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==About the group==
 
==About the group==
  
The applied bioinformatics group was founded in 2007 at the University of Queensland to lead a Bioinformatics node for the Australian Centre for Plant Functional Genomics and establish independent research in applied bioinformatics. Since this time, the group has attracted more than 6.5 M AU$ in competitive funds and is a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex plant genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation.  
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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.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 applied bioinformatics research in genetics and genomics.
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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@uq.edu.au David Edwards] for further information.
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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 Queensland's St Lucia campus in Brisbane, Australia.
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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 here [[publications_DE|'publications']]
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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]
 
 
 
 
 
 
  
 
==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.
 
 
 
  
 
===[[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
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:[[A differential kmer analysis pipeline]]
 
 
 
 
  
 
===Molecular marker discovery===
 
===Molecular marker discovery===
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:[[SNP discovery]]
 
:[[SNP discovery]]
  
:[[SSR discovery]]
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:[[SNParrayDB]]
 
 
:[[Genetic map visualisation]]
 
 
 
 
 
  
 
===Genome annotation and visualisation===
 
===Genome annotation and visualisation===
  
 
:[[Gene and genome annotation]]
 
:[[Gene and genome annotation]]
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:[http://daisychain.appliedbioinformatics.com.au Daisychain]
  
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===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:===
 
===Species of interest include:===
  
 +
:[[Amborella]]
  
 
:[[Brassica]]
 
:[[Brassica]]
  
 
:[[Chickpea]]
 
:[[Chickpea]]
 +
 +
:[[Soybean]]
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 +
:[[Other legumes]]
  
 
:[[Wheat]]
 
:[[Wheat]]
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 +
:[[Seagrass]]
  
 
:[[Metagenomics]]
 
:[[Metagenomics]]
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 +
===Publicly available data sets:===
 +
 +
:[[Yam bean assembly]]
 +
 +
===Supplementary Data:===
 +
 +
:[[PDH1 Comparative Legume Analysis]]
 +
:[[Supplementary Data Set]]
  
 
==Group members==
 
==Group members==
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===Postdocs===
 
===Postdocs===
  
 +
[[Hawlader Al-Mamun]]
  
[[Kenneth Chan]]
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[[Monica Danilevicz]]
  
Positions available, please contact David Edwards if interested  
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Positions available, please contact David Edwards if interested.
  
===Researchers===
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===Research Assistants===
  
 
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Positions available, please contact David Edwards if interested
[[Yang Liu (Ben)]]
 
  
 
===PhD students===
 
===PhD students===
  
[[Salman Alamery]]
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[[Benjamin Nestor]]
 
 
[[Philipp Bayer]]
 
  
[[Agnieszka Golicz]]
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[[Shriprabha Upadhyaya]]
  
[[Kaitao Lai]]
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Positions available, please contact David Edwards if interested
  
[[Michal Lorenc]]
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=== Master students ===
  
[[Paula Andrea Martinez]]
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[[Tessa Macnish]]<br>
 
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[[Michael Mckay]]<br>
[[Paul Visendi Muhindira]]
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[[Shameela Mohamedikbal]]<br>
 
 
[[Pradeep Ruperao]]
 
 
 
[[Manuel Zander]]
 
 
 
Positions available, please contact David Edwards if interested
 
  
 
=== Honours students ===
 
=== Honours students ===
  
Positions available, please contact David Edwards if interested  
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Positions available, please contact David Edwards if interested
  
 
=== Interns ===
 
=== Interns ===
 
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[[Connor McPhan]]
[[Michael Whitehead]]
 
  
 
Positions available, please contact David Edwards if interested
 
Positions available, please contact David Edwards if interested
  
 +
===Associates===
  
 +
[[Philipp Bayer]]
  
===Alumni===
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===[[Alumni]]===
 
 
 
 
Nikki Appleby
 
 
 
Jacqueline Batley
 
 
 
[[Paul Berkman]]
 
 
 
Terry Clark
 
 
 
Chris Duran
 
 
 
Mike Imelfort
 
 
 
Tristan de Jong
 
 
 
Hong Ching Lee
 
 
 
Edmund Ling
 
 
 
Sahana Manoli
 
 
 
Daniel Marshall
 
 
 
Thomas Schumann
 
 
 
Adam Skarshewski
 
 
 
Lars Smits
 
 
 
Jiri Stiller
 
 
 
Nikolay Terentyev
 
 
 
Sonika Tyagi
 
 
 
Megan Vardy
 
 
 
Ping Zhang
 
  
 
===Positions available===
 
===Positions available===
  
There are current positions availble 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@uq.edu.au.
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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.