• The University of Western Australia (M084), 35 Stirling Highway,

    6009 Perth

    Australia

1992 …2023
If you made any changes in Pure these will be visible here soon.

Personal profile

Biography

To view a managed list of my publications, please go to Google Scholar.

 

I gained an Honours degree in agriculture from the University of Nottingham and a PhD from the Department of Plant Science, University of Cambridge, UK. I have engaged in research in a range of organisms but with a focus on crop plant genomics. Following my PhD studies which identified functionally conserved genes between plants and fungi, I worked briefly in the Genetics Department of the University of Cambridge on rice genome structure before joining Long Ashton Research Station, Bristol, UK. During my time in Bristol, I studied tissue specific gene regulation, cereal gene function and bioinformatics. We developed cereal microarrays for both high throughput transposon mutagenesis and gene expression profiling along with computational tools for sequence data analysis and molecular marker discovery.

I joined the Victorian Department of Primary Industries in 2002 to lead a team in Brassica genomics and establish capabilities in bioinformatics. I established a strawberry genomics program and led Australia’s participation in the Multinational Brassica Genome Project. The computational biology group was particularly successful, with established international linkages and capabilities demonstrated through student and staff training as well as numerous peer reviewed publications.

In 2007, I moved to the University of Queensland as an Associate Professor (level D) to support bioinformatics for the Australian Centre for Plant Functional Genomics and establish a research group in applied bioinformatics. In 2011 I was promoted to Professor (level E). During this period, I established a dedicated applied bioinformatics research group and contributed to honours and masters level courses in plant science and bioinformatics. Research during this period led to 69 peer reviewed publications including high impact journals such as Science (4), Nature Genetics, Nature Biotechnology, Nature Communications and Genome Biology (3), funded by more than $10m in competitive research grants. In January 2015 I accepted an ongoing position as Professor in cereal genomics at the University of Western Australia. My current research activities include the characterisation of complex plant genomes, translational genomics and genome informatics, with a focus on wheat, Brassica and chickpea crops. Details of my current research activities and links to publications are available through my group home page: http://www.appliedbioinformatics.com.au/

Previous positions

Academic history:

PhD University of Cambridge 2000
BSc (Hons) University of Nottingham 1989

Recent posts:

2015 - present Professor, University of Western Australia, Crawley, Australia
2011 - 2015 Professor, University of Queensland, Brisbane, Australia
2007 - 2011 Associate Professor, University of Queensland, Brisbane, Australia
2002 - 2007 Plant Biotechnology Centre, Melbourne, Australia.
1997 - 2002 IACR Long Ashton, University of Bristol, UK.

Keywords

  • Genomics: structure, expression and variation
  • Bioinformatics
  • Crop improvement
  • Evolution
  • Climate change

Network Recent external collaboration on country level. Dive into details by clicking on the dots.

Research Output 1992 2019

5 Citations (Scopus)

Adapting legume crops to climate change using genomic approaches

Mousavi-Derazmahalleh, M., Bayer, P. E., Hane, J. K., Babu, V., Nguyen, H. T., Nelson, M. N., Erskine, W., Varshney, R. K., Papa, R. & Edwards, D., 30 Jan 2019, In : Plant Cell and Environment. 42, 1, p. 6-19

Research output: Contribution to journalReview article

Open Access
Climate Change
Fabaceae
legumes
climate change
genomics

A differential k-mer analysis pipeline for comparing RNA-Seq transcriptome and meta-transcriptome datasets without a reference

Chan, C. K. K., Rosic, N., Lorenc, M. T., Visendi, P., Lin, M., Kaniewska, P., Ferguson, B. J., Gresshoff, P. M., Batley, J. & Edwards, D., 1 Mar 2019, In : Functional and Integrative Genomics. 19, 2, p. 363-371 9 p.

Research output: Contribution to journalArticle

Transcriptome
RNA
Genome
Gene Expression
Anthozoa

Construction and comparison of three reference-quality genome assemblies for soybean

Valliyodan, B., Cannon, S. B., Bayer, P. E., Shu, S., Brown, A. V., Ren, L., Jenkins, J., Chung, C. Y-L., Chan, T-F., Daum, C. G., Plott, C., Hastie, A., Baruch, K., Barry, K. W., Huang, W., Patil, G., Varshney, R. K., Hu, H., Batley, J., Yuan, Y. & 10 othersSong, Q., Stupar, R. M., Goodstein, D. M., Stacey, G., Lam, H-M., Jackson, S. A., Schmutz, J., Grimwood, J., Edwards, D. & Nguyen, H. T., 21 Aug 2019, In : The Plant Journal. 39 p.

Research output: Contribution to journalArticle

Glycine soja
genome assembly
Soybeans
Genome
soybeans

CropSNPdb: a database of SNP array data for Brassica crops and hexaploid bread wheat

Scheben, A., Verpaalen, B., Lawley, C. T., Chan, C-K. K., Bayer, P. E., Batley, J. & Edwards, D., Apr 2019, In : Plant Journal. 98, 1, p. 142-152 11 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia

Schneider, M. V., Griffin, P. C., Tyagi, S., Flannery, M., Dayalan, S., Gladman, S., Watson-Haigh, N., Bayer, P. E., Charleston, M., Cooke, I., Cook, R., Edwards, R. J., Edwards, D., Gorse, D., McConville, M., Powell, D., Wilkins, M. R. & Lonie, A., Mar 2019, In : Briefings in Bioinformatics. 20, 2, p. 384-389 6 p.

Research output: Contribution to journalArticle

Open Access
Biological Science Disciplines
Bioinformatics
Computational Biology
Research Personnel
Research

Datasets

Pigeon pea pangenome contig assembly, annotation, SNPs, PAV

Zhao, J. (Creator), Bayer, P. (Creator), Ruperao, P. (Creator), Saxena, R. (Creator), Khan, M. A. W. (Creator), Golicz, A. (Creator), Nguyen, H. (Creator), Batley, J. (Creator), Edwards, D. (Creator), Varshney, R. (Creator), The University of Western Australia, 4 Apr 2019

Dataset

File

Supplementary data for manuscript:"High intraspecific diversity of Restorer-of-fertility-like genes in barley"

Melonek, J. (Creator), Zhou, R. (Creator), Bayer, P. (Creator), Edwards, D. (Creator), Stein, N. (Creator), Small, I. (Creator), The University of Western Australia, 21 Sep 2018

Dataset

File
File

Assembly and comparison of two closely related Brassica napus genomes

Bayer, P. (Creator), Hurgobin, B. (Creator), Golicz, A. A. (Creator), Chan, C. K. (Creator), Yuan, Y. (Creator), Lee, H. (Creator), Renton, M. (Creator), Meng, J. (Creator), Li, R. (Creator), Long, Y. (Creator), Zou, J. (Creator), Bancroft, I. (Creator), Chalhoub, B. (Creator), King, G. J. (Creator), Batley, J. (Creator), Edwards, D. (Creator), Zenodo, 17 Mar 2017

Dataset

Projects 2014 2023