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	==About the group==		==About the group==
−	Dr [[Jacqueline Batley]] Joined the University of Queensland in 2007 and was awarded an ARC QEII fellowship in 2008. .	+	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.
−	Our current research activities include doing lots of interesting stuff.	+	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 receives funding from the [http://www.acpfg.com.au/ Australian Centre for Plant Functional Genomics], the [http://www.uq.edu.au/ University of Queensland], 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 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@uwa.edu.au David Edwards] for further information.
−	The group is led by [[Jacqueline Batley]] and consists of XX full time researchers. We offer training in applied genetics and genomics at all levels and [[publications_JB|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:j.batley@uq.edu.au Jacqueline Batley] for further information.	+	We are based at the University of Western Australia's Crawley campus in Perth, Australia.
−	We are based at the University of Queensland's St Lucia campus in Brisbane, Australia.	+	==Publications==
		+	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]
−	===Information on public [[research|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.
−	===Information on [[people|group members]]===	+	===[[Genome sequencing]]===
		+
		+	:[http://www.wheatgenome.info Wheat genome sequencing]
		+
		+	:[http://www.brassicagenome.net Brassica genome sequencing]
		+
		+	:[http://www.cicer.info/ Chickpea genome sequencing]
		+
		+	:[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]
		+
		+	: [[Soybean]] genomics
		+
		+	:[[Metagenomics]]
		+
		+	:[[TAGdb]]
		+
		+	===Transcriptomics===
		+
		+	:[[A differential kmer analysis pipeline]]
		+
		+	===Molecular marker discovery===
		+
		+	:[[SNP discovery]]
		+
		+	:[[SNParrayDB]]
		+
		+	===Genome annotation and visualisation===
		+
		+	:[[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===
		+
		+	:[[KNetMiner collaboration with Rothamstead Research]]
		+
		+	===Species of interest include:===
		+
		+	:[[Amborella]]
		+
		+	:[[Brassica]]
		+
		+	:[[Chickpea]]
		+
		+	:[[Soybean]]
		+
		+	:[[Other legumes]]
		+
		+	:[[Wheat]]
		+
		+	:[[Seagrass]]
		+
		+	:[[Metagenomics]]
		+
		+	===Publicly available data sets:===
		+
		+	:[[Yam bean assembly]]
		+
		+	===Supplementary Data:===
		+
		+	:[[PDH1 Comparative Legume Analysis]]
		+	:[[Supplementary Data Set]]
		+
		+	==Group members==
		+
		+
		+
		+	===Group leader===
		+
		+	[[David Edwards]]
		+
		+
		+
		+	===Postdocs===
		+
		+	[[Hawlader Al-Mamun]]
		+
		+	[[Monica Danilevicz]]
		+
		+	Positions available, please contact David Edwards if interested.
		+
		+	===Research Assistants===
		+
		+	Positions available, please contact David Edwards if interested
		+
		+	===PhD students===
		+
		+	[[Benjamin Nestor]]
		+
		+	[[Shriprabha Upadhyaya]]
		+
		+	Positions available, please contact David Edwards if interested
		+
		+	=== Master students ===
		+
		+	[[Tessa Macnish]]<br>
		+	[[Michael Mckay]]<br>
		+	[[Shameela Mohamedikbal]]<br>
		+
		+	=== Honours students ===
		+
		+	Positions available, please contact David Edwards if interested
		+
		+	=== Interns ===
		+	[[Connor McPhan]]
		+
		+	Positions available, please contact David Edwards if interested
		+
		+	===Associates===
		+
		+	[[Philipp Bayer]]
		+
		+	===[[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.

---

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

Wheat genome sequencing

Brassica genome sequencing

Chickpea genome sequencing

Seagrass genome sequencing

Soybean genomics

Metagenomics

TAGdb

Transcriptomics

A differential kmer analysis pipeline

Molecular marker discovery

SNP discovery

SNParrayDB

Genome annotation and visualisation

Gene and genome annotation

Daisychain

Machine learning in Plant Biology

Image based high-throughput phenotyping of crops using neural networks

Knowledge networks

KNetMiner collaboration with Rothamstead Research

Species of interest include:

Amborella

Brassica

Chickpea

Soybean

Other legumes

Wheat

Seagrass

Metagenomics

Publicly available data sets:

Yam bean assembly

Supplementary Data:

PDH1 Comparative Legume Analysis

Supplementary Data Set

Group members

Group leader

David Edwards

Postdocs

Hawlader Al-Mamun

Monica Danilevicz

Positions available, please contact David Edwards if interested.

Research Assistants

Positions available, please contact David Edwards if interested

PhD students

Benjamin Nestor

Shriprabha Upadhyaya

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

Connor McPhan

Positions available, please contact David Edwards if interested

Associates

Philipp Bayer

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.