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==About the group== | ==About the group== | ||
| − | The applied bioinformatics group was founded in 2007 at the University of Queensland to | + | The applied bioinformatics group was founded in 2007 at the University of Queensland and moved to the University of Western Australia in January 2015. Since this time, the group has established itself as a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation. |
| − | The group receives funding from the [http://www. | + | The group receives funding from the [http://www.uwa.edu.au/ University of Western Australia], the [http://www.arc.gov.au/ Australian Research Council], the [http://www.grdc.com.au/ Grains Research and Development Corporation] and several industry partners to undertake applied bioinformatics research in genetics and genomics. |
| − | The group is led by Professor [[David Edwards]] and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and [[publications_DE|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:Dave.Edwards@ | + | The group is led by Professor [[David Edwards]] and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and [[publications_DE|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:Dave.Edwards@uwa.edu.au David Edwards] for further information. |
| − | We are based at the University of | + | We are based at the University of Western Australia's Crawley campus in Perth, Australia. |
==Publications== | ==Publications== | ||
| − | A current list of publications can be found | + | We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&hl=en Google Scholar] |
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==Public research projects== | ==Public research projects== | ||
The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups. | The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups. | ||
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===[[Genome sequencing]]=== | ===[[Genome sequencing]]=== | ||
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:[http://www.cicer.info/ Chickpea genome sequencing] | :[http://www.cicer.info/ Chickpea genome sequencing] | ||
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| + | :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing] | ||
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| + | : [[Soybean]] genomics | ||
:[[Metagenomics]] | :[[Metagenomics]] | ||
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===Transcriptomics=== | ===Transcriptomics=== | ||
| − | :A differential kmer analysis pipeline | + | :[[A differential kmer analysis pipeline]] |
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===Molecular marker discovery=== | ===Molecular marker discovery=== | ||
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:[[SNP discovery]] | :[[SNP discovery]] | ||
| − | :[[ | + | :[[SNParrayDB]] |
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===Genome annotation and visualisation=== | ===Genome annotation and visualisation=== | ||
:[[Gene and genome annotation]] | :[[Gene and genome annotation]] | ||
| + | :[http://daisychain.appliedbioinformatics.com.au Daisychain] | ||
| + | ===Machine learning in Plant Biology=== | ||
| + | :[[Image based high-throughput phenotyping of crops using neural networks]] | ||
| + | ===Knowledge networks=== | ||
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| + | :[[KNetMiner collaboration with Rothamstead Research]] | ||
===Species of interest include:=== | ===Species of interest include:=== | ||
| + | :[[Amborella]] | ||
:[[Brassica]] | :[[Brassica]] | ||
:[[Chickpea]] | :[[Chickpea]] | ||
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| + | :[[Soybean]] | ||
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| + | :[[Other legumes]] | ||
:[[Wheat]] | :[[Wheat]] | ||
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| + | :[[Seagrass]] | ||
:[[Metagenomics]] | :[[Metagenomics]] | ||
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| + | ===Publicly available data sets:=== | ||
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| + | :[[Yam bean assembly]] | ||
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| + | ===Supplementary Data:=== | ||
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| + | :[[PDH1 Comparative Legume Analysis]] | ||
| + | :[[Supplementary Data Set]] | ||
==Group members== | ==Group members== | ||
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===Postdocs=== | ===Postdocs=== | ||
| + | [[Hawlader Al-Mamun]] | ||
| − | [[ | + | [[Monica Danilevicz]] |
| − | Positions available, please contact David Edwards if interested | + | Positions available, please contact David Edwards if interested. |
| − | === | + | ===Research Assistants=== |
| − | + | Positions available, please contact David Edwards if interested | |
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===PhD students=== | ===PhD students=== | ||
| − | [[ | + | [[Benjamin Nestor]] |
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| − | [[ | + | [[Shriprabha Upadhyaya]] |
| − | + | Positions available, please contact David Edwards if interested | |
| − | + | === Master students === | |
| − | [[ | + | [[Tessa Macnish]]<br> |
| − | + | [[Michael Mckay]]<br> | |
| − | + | [[Shameela Mohamedikbal]]<br> | |
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| − | [[ | ||
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=== Honours students === | === Honours students === | ||
| − | Positions available, please contact David Edwards if interested | + | Positions available, please contact David Edwards if interested |
=== Interns === | === Interns === | ||
| − | + | [[Connor McPhan]] | |
| − | [[ | ||
Positions available, please contact David Edwards if interested | Positions available, please contact David Edwards if interested | ||
| + | ===Associates=== | ||
| + | [[Philipp Bayer]] | ||
| − | ===Alumni=== | + | ===[[Alumni]]=== |
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===Positions available=== | ===Positions available=== | ||
| − | There are current positions | + | There are current positions available at all levels including Postdoc, PhD students and Interns. Candidates should have a good understanding of one or more areas of Computing, Software development, Complex data analysis, Bioinformatics or Genomics. For consideration, please forward your cv and cover letter to Dave.Edwards@uwa.edu.au. |
Latest revision as of 01:46, 14 November 2023
About the group
The applied bioinformatics group was founded in 2007 at the University of Queensland and moved to the University of Western Australia in January 2015. Since this time, the group has established itself as a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation.
The group receives funding from the University of Western Australia, the Australian Research Council, the Grains Research and Development Corporation and several industry partners to undertake applied bioinformatics research in genetics and genomics.
The group is led by Professor David Edwards and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and publish widely in the fields of genomics, genetics and bioinformatics. Please contact David Edwards for further information.
We are based at the University of Western Australia's Crawley campus in Perth, Australia.
Publications
We publish extensively in major journals. A current list of publications can be found on Google Scholar
Public research projects
The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups.
Genome sequencing
- Soybean genomics
Transcriptomics
Molecular marker discovery
Genome annotation and visualisation
Machine learning in Plant Biology
Knowledge networks
Species of interest include:
Publicly available data sets:
Supplementary Data:
Group members
Group leader
Postdocs
Positions available, please contact David Edwards if interested.
Research Assistants
Positions available, please contact David Edwards if interested
PhD students
Positions available, please contact David Edwards if interested
Master students
Tessa Macnish
Michael Mckay
Shameela Mohamedikbal
Honours students
Positions available, please contact David Edwards if interested
Interns
Positions available, please contact David Edwards if interested
Associates
Alumni
Positions available
There are current positions available at all levels including Postdoc, PhD students and Interns. Candidates should have a good understanding of one or more areas of Computing, Software development, Complex data analysis, Bioinformatics or Genomics. For consideration, please forward your cv and cover letter to Dave.Edwards@uwa.edu.au.
