with arterial and venous disease

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

Genetics of varicose veins reveals polygenic architecture and genetic overlap with arterial and venous disease

2023

Journal Article

Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop Populus

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

Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop Populus

2022

Journal Article

Lipo-chitooligosaccharides induce specialized fungal metabolite profiles that modulate bacterial growth

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) e01052-22. doi: 10.1128/msystems.01052-22

Lipo-chitooligosaccharides induce specialized fungal metabolite profiles that modulate bacterial growth

2022

Other Outputs

RWRtoolkit: a set of command-line and R tools for performing Random-walk with Restart analyses on multiplex networks in any species

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.

RWRtoolkit: a set of command-line and R tools for performing Random-walk with Restart analyses on multiplex networks in any species

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

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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