Research output per year
Research output per year
Personal profile
Biography
In 2015 I finished my PhD at UQ creating a novel genotyping--by-sequencing method called skimGBS. I then moved to UWA to work with the Edwards group on plant breeding using computational methods. In 2018 I started a Forrest Fellowship where I worked on the genomics of wheat breeding and the applications of machine learning in genomics. In 2021 I started a DECRA where I work on modeling the evolutionary processes behind new genes and gene loss.
Roles and responsibilities
I'm a DECRA fellow associated with the group of Dave Edwards - I run my own research, help PhD students with their research, and look after the group's infrastructure.
I also run the Hacky Hour, every Tuesday at the Hackett Cafe at 2pm and online on Zoom, where we talk code and data and help people with code and data problems: https://twitter.com/hackyhouruwa
I am a member of the Research Committee for the UWA Institute of Data and a member of the Scientific Advisory Committee for the ARDC Machine Learning CoP.
Funding overview
UWA Research Collaboration Award, 'Microbe mediated alternative Nitrogen nutrition in Australian seagrasses'
GRDC, Identifying genetic contributors to canola blackleg resistance in the presence of environmental effects using Machine Learning
GRDC, Deep Learning for early detection and classification of crop disease and stress
ARC, DECRA: The Life and Death Of Plant Genes
Industrial relevance
Our group collaborates extensively with international breeding companies such as BASF and Intergrain.
Research
Plant genomics, plant pangenomics, machine learning, interpretable machine learning, computer-assisted breeding programs, Brassica, wheat, legumes, seagrasses
Languages
English
German
French
Japanese
German
French
Japanese
Expertise related to UN Sustainable Development Goals
In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):
Research expertise keywords
- plant genomics
- plant genetics
- bioinformatics
- computational biology
- Data Science
Fingerprint
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Network
Recent external collaboration on country/territory level. Dive into details by clicking on the dots or
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Amborella gene presence/absence variation is associated with abiotic stress responses that may contribute to environmental adaptation
Hu, H., Scheben, A., Verpaalen, B., Tirnaz, S., Bayer, P. E., Hodel, R. G. J., Batley, J., Soltis, D. E., Soltis, P. S. & Edwards, D., Feb 2022, In: New Phytologist. 233, 4, p. 1548-1555 8 p.Research output: Contribution to journal › Letter › peer-review
Open Access5 Citations (Web of Science) -
An SGSGeneloss-Based Method for Constructing a Gene Presence-Absence Table Using Mosdepth
Tay Fernandez, C. G., Marsh, J. I., Nestor, B. J., Gill, M., Golicz, A. A., Bayer, P. E. & Edwards, D., 2022, Plant Comparative Genomics. Pereira-Santana, A., Gamboa-Tuz, S. D. & Rodriguez-Zapata, L. C. (eds.). USA: Humana Press, p. 73-80 8 p. (Methods in molecular biology (Clifton, N.J.); vol. 2512).Research output: Chapter in Book/Conference paper › Chapter › peer-review
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A pan-genome and chromosome-length reference genome of narrow-leafed lupin (Lupinus angustifolius) reveals genomic diversity and insights into key industry and biological traits
Garg, G., Kamphuis, L. G., Bayer, P. E., Kaur, P., Dudchenko, O., Taylor, C. M., Frick, K. M., Foley, R. C., Gao, L. L., Lieberman Aiden, E., Edwards, D. & Singh, K. B., Sep 2022, In: The Plant Journal. 111, 5, p. 1252-1266 15 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Brassica napus genes Rlm4 and Rlm7, conferring resistance to Leptosphaeria maculans, are alleles of the Rlm9 wall-associated kinase-like resistance locus
Haddadi, P., Larkan, N. J., Van deWouw, A., Zhang, Y., Xiang Neik, T., Beynon, E., Bayer, P., Edwards, D., Batley, J. & Borhan, M. H., Jul 2022, In: Plant Biotechnology Journal. 20, 7, p. 1229-1231 3 p.Research output: Contribution to journal › Article › peer-review
Open Access5 Citations (Scopus) -
Copy Number Variation among Resistance Genes Analogues in Brassica napus
Dolatabadian, A., Yuan, Y., Bayer, P., Petereit, J., Severn-Ellis, A., Tirnaz, S., Patel, D., Edwards, D. & Batley, J., 4 Nov 2022, In: Genes. 13, 11, p. 1-17 17 p.Research output: Contribution to journal › Article › peer-review
Open Access
Datasets
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Nalanthamala psidii supplementary data
Severn-Ellis, A. (Creator), Schoeman, M. (Creator), Bayer, P. (Creator), Hane, J. K. (Creator), G. Rees, D. J. (Creator), Edwards, D. (Creator) & Batley, J. (Creator), The University of Western Australia, 8 Oct 2021
DOI: 10.26182/dbe0-mc39
Dataset
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Amborella pangenome and supplementary tables v4
Hu, R. (Creator), Scheben, A. P. (Creator), Verpaalen, B. (Creator), Bayer, P. (Creator), Tirnaz, S. (Creator), Hodel, R. G. J. (Creator), Batley, J. (Creator), Soltis, D. E. (Creator) & Edwards, D. (Creator), The University of Western Australia, 2 Jun 2021
DOI: 10.26182/2ewa-pd24
Dataset
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Amborella pangenome and supplementary tables v3
Hu, R. (Creator), Scheben, A. P. (Creator), Verpaalen, B. (Creator), Bayer, P. (Creator), Tirnaz, S. (Creator), Hodel, R. G. J. (Creator), Batley, J. (Creator), Soltis, D. E. (Creator), Soltis, P. S. (Creator) & Edwards, D. (Creator), The University of Western Australia, 20 Oct 2020
DOI: 10.26182/2a13-mg52
Dataset
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Amborella pangenome
Hu, R. (Creator), Scheben, A. P. (Creator), Verpaalen, B. (Creator), Tirnaz, S. (Creator), Bayer, P. (Creator), Hodel, R. G. J. (Creator), Batley, J. (Creator), Soltis, D. E. (Creator), Soltis, P. S. (Creator) & Edwards, D. (Creator), The University of Western Australia, 14 Feb 2020
Dataset
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Amborella pangenome and supplementary tables v2
Hu, R. (Creator), Scheben, A. P. (Creator), Verpaalen, B. (Creator), Bayer, P. (Creator), Tirnaz, S. (Creator), Hodel, R. G. J. (Creator), Batley, J. (Creator), Soltis, D. E. (Creator), Soltis, P. S. (Creator) & Edwards, D. (Creator), The University of Western Australia, 29 Sep 2020
Dataset
File
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Holsworth Wildlife Research Endowment
Batley, J., Edwards, D., Bayer, P., Thiele, K. & Craig, R.
1/01/22 → 31/12/24
Project: Research
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Microbe mediated alternative Nitrogen nutrition in Australian seagrasses
Bayer, P., Golicz, A., Fraser, M. & Bougoure, J.
The University of Western Australia
1/01/18 → 31/08/19
Project: Research