https://www.appliedbioinformatics.com.au/Edwards/api.php?action=feedcontributions&feedformat=atom&user=Dave 2026-04-18T22:43:48Z User contributions MediaWiki 1.28.0 https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Soybean&diff=1283 2024-06-18T06:58:53Z

<p>Dave: /* Soybean genomics */</p> <hr /> <div>== Soybean genomics ==<br /> <br /> <br /> <br /> === Soybean cqProt003 supplementary data ===<br /> <br /> <br /> This is the supplementary data for Marsh et al. <br /> <br /> [https://appliedbioinformatics.com.au/download/cqProt-003_Supplementary_Tables.xlsx Supplementary Tables]<br /> <br /> [https://appliedbioinformatics.com.au/download/cqProt-003_Supplementary_Figures.docx Supplementary Figures]<br /> <br /> Files contain Gm20 with Wm82.a1.v4 reference<br /> <br /> [https://appliedbioinformatics.com.au/download/Gm20.INDELs.vcf.gz Raw Indels]<br /> <br /> [https://appliedbioinformatics.com.au/download/Gm20.SNPs.vcf.gz Raw SNPs]<br /> <br /> [https://appliedbioinformatics.com.au/download/filtered_biallelic_Gm20.INs.vcf.gz Filtered Insertions reformatted to biallelic]<br /> <br /> [https://appliedbioinformatics.com.au/download/filtered_biallelic_Gm20.DELs.vcf.gz Filtered Deletions reformatted to biallelic]<br /> <br /> [https://appliedbioinformatics.com.au/download/HM_input.tar.gz HaplotypeMiner input]<br /> <br /> [https://appliedbioinformatics.com.au/download/protein_Gm20.SNPs.id.biallic_maf_0.01_geno_0.1.vcf.gz Filtered SNPs]<br /> <br /> === Soybean pangenome ===<br /> <br /> Supplementary information relating to Bayer et al. 2021, [https://acsess.onlinelibrary.wiley.com/doi/10.1002/tpg2.20109 Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding], is available below.<br /> <br /> [https://www.appliedbioinformatics.com.au/soybean JBrowse genome viewer]<br /> <br /> Supplementary Tables: [https://www.appliedbioinformatics.com.au/download/Soybean_pangenome_Supp_Tables.xlsx Download here]<br /> <br /> The data can also be viewed on [https://soybase.org/projects/SoyBase.C2020.02.php soybase] and [https://research-repository.uwa.edu.au/en/datasets/soybean-pangenome-snps-assembly-annotation-pav UWA Research Repository].<br /> <br /> ===Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean===<br /> <br /> [ Supplementary tables]</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Soybean&diff=1282 2024-06-18T06:55:20Z

<p>Dave: /* Soybean genomics */</p> <hr /> <div>== Soybean genomics ==<br /> <br /> <br /> <br /> === Soybean cqProt003 supplementary data ===<br /> <br /> <br /> This is the supplementary data for Marsh et al. <br /> <br /> [https://appliedbioinformatics.com.au/download/cqProt-003_Supplementary_Tables.xlsx Supplementary Tables]<br /> <br /> [https://appliedbioinformatics.com.au/download/cqProt-003_Supplementary_Figures.docx Supplementary Figures]<br /> <br /> Files contain Gm20 with Wm82.a1.v4 reference<br /> <br /> [https://appliedbioinformatics.com.au/download/Gm20.INDELs.vcf.gz Raw Indels]<br /> <br /> [https://appliedbioinformatics.com.au/download/Gm20.SNPs.vcf.gz Raw SNPs]<br /> <br /> [https://appliedbioinformatics.com.au/download/filtered_biallelic_Gm20.INs.vcf.gz Filtered Insertions reformatted to biallelic]<br /> <br /> [https://appliedbioinformatics.com.au/download/filtered_biallelic_Gm20.DELs.vcf.gz Filtered Deletions reformatted to biallelic]<br /> <br /> [https://appliedbioinformatics.com.au/download/HM_input.tar.gz HaplotypeMiner input]<br /> <br /> [https://appliedbioinformatics.com.au/download/protein_Gm20.SNPs.id.biallic_maf_0.01_geno_0.1.vcf.gz Filtered SNPs]<br /> <br /> === Soybean pangenome ===<br /> <br /> Supplementary information relating to Bayer et al. 2021, [https://acsess.onlinelibrary.wiley.com/doi/10.1002/tpg2.20109 Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding], is available below.<br /> <br /> [https://www.appliedbioinformatics.com.au/soybean JBrowse genome viewer]<br /> <br /> Supplementary Tables: [https://www.appliedbioinformatics.com.au/download/Soybean_pangenome_Supp_Tables.xlsx Download here]<br /> <br /> The data can also be viewed on [https://soybase.org/projects/SoyBase.C2020.02.php soybase] and [https://research-repository.uwa.edu.au/en/datasets/soybean-pangenome-snps-assembly-annotation-pav UWA Research Repository].<br /> <br /> ===Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean===<br /> <br /> Supplementary tables</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Shameela_Mohamedikbal&diff=1280 2023-11-14T01:47:30Z

<p>Dave: Created page with &quot;'''Shameela Mohamedikbal''' My name is Shameela, and I am currently completing my Master’s in Biotechnology with a specialization in Genetics and Genomics at UWA. My disser...&quot;</p> <hr /> <div>'''Shameela Mohamedikbal'''<br /> <br /> My name is Shameela, and I am currently completing my Master’s in Biotechnology with a specialization in Genetics and Genomics at UWA. My dissertation project is on identifying the genomic regions and haplotype structures associated with flowering time variation in soybean using advanced bioinformatics approaches. <br /> <br /> <br /> Areas of Interest: <br /> <br /> Bioinformatics, Population Genomics, Agriculture, Data Science<br /> <br /> <br /> Academic History:<br /> <br /> 2021 – present: Master of Biotechnology at the University of Western Australia (Australia), with dissertation project titled “Genome-Wide Association Study and Haplotype Analysis for Flowering Time in Soybean” supervised by Prof. Dave Edwards and Dr. Hawlader Al-Mamun<br /> <br /> Bachelor of Technology (B.Tech) in Biotechnology and Biochemical Engineering, at the University of Kerala (India) with project titled “Isolation and Sequencing of an Unknown Gene from a c-DNA Library” supervised by Dr. Priya Srinivas at Rajiv Gandhi Centre for Biotechnology, Kerala, India<br /> <br /> <br /> Contact:<br /> 23140255@student.uwa.edu.au</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=1279 2023-11-14T01:46:36Z

<p>Dave: /* Master students */</p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> : [[Soybean]] genomics<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SNParrayDB]]<br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> :[http://daisychain.appliedbioinformatics.com.au Daisychain]<br /> <br /> ===Machine learning in Plant Biology===<br /> :[[Image based high-throughput phenotyping of crops using neural networks]]<br /> <br /> ===Knowledge networks===<br /> <br /> :[[KNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> :[[Amborella]]<br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Soybean]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Metagenomics]]<br /> <br /> ===Publicly available data sets:===<br /> <br /> :[[Yam bean assembly]]<br /> <br /> ===Supplementary Data:===<br /> <br /> :[[PDH1 Comparative Legume Analysis]]<br /> :[[Supplementary Data Set]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> [[Hawlader Al-Mamun]]<br /> <br /> [[Monica Danilevicz]]<br /> <br /> Positions available, please contact David Edwards if interested.<br /> <br /> ===Research Assistants===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===PhD students===<br /> <br /> [[Benjamin Nestor]]<br /> <br /> [[Shriprabha Upadhyaya]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> <br /> [[Tessa Macnish]]&lt;br&gt;<br /> [[Michael Mckay]]&lt;br&gt;<br /> [[Shameela Mohamedikbal]]&lt;br&gt;<br /> <br /> === Honours students ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> [[Connor McPhan]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Associates===<br /> <br /> [[Philipp Bayer]]<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Monica_Danilevicz&diff=1278 2023-11-08T09:56:17Z

<p>Dave: </p> <hr /> <div><br /> Hi, <br /> <br /> I am a postdoc at the University of Western Australia, after finishing my PhD in the group supported by the Forrest Research Foundation scholarship. My research in the group has focused on combining multidimensional datasets (describing the plant traits and environment) and training deep learning models for early yield prediction of crops, preliminary selection of crop varieties under field trial, and distinguishing visually similar plant species for weed detection. Advances in camera technology and artificial intelligence are transforming how we can observe plant development, enabling the development of more productive crop varieties, so my focus has been on their use for Australian agriculture. <br /> <br /> Before joining the group, I completed my Bachelor's and Master's degrees in Brazil at the Universidade Federal do Rio de Janeiro, looking into the interaction of crops (mainly maize and sugarcane) with beneficial bacteria when subjected to water deficit stress. There, I primarily worked with bioinformatics, doing some RNA-seq analysis and looking into the expression of microRNAs and long non-coding RNAs.<br /> <br /> <br /> <br /> == Areas of Interest ==<br /> <br /> Plant Biology, Plant Genetics, Machine learning, Deep neural networks, Bioinformatics, Data Science, Plant Phenotyping.<br /> <br /> <br /> == Academic History ==<br /> <br /> '''2019 to 2023''' Ph.D. in Biological Sciences at the University of Western Australia (Australia), supervised by Prof. David Edwards, Prof. Mohammed Bennamoun, Dr. Philipp Bayer and Prof. Jacqueline Batley.<br /> <br /> '''2017 - 2019''' MA in Plant Biotechnology with Honors at Universidade Federal do Rio de Janeiro (Brazil), supervised by Prof. Paulo C.G. Ferreira and Dr. Flavia Thiebaut. Honors project title “Uncovering long non-coding RNAs in copaiba and maize”.<br /> <br /> '''2011 - 2016''' Bsc. in Biotechnology at Universidade Federal do Rio de Janeiro (Brazil), supervised by Prof. Paulo C.G. Ferreira, with an exchange period at Australia National University (Australia). Dissertation title “Expression analysis of microRNAs from maize associated to beneficial bacteria and subjected to hydric deficit stress”.<br /> <br /> <br /> == Publications ==<br /> <br /> Current record of publication is available at [https://scholar.google.com.au/citations?user=SIPvegsAAAAJ&amp;hl=en&amp;oi=ao]<br /> <br /> <br /> == Contact ==<br /> <br /> monica.danilevicz@research.uwa.edu.au</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Michael_Mckay&diff=1277 2023-11-03T00:44:43Z

<p>Dave: Created page with &quot;My name is Michael Mckay, I am currently completing my masters degree with dissertation at UWA. After completing my undergraduate degree at Curtin University, I wanted to get...&quot;</p> <hr /> <div>My name is Michael Mckay, I am currently completing my masters degree with dissertation at UWA. After completing my undergraduate degree at Curtin University, I wanted to get into the field of Bioinformatics as it was an exciting new field of development particularly in my interest area of genetics. My dissertation project is training deep learning models to perform image segmentation to recognise agricultural crop species, in my case canola, in order to map weeds in fields. The project offered a unique approach as it targets crop structures rather than weed structures, increasing its versatility of application in precision agriculture technologies.<br /> <br /> Areas of Interest: Genetics, Bioinformatics, Deep-learning, Data Science, Agriculture, Aquaculture<br /> <br /> Academic history:<br /> <br /> July 2021 to present: Master of Bioinformatics at the University of Western Australia (Australia). Supervised by Prof. David Edwards and Dr. Monica Danilevicz <br /> January 2020 to November 2020: Honours in Biomedical Science in collaboration with CSIRO, Investigating Manganese oxidating organisms and their impact on desirable earth elements.<br /> 2017 to 2019: Molecular Genetics and Biotechnology at Curtin University<br /> <br /> Publications:<br /> N/A</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=1276 2023-11-01T23:45:37Z

<p>Dave: /* Postdocs */</p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> : [[Soybean]] genomics<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SNParrayDB]]<br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> :[http://daisychain.appliedbioinformatics.com.au Daisychain]<br /> <br /> ===Machine learning in Plant Biology===<br /> :[[Image based high-throughput phenotyping of crops using neural networks]]<br /> <br /> ===Knowledge networks===<br /> <br /> :[[KNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> :[[Amborella]]<br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Soybean]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Metagenomics]]<br /> <br /> ===Publicly available data sets:===<br /> <br /> :[[Yam bean assembly]]<br /> <br /> ===Supplementary Data:===<br /> <br /> :[[PDH1 Comparative Legume Analysis]]<br /> :[[Supplementary Data Set]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> [[Hawlader Al-Mamun]]<br /> <br /> [[Monica Danilevicz]]<br /> <br /> Positions available, please contact David Edwards if interested.<br /> <br /> ===Research Assistants===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===PhD students===<br /> <br /> [[Benjamin Nestor]]<br /> <br /> [[Shriprabha Upadhyaya]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> <br /> [[Tessa Macnish]]&lt;br&gt;<br /> [[Michael Mckay]]&lt;br&gt;<br /> <br /> === Honours students ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> [[Connor McPhan]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Associates===<br /> <br /> [[Philipp Bayer]]<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=1275 2023-11-01T23:45:27Z

<p>Dave: /* Postdocs */</p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> : [[Soybean]] genomics<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SNParrayDB]]<br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> :[http://daisychain.appliedbioinformatics.com.au Daisychain]<br /> <br /> ===Machine learning in Plant Biology===<br /> :[[Image based high-throughput phenotyping of crops using neural networks]]<br /> <br /> ===Knowledge networks===<br /> <br /> :[[KNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> :[[Amborella]]<br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Soybean]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Metagenomics]]<br /> <br /> ===Publicly available data sets:===<br /> <br /> :[[Yam bean assembly]]<br /> <br /> ===Supplementary Data:===<br /> <br /> :[[PDH1 Comparative Legume Analysis]]<br /> :[[Supplementary Data Set]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> [[Hawlader Al-Mamun]]<br /> <br /> [[Monica Danilevicz]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested.<br /> <br /> ===Research Assistants===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===PhD students===<br /> <br /> [[Benjamin Nestor]]<br /> <br /> [[Shriprabha Upadhyaya]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> <br /> [[Tessa Macnish]]&lt;br&gt;<br /> [[Michael Mckay]]&lt;br&gt;<br /> <br /> === Honours students ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> [[Connor McPhan]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Associates===<br /> <br /> [[Philipp Bayer]]<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=1274 2023-11-01T23:45:17Z

<p>Dave: /* Research Assistants */</p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> : [[Soybean]] genomics<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SNParrayDB]]<br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> :[http://daisychain.appliedbioinformatics.com.au Daisychain]<br /> <br /> ===Machine learning in Plant Biology===<br /> :[[Image based high-throughput phenotyping of crops using neural networks]]<br /> <br /> ===Knowledge networks===<br /> <br /> :[[KNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> :[[Amborella]]<br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Soybean]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Metagenomics]]<br /> <br /> ===Publicly available data sets:===<br /> <br /> :[[Yam bean assembly]]<br /> <br /> ===Supplementary Data:===<br /> <br /> :[[PDH1 Comparative Legume Analysis]]<br /> :[[Supplementary Data Set]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> [[Hawlader Al-Mamun]]<br /> <br /> [[Monica Danilevicz]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested.<br /> <br /> <br /> ===Research Assistants===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===PhD students===<br /> <br /> [[Benjamin Nestor]]<br /> <br /> [[Shriprabha Upadhyaya]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> <br /> [[Tessa Macnish]]&lt;br&gt;<br /> [[Michael Mckay]]&lt;br&gt;<br /> <br /> === Honours students ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> [[Connor McPhan]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Associates===<br /> <br /> [[Philipp Bayer]]<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=1273 2023-11-01T23:44:58Z

<p>Dave: </p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> : [[Soybean]] genomics<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SNParrayDB]]<br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> :[http://daisychain.appliedbioinformatics.com.au Daisychain]<br /> <br /> ===Machine learning in Plant Biology===<br /> :[[Image based high-throughput phenotyping of crops using neural networks]]<br /> <br /> ===Knowledge networks===<br /> <br /> :[[KNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> :[[Amborella]]<br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Soybean]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Metagenomics]]<br /> <br /> ===Publicly available data sets:===<br /> <br /> :[[Yam bean assembly]]<br /> <br /> ===Supplementary Data:===<br /> <br /> :[[PDH1 Comparative Legume Analysis]]<br /> :[[Supplementary Data Set]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> [[Hawlader Al-Mamun]]<br /> <br /> [[Monica Danilevicz]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested.<br /> <br /> <br /> ===Research Assistants===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> <br /> ===PhD students===<br /> <br /> [[Benjamin Nestor]]<br /> <br /> [[Shriprabha Upadhyaya]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> <br /> [[Tessa Macnish]]&lt;br&gt;<br /> [[Michael Mckay]]&lt;br&gt;<br /> <br /> === Honours students ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> [[Connor McPhan]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Associates===<br /> <br /> [[Philipp Bayer]]<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=David_Edwards&diff=1272 2023-11-01T23:44:10Z

<p>Dave: </p> <hr /> <div>== David Edwards ==<br /> <br /> ===Academic history: ===<br /> <br /> PhD University of Cambridge 2000<br /> <br /> BSc (Hons) University of Nottingham 1989<br /> <br /> ===Posts held:===<br /> <br /> *2015 - present Professor University of Western Australia.<br /> *2012 - 2015 Professor University of Queensland.<br /> *2007 - 2011 Associate Professor University of Queensland. <br /> *2002 - 2007 Plant Biotechnology Centre, Victoria, Australia. <br /> *1997 - 2002 IACR Long Ashton, University of Bristol, UK. <br /> *1996 - 1997 Genetics Dept. University of Cambridge, UK. <br /> <br /> I gained an Honours degree in agriculture from the University of Nottingham and a PhD from the Department of Plant Science, University of Cambridge. I have held positions within academia (University of Adelaide, Australia; University of Cambridge, UK; and McGill University, Canada), government (Long Ashton Research Centre, UK, Department of Primary Industries, Victoria, Australia) and industry (ICI seeds, UK). I moved to The University of Queensland, Australia in 2007 as an Associate Professor and Principal Research Fellow to support bioinformatics for the Australian Centre for Plant Functional Genomics, and promoted to Professor in 2012. In January 2015 I moved to The University of Western Australia. <br /> <br /> ===Interests:===<br /> <br /> My research interests include applied agricultural biotechnology, the structure and expression of plant genomes, the discovery and application of molecular genetic markers and their application for applied crop improvement, with a focus on crops. We apply a range of applied bioinformatics methods including machine learning for image, genomics and text data analysis. I established and coordinate a Master of Bioinformatics course as well as microcredentials in applied bioinformatics at UWA. To promote the field of applied bioinformatics and support the growing bioinformatics community in Western Australia, I established and lead the UWA [https://www.appliedbioinformatics.com.au/ Centre for Applied Bioinformatics] with members across universities, hospitals and research institutes in Western Australia and internationally.<br /> <br /> <br /> *A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> <br /> ===Contact:===<br /> <br /> University of Western Australia<br /> <br /> Perth, Australia<br /> <br /> email: Dave.Edwards@uwa.edu.au</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=David_Edwards&diff=1271 2023-11-01T23:43:24Z

<p>Dave: </p> <hr /> <div>== David Edwards ==<br /> <br /> ===Academic history: ===<br /> <br /> PhD University of Cambridge 2000<br /> <br /> BSc (Hons) University of Nottingham 1989<br /> <br /> ===Posts held:===<br /> <br /> *2015 - present Professor University of Western Australia.<br /> *2012 - 2015 Professor University of Queensland.<br /> *2007 - 2011 Associate Professor University of Queensland. <br /> *2002 - 2007 Plant Biotechnology Centre, Victoria, Australia. <br /> *1997 - 2002 IACR Long Ashton, University of Bristol, UK. <br /> *1996 - 1997 Genetics Dept. University of Cambridge, UK. <br /> <br /> I gained an Honours degree in agriculture from the University of Nottingham and a PhD from the Department of Plant Science, University of Cambridge. I have held positions within academia (University of Adelaide, Australia; University of Cambridge, UK; and McGill University, Canada), government (Long Ashton Research Centre, UK, Department of Primary Industries, Victoria, Australia) and industry (ICI seeds, UK). I moved to The University of Queensland, Australia in 2007 as an Associate Professor and Principal Research Fellow to support bioinformatics for the Australian Centre for Plant Functional Genomics, and promoted to Professor in 2012. In January 2015 I moved to The University of Western Australia. <br /> <br /> <br /> ===Interests:===<br /> <br /> My research interests include applied agricultural biotechnology, the structure and expression of plant genomes, the discovery and application of molecular genetic markers and their application for applied crop improvement, with a focus on crops. We apply a range of applied bioinformatics methods including machine learning for image, genomics and text data analysis. I established and coordinate a Master of Bioinformatics course as well as microcredentials in applied bioinformatics at UWA. To promote the field of applied bioinformatics and support the growing bioinformatics community in Western Australia, I established and lead the UWA [https://www.appliedbioinformatics.com.au/ Centre for Applied Bioinformatics] with members across universities, hospitals and research institutes in Western Australia and internationally.<br /> <br /> *A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ===Contact:===<br /> <br /> University of Western Australia<br /> <br /> Perth, Australia<br /> <br /> email: Dave.Edwards@uwa.edu.au</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=David_Edwards&diff=1270 2023-11-01T23:38:45Z

<p>Dave: /* Posts held: */</p> <hr /> <div>== David Edwards ==<br /> <br /> ===Academic history: ===<br /> <br /> PhD University of Cambridge 2000<br /> <br /> BSc (Hons) University of Nottingham 1989<br /> <br /> ===Posts held:===<br /> <br /> *2015 - present Professor University of Western Australia.<br /> *2012 - 2015 Professor University of Queensland.<br /> *2007 - 2011 Associate Professor University of Queensland. <br /> *2002 - 2007 Plant Biotechnology Centre, Victoria, Australia. <br /> *1997 - 2002 IACR Long Ashton, University of Bristol, UK. <br /> *1996 - 1997 Genetics Dept. University of Cambridge, UK. <br /> <br /> I gained an Honours degree in agriculture from the University of Nottingham and a PhD from the Department of Plant Science, University of Cambridge. I have held positions within academia (University of Adelaide, Australia; University of Cambridge, UK; and McGill University, Canada), government (Long Ashton Research Centre, UK, Department of Primary Industries, Victoria, Australia) and industry (ICI seeds, UK). I moved to The University of Queensland, Australia in 2007 as an Associate Professor and Principal Research Fellow to support bioinformatics for the Australian Centre for Plant Functional Genomics, and promoted to Professor in 2012. In January 2015 I moved to The University of Western Australia. My research interests include applied agricultural biotechnology, the structure and expression of plant genomes, the discovery and application of molecular genetic markers and their application for applied crop improvement, with a focus on crops. We apply a range of applied bioinformatics methods including machine learning for image, genomics and text data analysis.<br /> <br /> *A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ===Contact:===<br /> <br /> University of Western Australia<br /> <br /> Perth, Australia<br /> <br /> email: Dave.Edwards@uwa.edu.au</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Mitchell_Gill&diff=1269 2023-11-01T23:35:40Z

<p>Dave: /* Project */</p> <hr /> <div><br /> == Project ==<br /> <br /> Trait Prediction in Soybean Through Deep Learning Techniques. - Note, Mitchell left the group after one year of his PhD studies to accept an employment offer in industry.<br /> <br /> == Supervisors ==<br /> <br /> Dr Philipp Bayer<br /> <br /> Professor David Edwards<br /> <br /> == Academic achievements ==<br /> <br /> 2016-2018: Bachelor of Science. Majoring in Genetics &amp; Computer Science<br /> <br /> 2019-Current: Masters of Biotechnology specialising in Genetics &amp; Genomics<br /> <br /> <br /> == Research area ==<br /> <br /> Applications of Deep Learning within a genomic context<br /> <br /> Bioinformatics<br /> <br /> <br /> == Contact ==<br /> <br /> 21953849@student.uwa.edu.au</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Mitchell_Gill&diff=1268 2023-11-01T23:35:04Z

<p>Dave: /* Supervisors */</p> <hr /> <div><br /> == Project ==<br /> <br /> Trait Prediction in Soybean Through Deep Learning Techniques. - Note, Mitchell left the group after one year to accept an employment offer in industry.<br /> <br /> == Supervisors ==<br /> <br /> Dr Philipp Bayer<br /> <br /> Professor David Edwards<br /> <br /> == Academic achievements ==<br /> <br /> 2016-2018: Bachelor of Science. Majoring in Genetics &amp; Computer Science<br /> <br /> 2019-Current: Masters of Biotechnology specialising in Genetics &amp; Genomics<br /> <br /> <br /> == Research area ==<br /> <br /> Applications of Deep Learning within a genomic context<br /> <br /> Bioinformatics<br /> <br /> <br /> == Contact ==<br /> <br /> 21953849@student.uwa.edu.au</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Mitchell_Gill&diff=1267 2023-11-01T23:34:52Z

<p>Dave: </p> <hr /> <div><br /> == Project ==<br /> <br /> Trait Prediction in Soybean Through Deep Learning Techniques. - Note, Mitchell left the group after one year to accept an employment offer in industry.<br /> <br /> == Supervisors ==<br /> <br /> Dr Philipp Bayer<br /> Professor David Edwards<br /> <br /> == Academic achievements ==<br /> <br /> 2016-2018: Bachelor of Science. Majoring in Genetics &amp; Computer Science<br /> <br /> 2019-Current: Masters of Biotechnology specialising in Genetics &amp; Genomics<br /> <br /> <br /> == Research area ==<br /> <br /> Applications of Deep Learning within a genomic context<br /> <br /> Bioinformatics<br /> <br /> <br /> == Contact ==<br /> <br /> 21953849@student.uwa.edu.au</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Alumni&diff=1266 2023-11-01T23:32:11Z

<p>Dave: </p> <hr /> <div>'''PhD graduates'''<br /> <br /> [[Monica Danilevicz]]<br /> <br /> [[Robyn Anderson]]<br /> <br /> [[Cassandria Tay Fernandez]]<br /> <br /> [[Jacob Marsh]]<br /> <br /> [[Ricky Hu]]<br /> <br /> [[Clementine Merce]]<br /> <br /> [[Andy Yuan]]<br /> <br /> [[Armin Scheben]]<br /> <br /> [[Bhavna Hurgobin]]<br /> <br /> [[Juan Montenegro]]<br /> <br /> [[Seyedehmahsa Mousaviderazmahalleh (Mahsa Mousavi)]]<br /> <br /> [[Jenny (HueyTyng) Lee]]<br /> <br /> [[Agnieszka Golicz]]<br /> <br /> [[Paul Visendi Muhindira]]<br /> <br /> [[Paula Andrea Martinez]]<br /> <br /> [[Philipp Bayer]]<br /> <br /> [[Pradeep Ruperao]]<br /> <br /> [[Michal Lorenc]]<br /> <br /> [[Kaitao Lai]]<br /> <br /> [[Paul Berkman]]<br /> <br /> Chris Duran<br /> <br /> Mike Imelfort<br /> <br /> Jatinder Kaur<br /> <br /> Christopher Love<br /> <br /> <br /> '''Masters graduates'''<br /> <br /> [[Xuesong Wang]]<br /> <br /> [[Dimity Smith]]<br /> <br /> [[Ruolan Zhao]]<br /> <br /> [[Aidan Charles]]<br /> <br /> [[Rikard Nyman]]<br /> <br /> [[Eva Song]]<br /> <br /> Patricia Angelica Vera<br /> <br /> Nikki Appleby (MSc)<br /> <br /> <br /> '''Senior researchers and postdocs'''<br /> <br /> [[Philipp Bayer]]<br /> <br /> [[Kenneth Chan]]<br /> <br /> Terry Clark<br /> <br /> [[Pradeep Ruperao]]<br /> <br /> Hong Ching Lee<br /> <br /> [[Jenny (HueyTyng) Lee]]<br /> <br /> Edmund Ling<br /> <br /> Daniel Marshall<br /> <br /> Jiri Stiller<br /> <br /> Ping Zhang<br /> <br /> <br /> '''Research assistants'''<br /> <br /> <br /> Sahana Manoli<br /> <br /> Adam Skarshewski<br /> <br /> Sonika Tyagi<br /> <br /> Yang Liu (Ben)<br /> <br /> <br /> '''Interns'''<br /> <br /> <br /> Tristan de Jong<br /> <br /> Thomas Schumann<br /> <br /> Lars Smits<br /> <br /> Nikolay Terentyev<br /> <br /> Tek-Jun Ling<br /> <br /> [[Oliver Schliebs]]<br /> <br /> Brent Verpaalen<br /> <br /> <br /> '''Other'''<br /> <br /> [[Mitchell Gill]]</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Alumni&diff=1265 2023-11-01T23:30:05Z

<p>Dave: </p> <hr /> <div>'''PhD graduates'''<br /> <br /> [[Monica Danilevicz]]<br /> <br /> [[Robyn Anderson]]<br /> <br /> [[Cassandria Tay Fernandez]]<br /> <br /> [[Jacob Marsh]]<br /> <br /> [[Mitchell Gill]]<br /> <br /> [[Ricky Hu]]<br /> <br /> [[Clementine Merce]]<br /> <br /> [[Andy Yuan]]<br /> <br /> [[Armin Scheben]]<br /> <br /> [[Bhavna Hurgobin]]<br /> <br /> [[Juan Montenegro]]<br /> <br /> [[Seyedehmahsa Mousaviderazmahalleh (Mahsa Mousavi)]]<br /> <br /> [[Jenny (HueyTyng) Lee]]<br /> <br /> [[Agnieszka Golicz]]<br /> <br /> [[Paul Visendi Muhindira]]<br /> <br /> [[Paula Andrea Martinez]]<br /> <br /> [[Philipp Bayer]]<br /> <br /> [[Pradeep Ruperao]]<br /> <br /> [[Michal Lorenc]]<br /> <br /> [[Kaitao Lai]]<br /> <br /> [[Paul Berkman]]<br /> <br /> Chris Duran<br /> <br /> Mike Imelfort<br /> <br /> Jatinder Kaur<br /> <br /> Christopher Love<br /> <br /> <br /> '''Masters graduates'''<br /> <br /> [[Xuesong Wang]]<br /> <br /> [[Dimity Smith]]<br /> <br /> [[Ruolan Zhao]]<br /> [[Aidan Charles]]&lt;br&gt;<br /> [[Rikard Nyman]]<br /> [[Eva Song]]&lt;br&gt;<br /> <br /> Patricia Angelica Vera<br /> <br /> Nikki Appleby (MSc)<br /> <br /> <br /> '''Senior researchers and postdocs'''<br /> <br /> [[Philipp Bayer]]<br /> <br /> [[Kenneth Chan]]<br /> <br /> Terry Clark<br /> <br /> [[Pradeep Ruperao]]<br /> <br /> Hong Ching Lee<br /> <br /> [[Jenny (HueyTyng) Lee]]<br /> <br /> Edmund Ling<br /> <br /> Daniel Marshall<br /> <br /> Jiri Stiller<br /> <br /> Ping Zhang<br /> <br /> <br /> '''Research assistants'''<br /> <br /> <br /> Sahana Manoli<br /> <br /> Adam Skarshewski<br /> <br /> Sonika Tyagi<br /> <br /> Yang Liu (Ben)<br /> <br /> <br /> '''Interns'''<br /> <br /> <br /> Tristan de Jong<br /> <br /> Thomas Schumann<br /> <br /> Lars Smits<br /> <br /> Nikolay Terentyev<br /> <br /> Tek-Jun Ling<br /> <br /> [[Oliver Schliebs]]<br /> <br /> Brent Verpaalen</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=1264 2023-11-01T23:28:25Z

<p>Dave: </p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> : [[Soybean]] genomics<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SNParrayDB]]<br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> :[http://daisychain.appliedbioinformatics.com.au Daisychain]<br /> <br /> ===Machine learning in Plant Biology===<br /> :[[Image based high-throughput phenotyping of crops using neural networks]]<br /> <br /> ===Knowledge networks===<br /> <br /> :[[KNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> :[[Amborella]]<br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Soybean]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Metagenomics]]<br /> <br /> ===Publicly available data sets:===<br /> <br /> :[[Yam bean assembly]]<br /> <br /> ===Supplementary Data:===<br /> <br /> :[[PDH1 Comparative Legume Analysis]]<br /> :[[Supplementary Data Set]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> [[Hawlader Al-Mamun]]<br /> <br /> [[Monica Danilevicz]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested.<br /> <br /> ===Research Assistants===<br /> <br /> <br /> <br /> ===PhD students===<br /> <br /> [[Benjamin Nestor]]<br /> <br /> [[Shriprabha Upadhyaya]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> <br /> [[Tessa Macnish]]&lt;br&gt;<br /> [[Michael Mckay]]&lt;br&gt;<br /> <br /> === Honours students ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> [[Connor McPhan]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Associates===<br /> <br /> [[Philipp Bayer]]<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=1263 2023-11-01T23:27:29Z

<p>Dave: </p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> : [[Soybean]] genomics<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SNParrayDB]]<br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> :[http://daisychain.appliedbioinformatics.com.au Daisychain]<br /> <br /> ===Machine learning in Plant Biology===<br /> :[[Image based high-throughput phenotyping of crops using neural networks]]<br /> <br /> ===Knowledge networks===<br /> <br /> :[[KNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> :[[Amborella]]<br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Soybean]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Metagenomics]]<br /> <br /> ===Publicly available data sets:===<br /> <br /> :[[Yam bean assembly]]<br /> <br /> ===Supplementary Data:===<br /> <br /> :[[PDH1 Comparative Legume Analysis]]<br /> :[[Supplementary Data Set]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> [[Hawlader Al-Mamun]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested.<br /> <br /> ===Research Assistants===<br /> <br /> <br /> <br /> ===PhD students===<br /> <br /> [[Benjamin Nestor]]<br /> <br /> [[Shriprabha Upadhyaya]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> <br /> [[Tessa Macnish]]&lt;br&gt;<br /> [[Michael Mckay]]&lt;br&gt;<br /> <br /> <br /> === Honours students ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> [[Connor McPhan]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Associates===<br /> <br /> [[Philipp Bayer]]<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=File:Apbg_logo_FINAL_design2.png&diff=1209 2022-01-21T04:28:52Z

<p>Dave: logo</p> <hr /> <div>logo</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=1193 2021-09-04T02:16:57Z

<p>Dave: /* Species of interest include: */</p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> : [[Soybean]] genomics<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SNParrayDB]]<br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> :[http://daisychain.appliedbioinformatics.com.au Daisychain]<br /> <br /> ===Machine learning in Plant Biology===<br /> :[[Image based high-throughput phenotyping of crops using neural networks]]<br /> <br /> ===Knowledge networks===<br /> <br /> :[[KNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> :[[Amborella]]<br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Soybean]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Metagenomics]]<br /> <br /> ===Publicly available data sets:===<br /> <br /> :[[Yam bean assembly]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> <br /> [[Philipp Bayer]]<br /> <br /> [[Jakob Petereit]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Research Assistants===<br /> <br /> <br /> <br /> ===PhD students===<br /> <br /> [[Monica Danilevicz]]<br /> <br /> [[Robyn Anderson]]<br /> <br /> [[Cassandria Tay Fernandez]]<br /> <br /> [[Jacob Marsh]]<br /> <br /> [[Mitchell Gill]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> <br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Honours students ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=1192 2021-09-04T02:16:46Z

<p>Dave: /* Species of interest include: */</p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> : [[Soybean]] genomics<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SNParrayDB]]<br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> :[http://daisychain.appliedbioinformatics.com.au Daisychain]<br /> <br /> ===Machine learning in Plant Biology===<br /> :[[Image based high-throughput phenotyping of crops using neural networks]]<br /> <br /> ===Knowledge networks===<br /> <br /> :[[KNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> :[[Amboella]]<br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Soybean]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Metagenomics]]<br /> <br /> ===Publicly available data sets:===<br /> <br /> :[[Yam bean assembly]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> <br /> [[Philipp Bayer]]<br /> <br /> [[Jakob Petereit]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Research Assistants===<br /> <br /> <br /> <br /> ===PhD students===<br /> <br /> [[Monica Danilevicz]]<br /> <br /> [[Robyn Anderson]]<br /> <br /> [[Cassandria Tay Fernandez]]<br /> <br /> [[Jacob Marsh]]<br /> <br /> [[Mitchell Gill]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> <br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Honours students ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=1191 2021-09-04T02:15:03Z

<p>Dave: /* PhD students */</p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> : [[Soybean]] genomics<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SNParrayDB]]<br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> :[http://daisychain.appliedbioinformatics.com.au Daisychain]<br /> <br /> ===Machine learning in Plant Biology===<br /> :[[Image based high-throughput phenotyping of crops using neural networks]]<br /> <br /> ===Knowledge networks===<br /> <br /> :[[KNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Soybean]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Metagenomics]]<br /> <br /> <br /> ===Publicly available data sets:===<br /> <br /> :[[Yam bean assembly]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> <br /> [[Philipp Bayer]]<br /> <br /> [[Jakob Petereit]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Research Assistants===<br /> <br /> <br /> <br /> ===PhD students===<br /> <br /> [[Monica Danilevicz]]<br /> <br /> [[Robyn Anderson]]<br /> <br /> [[Cassandria Tay Fernandez]]<br /> <br /> [[Jacob Marsh]]<br /> <br /> [[Mitchell Gill]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> <br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Honours students ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=1190 2021-09-04T02:14:37Z

<p>Dave: /* Master students */</p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> : [[Soybean]] genomics<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SNParrayDB]]<br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> :[http://daisychain.appliedbioinformatics.com.au Daisychain]<br /> <br /> ===Machine learning in Plant Biology===<br /> :[[Image based high-throughput phenotyping of crops using neural networks]]<br /> <br /> ===Knowledge networks===<br /> <br /> :[[KNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Soybean]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Metagenomics]]<br /> <br /> <br /> ===Publicly available data sets:===<br /> <br /> :[[Yam bean assembly]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> <br /> [[Philipp Bayer]]<br /> <br /> [[Jakob Petereit]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Research Assistants===<br /> <br /> <br /> <br /> ===PhD students===<br /> <br /> [[Monica Danilevicz]]<br /> <br /> [[Robyn Anderson]]<br /> <br /> [[Cassandria Tay Fernandez]]<br /> <br /> [[Jacob Marsh]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> <br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Honours students ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Alumni&diff=1189 2021-09-04T02:14:16Z

<p>Dave: </p> <hr /> <div>'''PhD graduates'''<br /> <br /> [[Ricky Hu]]<br /> <br /> [[Clementine Merce]]<br /> <br /> [[Andy Yuan]]<br /> <br /> [[Armin Scheben]]<br /> <br /> [[Bhavna Hurgobin]]<br /> <br /> [[Juan Montenegro]]<br /> <br /> [[Seyedehmahsa Mousaviderazmahalleh (Mahsa Mousavi)]]<br /> <br /> [[Jenny (HueyTyng) Lee]]<br /> <br /> [[Agnieszka Golicz]]<br /> <br /> [[Paul Visendi Muhindira]]<br /> <br /> [[Paula Andrea Martinez]]<br /> <br /> [[Philipp Bayer]]<br /> <br /> [[Pradeep Ruperao]]<br /> <br /> [[Michal Lorenc]]<br /> <br /> [[Kaitao Lai]]<br /> <br /> [[Paul Berkman]]<br /> <br /> Chris Duran<br /> <br /> Mike Imelfort<br /> <br /> Jatinder Kaur<br /> <br /> Christopher Love<br /> <br /> <br /> '''Masters graduates'''<br /> <br /> [[Xuesong Wang]]<br /> <br /> [[Dimity Smith]]<br /> <br /> [[Ruolan Zhao]]<br /> <br /> Patricia Angelica Vera<br /> <br /> Nikki Appleby (MSc)<br /> <br /> <br /> '''Senior researchers and postdocs'''<br /> <br /> <br /> [[Kenneth Chan]]<br /> <br /> Terry Clark<br /> <br /> [[Pradeep Ruperao]]<br /> <br /> Hong Ching Lee<br /> <br /> [[Jenny (HueyTyng) Lee]]<br /> <br /> Edmund Ling<br /> <br /> Daniel Marshall<br /> <br /> Jiri Stiller<br /> <br /> Ping Zhang<br /> <br /> <br /> '''Research assistants'''<br /> <br /> <br /> Sahana Manoli<br /> <br /> Adam Skarshewski<br /> <br /> Sonika Tyagi<br /> <br /> Yang Liu (Ben)<br /> <br /> <br /> '''Interns'''<br /> <br /> <br /> Tristan de Jong<br /> <br /> Thomas Schumann<br /> <br /> Lars Smits<br /> <br /> Nikolay Terentyev<br /> <br /> Tek-Jun Ling<br /> <br /> [[Oliver Schliebs]]<br /> <br /> Brent Verpaalen</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=1188 2021-09-04T02:13:19Z

<p>Dave: /* PhD students */</p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> : [[Soybean]] genomics<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SNParrayDB]]<br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> :[http://daisychain.appliedbioinformatics.com.au Daisychain]<br /> <br /> ===Machine learning in Plant Biology===<br /> :[[Image based high-throughput phenotyping of crops using neural networks]]<br /> <br /> ===Knowledge networks===<br /> <br /> :[[KNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Soybean]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Metagenomics]]<br /> <br /> <br /> ===Publicly available data sets:===<br /> <br /> :[[Yam bean assembly]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> <br /> [[Philipp Bayer]]<br /> <br /> [[Jakob Petereit]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Research Assistants===<br /> <br /> <br /> <br /> ===PhD students===<br /> <br /> [[Monica Danilevicz]]<br /> <br /> [[Robyn Anderson]]<br /> <br /> [[Cassandria Tay Fernandez]]<br /> <br /> [[Jacob Marsh]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> [[Xuesong Wang]]<br /> <br /> [[Dimity Smith]]<br /> <br /> [[Ruolan Zhao]]<br /> <br /> [[Mitchell Gill]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Honours students ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Alumni&diff=1187 2021-09-04T02:12:48Z

<p>Dave: </p> <hr /> <div>'''PhD graduates'''<br /> <br /> [[Ricky Hu]]<br /> <br /> [[Clementine Merce]]<br /> <br /> [[Andy Yuan]]<br /> <br /> [[Armin Scheben]]<br /> <br /> [[Bhavna Hurgobin]]<br /> <br /> [[Juan Montenegro]]<br /> <br /> [[Seyedehmahsa Mousaviderazmahalleh (Mahsa Mousavi)]]<br /> <br /> [[Jenny (HueyTyng) Lee]]<br /> <br /> [[Agnieszka Golicz]]<br /> <br /> [[Paul Visendi Muhindira]]<br /> <br /> [[Paula Andrea Martinez]]<br /> <br /> [[Philipp Bayer]]<br /> <br /> [[Pradeep Ruperao]]<br /> <br /> [[Michal Lorenc]]<br /> <br /> [[Kaitao Lai]]<br /> <br /> [[Paul Berkman]]<br /> <br /> Chris Duran<br /> <br /> Mike Imelfort<br /> <br /> Jatinder Kaur<br /> <br /> Christopher Love<br /> <br /> <br /> '''Masters graduates'''<br /> <br /> Patricia Angelica Vera<br /> <br /> Nikki Appleby (MSc)<br /> <br /> <br /> '''Senior researchers and postdocs'''<br /> <br /> <br /> [[Kenneth Chan]]<br /> <br /> Terry Clark<br /> <br /> [[Pradeep Ruperao]]<br /> <br /> Hong Ching Lee<br /> <br /> [[Jenny (HueyTyng) Lee]]<br /> <br /> Edmund Ling<br /> <br /> Daniel Marshall<br /> <br /> Jiri Stiller<br /> <br /> Ping Zhang<br /> <br /> <br /> '''Research assistants'''<br /> <br /> <br /> Sahana Manoli<br /> <br /> Adam Skarshewski<br /> <br /> Sonika Tyagi<br /> <br /> Yang Liu (Ben)<br /> <br /> <br /> '''Interns'''<br /> <br /> <br /> Tristan de Jong<br /> <br /> Thomas Schumann<br /> <br /> Lars Smits<br /> <br /> Nikolay Terentyev<br /> <br /> Tek-Jun Ling<br /> <br /> [[Oliver Schliebs]]<br /> <br /> Brent Verpaalen</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=1186 2021-09-04T02:11:12Z

<p>Dave: /* Publicly available data sets: */</p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> : [[Soybean]] genomics<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SNParrayDB]]<br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> :[http://daisychain.appliedbioinformatics.com.au Daisychain]<br /> <br /> ===Machine learning in Plant Biology===<br /> :[[Image based high-throughput phenotyping of crops using neural networks]]<br /> <br /> ===Knowledge networks===<br /> <br /> :[[KNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Soybean]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Metagenomics]]<br /> <br /> <br /> ===Publicly available data sets:===<br /> <br /> :[[Yam bean assembly]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> <br /> [[Philipp Bayer]]<br /> <br /> [[Jakob Petereit]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Research Assistants===<br /> <br /> <br /> <br /> ===PhD students===<br /> <br /> [[Habib Rijzaani]]<br /> <br /> [[Ricky Hu]]<br /> <br /> [[Clementine Merce]]<br /> <br /> [[Monica Danilevicz]]<br /> <br /> [[Robyn Anderson]]<br /> <br /> [[Cassandria Tay Fernandez]]<br /> <br /> [[Jacob Marsh]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> [[Xuesong Wang]]<br /> <br /> [[Dimity Smith]]<br /> <br /> [[Ruolan Zhao]]<br /> <br /> [[Mitchell Gill]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Honours students ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Soybean&diff=1176 2020-09-01T02:51:25Z

<p>Dave: </p> <hr /> <div>We have been working to develop and analyse a large collection of soybean germplasm. A manuscript has been submitted and supplementary information relating to this manuscript is available below.<br /> <br /> [http://www.appliedbioinformatics.com.au/soybean JBrowse genome viewer]<br /> <br /> Supplementary Tables: [http://www.appliedbioinformatics.com.au/download/Soybean_pangenome_Supp_Tables.xlsx Download here]<br /> <br /> The data can also be viewed on [https://soybase.org/projects/SoyBase.C2020.02.php soybase]</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Soybean&diff=1175 2020-09-01T02:49:52Z

<p>Dave: </p> <hr /> <div>We have been working to develop and analyse a large collection of soybean germplasm. A manuscript has been submitted and supplementary information relating to this manuscript is available below.<br /> <br /> [http://www.appliedbioinformatics.com.au/soybean JBrowse genome viewer]<br /> <br /> The data can also be viewed on [https://soybase.org/projects/SoyBase.C2020.02.php soybase]<br /> <br /> Supplementary Tables: [http://www.appliedbioinformatics.com.au/download/Soybean_pangenome_Supp_Tables.xlsx Download here]</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Soybean&diff=1174 2020-09-01T02:48:35Z

<p>Dave: </p> <hr /> <div>We have been working to develop and analyse a large collection of soybean germplasm. A manuscript has been submitted and supplementary information relating to this manuscript is available below.<br /> <br /> [http://www.appliedbioinformatics.com.au/soybean JBrowse genome viewer]<br /> <br /> Supplementary Tables: [http://www.appliedbioinformatics.com.au/download/Soybean_pangenome_Supp_Tables.xlsx Download here]</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=1173 2020-09-01T02:46:43Z

<p>Dave: /* Genome sequencing */</p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> : [[Soybean]] genomics<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SNParrayDB]]<br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> :[http://daisychain.appliedbioinformatics.com.au Daisychain]<br /> <br /> ===Machine learning in Plant Biology===<br /> :[[Image based high-throughput phenotyping of crops using neural networks]]<br /> <br /> ===Knowledge networks===<br /> <br /> :[[QTLNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Soybean]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Metagenomics]]<br /> <br /> <br /> ===Publicly available data sets:===<br /> <br /> :[[Sample data]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> <br /> [[Philipp Bayer]]<br /> <br /> [[Jakob Petereit]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Research Assistants===<br /> <br /> <br /> <br /> ===PhD students===<br /> <br /> [[Habib Rijzaani]]<br /> <br /> [[Ricky Hu]]<br /> <br /> [[Clementine Merce]]<br /> <br /> [[Monica Danilevicz]]<br /> <br /> [[Robyn Anderson]]<br /> <br /> [[Cassandria Tay Fernandez]]<br /> <br /> [[Jacob Marsh]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> [[Xuesong Wang]]<br /> <br /> [[Dimity Smith]]<br /> <br /> [[Ruolan Zhao]]<br /> <br /> [[Mitchell Gill]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Honours students ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> [[Callum Corkill]]<br /> <br /> [[Gareth Tay Fernandez]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Soybean&diff=1171 2020-08-18T01:10:27Z

<p>Dave: Created page with &quot;We have been working to develop and analyse a large collection of soybean germplasm. A manuscript has been submitted and supplementary information relating to this manuscript...&quot;</p> <hr /> <div>We have been working to develop and analyse a large collection of soybean germplasm. A manuscript has been submitted and supplementary information relating to this manuscript is available below.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Other_legumes&diff=1170 2020-08-18T01:07:46Z

<p>Dave: </p> <hr /> <div>In addition to chickpea and soybean, we contribute to a range of legume genome projects including.<br /> <br /> Pea: We are members of an international consortium to sequence the pea genome, led by INRA, France. <br /> <br /> Pigeonpea: We are working with colleagues at ICRISAT on pigeonpea genomics<br /> <br /> Lentil: We are members of an international consortium to sequence the lentil genome led by Kirstin Bett in Saskatoon, we are sequencing isolated chromosomes (from Jaroslav Dolezel) and undertaking skimGBS to assess contig assembly quality and placement.<br /> <br /> Lupin: I contribute to a lupin genome project with CSIRO<br /> <br /> Clover: I contribute to a clover genome project at UWA<br /> <br /> Pongamia: I have previously contributed towards the analysis of the Pongamia Pinnata genome in a project led by Peter Gresshoff at the University of Queensland<br /> <br /> <br /> Back to [[Main_Page]]</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=1169 2020-08-18T01:06:38Z

<p>Dave: </p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SNParrayDB]]<br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> :[http://daisychain.appliedbioinformatics.com.au Daisychain]<br /> <br /> ===Machine learning in Plant Biology===<br /> :[[Image based high-throughput phenotyping of crops using neural networks]]<br /> <br /> ===Knowledge networks===<br /> <br /> :[[QTLNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Soybean]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Metagenomics]]<br /> <br /> <br /> ===Publicly available data sets:===<br /> <br /> :[[Sample data]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> <br /> [[Philipp Bayer]]<br /> <br /> [[Jakob Petereit]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Research Assistants===<br /> <br /> <br /> <br /> ===PhD students===<br /> <br /> [[Habib Rijzaani]]<br /> <br /> [[Ricky Hu]]<br /> <br /> [[Clementine Merce]]<br /> <br /> [[Monica Danilevicz]]<br /> <br /> [[Robyn Anderson]]<br /> <br /> [[Cassandria Tay Fernandez]]<br /> <br /> [[Jacob Marsh]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> [[Xuesong Wang]]<br /> <br /> [[Dimity Smith]]<br /> <br /> [[Ruolan Zhao]]<br /> <br /> [[Mitchell Gill]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Honours students ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> [[Callum Corkill]]<br /> <br /> [[Gareth Tay Fernandez]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=David_Edwards&diff=1156 2020-03-19T00:35:53Z

<p>Dave: </p> <hr /> <div>== David Edwards ==<br /> <br /> ===Academic history: ===<br /> <br /> PhD University of Cambridge 2000<br /> <br /> BSc (Hons) University of Nottingham 1989<br /> <br /> ===Posts held:===<br /> <br /> *2015 - present Professor University of Western Australia.<br /> *2012 - 2015 Professor University of Queensland.<br /> *2007 - 2011 Associate Professor University of Queensland. <br /> *2002 - 2007 Plant Biotechnology Centre, Victoria, Australia. <br /> *1997 - 2002 IACR Long Ashton, University of Bristol, UK. <br /> *1996 - 1997 Genetics Dept. University of Cambridge, UK. <br /> <br /> I gained an Honours degree in agriculture from the University of Nottingham and a PhD from the Department of Plant Science, University of Cambridge. I have held positions within academia (University of Adelaide, Australia; University of Cambridge, UK; and McGill University, Canada), government (Long Ashton Research Centre, UK, Department of Primary Industries, Victoria, Australia) and industry (ICI seeds, UK). I moved to The University of Queensland, Australia in 2007 as an Associate Professor and Principal Research Fellow to support bioinformatics for the Australian Centre for Plant Functional Genomics, and promoted to Professor in 2012. In January 2015 I moved to The University of Western Australia. My research interests include applied agricultural biotechnology, the structure and expression of plant genomes, the discovery and application of molecular genetic markers and applied bioinformatics, with a focus on crops.<br /> <br /> *A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ===Contact:===<br /> <br /> University of Western Australia<br /> <br /> Perth, Australia<br /> <br /> email: Dave.Edwards@uwa.edu.au</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=SNParrayDB&diff=1103 2018-11-26T09:47:40Z

<p>Dave: /* Link */</p> <hr /> <div>==Introduction==<br /> Advances in sequencing technology have led to a rapid rise of available genomic data for plants, driving new insights into the evolution and domestication of crops. Single nucleotide polymorphisms are a major component of crop diversity and are invaluable as genetic markers in breeding programs. To address the lack of SNP data provided by major databases and to make this data more easily accessible to researchers and breeders, we have developed SNParrayDB, the first database which focuses on SNP array data from oilseed rape (Brassica napus) and bread wheat (Triticum aestivum). SNParrayDB is a comprehensive web-portal providing a database of large-scale genome variation from the Brassica 60K Illumina Infinium™ array for 446 lines from 19 countries and from the Infinium iSelect Wheat 90k array for 309 lines. We include data from three recently published SNP assay datasets (Mason et al., 2015; Qian et al., 2014; Xu et al., 2016) and provide search, download and upload utilities for users. SNParrayDB is a useful starting point for a range of genomics and molecular breeding activities for oilseed rape and wheat.<br /> <br /> ==Link==<br /> The Crop SNParrayDB can be accessed here: http://snpdb.appliedbioinformatics.com.au/<br /> <br /> ==Using SNParrayDB==<br /> <br /> ===Scan a genomic region for SNPs===<br /> A comparative search query between the cultivars Karat and Marnoo for SNPs in a region of chromosome A01 can be carried out from the landing page, by inputting species, lines, chromosome and coordinates (Fig. 1).<br /> [[File:CropSNPdb_Search.png|200px|thumb|right|'''Figure 1''' Overview of the Search page for querying SNPs]]<br /> <br /> The search result is dumped to the screen in tabular format. Additional information on the SNP can be accessed by clicking on the SNP row, which brings up a pop-up box with all additional SNP metadata (Fig. 2).<br /> [[File:Mypic.png|200px|thumb|right|'''Figure 2''' Result of an example search for SNPs between the oilseed rape lines Karat and Marnoo]]<br /> <br /> ===Bulk download SNPs by chromosome===<br /> Users can download all canola genotypes hosted by the database by chromosome as comma-delimited tabular files (Fig. 3).<br /> [[File:CropSNPdb_Download.png|200px|thumb|right|'''Figure 3''' Download page of Crop SNParrayDB]]<br /> <br /> ===Submit SNPs===<br /> User can upload their own oilseed rape SNP array data using the submission portal of Crop SNParrayDB (Fig.4). A genotype matrix and a list of line names and accessions should be uploaded. Example files with correct formatting can be downloaded from the page.<br /> [[File:CropSNPdb_Submit.png|200px|thumb|right|'''Figure 4''' Submission portal of Crop SNParrayDB]]<br /> <br /> ===References===<br /> *Mason AS, Zhang J, Tollenaere R, Vasquez Teuber P, Dalton-Morgan J, Hu L, Yan G, Edwards D, Redden R, Batley J. 2015. High-throughput genotyping for species identification and diversity assessment in germplasm collections. Mol Ecol Resour 15(5): 1091-1101.<br /> *Qian LW, Qian W, Snowdon RJ. 2014. Sub-genomic selection patterns as a signature of breeding in the allopolyploid Brassica napus genome. BMC Genomics 15.<br /> *Xu LP, Hu KN, Zhang ZQ, Guan CY, Chen S, Hua W, Li JN, Wen J, Yi B, Shen JX, et al. 2016. Genome-wide association study reveals the genetic architecture of flowering time in rapeseed (Brassica napus L.). DNA Research 23(1): 43-52.<br /> *The Triticeae Toolbox (T3) (http://triticeaetoolbox.org/)<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> Back to [[Main_Page|main page]]</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=1102 2018-07-19T08:00:19Z

<p>Dave: </p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SNParrayDB]]<br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> <br /> ===Knowledge networks===<br /> <br /> :[[QTLNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Metagenomics]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> <br /> [[Philipp Bayer]]<br /> <br /> <br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Research Assistants===<br /> <br /> <br /> <br /> ===PhD students===<br /> <br /> <br /> Primary supervisor:<br /> <br /> [[Habib Rijzaani]]<br /> <br /> [[Andy Yuan]]<br /> <br /> [[Armin Scheben]]<br /> <br /> [[Ricky Hu]]<br /> <br /> [[Clementine Merce]]<br /> <br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Honours students ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> <br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Alumni&diff=1101 2018-07-19T08:00:02Z

<p>Dave: </p> <hr /> <div>'''PhD graduates'''<br /> <br /> [[Bhavna Hurgobin]]<br /> <br /> [[Juan Montenegro]]<br /> <br /> [[Seyedehmahsa Mousaviderazmahalleh (Mahsa Mousavi)]]<br /> <br /> [[Jenny (HueyTyng) Lee]]<br /> <br /> [[Agnieszka Golicz]]<br /> <br /> [[Paul Visendi Muhindira]]<br /> <br /> [[Paula Andrea Martinez]]<br /> <br /> [[Philipp Bayer]]<br /> <br /> [[Pradeep Ruperao]]<br /> <br /> [[Michal Lorenc]]<br /> <br /> [[Kaitao Lai]]<br /> <br /> [[Paul Berkman]]<br /> <br /> Chris Duran<br /> <br /> Mike Imelfort<br /> <br /> Jatinder Kaur<br /> <br /> Christopher Love<br /> <br /> <br /> '''Masters graduates'''<br /> <br /> Patricia Angelica Vera<br /> <br /> Nikki Appleby (MSc)<br /> <br /> <br /> '''Senior researchers and postdocs'''<br /> <br /> <br /> [[Kenneth Chan]]<br /> <br /> Terry Clark<br /> <br /> [[Pradeep Ruperao]]<br /> <br /> Hong Ching Lee<br /> <br /> [[Jenny (HueyTyng) Lee]]<br /> <br /> Edmund Ling<br /> <br /> Daniel Marshall<br /> <br /> Jiri Stiller<br /> <br /> Ping Zhang<br /> <br /> <br /> '''Research assistants'''<br /> <br /> <br /> Sahana Manoli<br /> <br /> Adam Skarshewski<br /> <br /> Sonika Tyagi<br /> <br /> Yang Liu (Ben)<br /> <br /> <br /> '''Interns'''<br /> <br /> <br /> Tristan de Jong<br /> <br /> Thomas Schumann<br /> <br /> Lars Smits<br /> <br /> Nikolay Terentyev<br /> <br /> Tek-Jun Ling<br /> <br /> [[Oliver Schliebs]]</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=1100 2018-07-19T07:56:49Z

<p>Dave: </p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SNParrayDB]]<br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> <br /> ===Knowledge networks===<br /> <br /> :[[QTLNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Metagenomics]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> [[Kenneth Chan]]<br /> [[Philipp Bayer]]<br /> <br /> [[Jenny (HueyTyng) Lee]]<br /> <br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Research Assistants===<br /> <br /> <br /> <br /> ===PhD students===<br /> <br /> <br /> Primary supervisor:<br /> <br /> [[Habib Rijzaani]]<br /> <br /> [[Andy Yuan]]<br /> <br /> [[Armin Scheben]]<br /> <br /> [[Bhavna Hurgobin]]<br /> <br /> [[Juan Montenegro]]<br /> <br /> [[Seyedehmahsa Mousaviderazmahalleh (Mahsa Mousavi)]]<br /> <br /> [[Ricky Hu]]<br /> <br /> [[Clementine Merce]]<br /> <br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Honours students ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> <br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Alumni&diff=1023 2017-10-06T09:33:10Z

<p>Dave: </p> <hr /> <div>'''PhD graduates'''<br /> <br /> <br /> <br /> [[Agnieszka Golicz]]<br /> <br /> [[Paul Visendi Muhindira]]<br /> <br /> [[Paula Andrea Martinez]]<br /> <br /> [[Philipp Bayer]]<br /> <br /> [[Pradeep Ruperao]]<br /> <br /> [[Michal Lorenc]]<br /> <br /> [[Kaitao Lai]]<br /> <br /> [[Paul Berkman]]<br /> <br /> Chris Duran<br /> <br /> Mike Imelfort<br /> <br /> Jatinder Kaur<br /> <br /> Christopher Love<br /> <br /> <br /> '''Masters graduates'''<br /> <br /> Patricia Angelica Vera<br /> <br /> Nikki Appleby (MSc)<br /> <br /> <br /> '''Senior researchers and postdocs'''<br /> <br /> <br /> Terry Clark<br /> <br /> [[Pradeep Ruperao]]<br /> <br /> Hong Ching Lee<br /> <br /> Edmund Ling<br /> <br /> Daniel Marshall<br /> <br /> Jiri Stiller<br /> <br /> Ping Zhang<br /> <br /> <br /> '''Research assistants'''<br /> <br /> <br /> Sahana Manoli<br /> <br /> Adam Skarshewski<br /> <br /> Sonika Tyagi<br /> <br /> Yang Liu (Ben)<br /> <br /> <br /> '''Interns'''<br /> <br /> <br /> Tristan de Jong<br /> <br /> Thomas Schumann<br /> <br /> Lars Smits<br /> <br /> Nikolay Terentyev<br /> <br /> Tek-Jun Ling<br /> <br /> [[Oliver Schliebs]]</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=1022 2017-10-06T09:32:40Z

<p>Dave: /* Group members */</p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> <br /> <br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SSR discovery]]<br /> <br /> :[[Genetic map visualisation]]<br /> <br /> <br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> <br /> <br /> ===Knowledge networks===<br /> <br /> :[[QTLNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Metagenomics]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> <br /> [[Kenneth Chan]]<br /> <br /> [[Philipp Bayer]]<br /> <br /> [[Jenny (HueyTyng) Lee]]<br /> <br /> <br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Research Assistants===<br /> <br /> <br /> <br /> ===PhD students===<br /> <br /> <br /> Primary supervisor:<br /> <br /> [[Habib Rijzaani]]<br /> <br /> [[Andy Yuan]]<br /> <br /> [[Armin Scheben]]<br /> <br /> [[Bhavna Hurgobin]]<br /> <br /> [[Juan Montenegro]]<br /> <br /> [[Seyedehmahsa Mousaviderazmahalleh (Mahsa Mousavi)]]<br /> <br /> [[Ricky Hu]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> <br /> === Honours students ===<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> <br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=QTLNetMiner_collaboration_with_Rothamstead_Research&diff=1020 2017-09-01T05:35:59Z

<p>Dave: </p> <hr /> <div>QTLNetMiner<br /> <br /> Rothamstead Research has developed [https://ondex.rothamsted.ac.uk/QTLNetMiner/ QTLNetMiner], a system of knowledge networks that connect information about genes, proteins, QTLs, SNPs, publications and more in one graph-based database. Users can use this network to gather knowledge about their genes of interest.<br /> <br /> We have started to collaborate with Rothamstead Research on this project and are hosting our [https://qtlnetminerboleracea.appliedbioinformatics.com.au own ''Brassica oleracea'' instance]. Work is currently underway to expand the functionality of QTLNetMiner and to add more instances for other species of interest.<br /> <br /> <br /> Back to [[Main_Page|main page]]</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Metagenomics&diff=1002 2017-05-27T05:20:46Z

<p>Dave: </p> <hr /> <div>The applied bioinformatics group has extended research experience and interests from crop genomes to metagenomics. <br /> <br /> <br /> <br /> Back to Back to [[Main_Page]]</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Other_legumes&diff=1001 2017-05-27T05:20:07Z

<p>Dave: </p> <hr /> <div>In addition to chickpea, we contribute to a range of legume genome projects including.<br /> <br /> Soybean: We contribute to an international collaboration on soybean genomics with researchers in the US and India<br /> <br /> Pea: We are members of an international consortium to sequence the pea genome, led by INRA, France. <br /> <br /> Pigeonpea: We are working with colleagues at ICRISAT on pigeonpea genomics<br /> <br /> Lentil: We are members of an international consortium to sequence the lentil genome led by Kirstin Bett in Saskatoon, we are sequencing isolated chromosomes (from Jaroslav Dolezel) and undertaking skimGBS to assess contig assembly quality and placement.<br /> <br /> Lupin: I contribute to a lupin genome project with CSIRO<br /> <br /> Clover: I contribute to a clover genome project at UWA<br /> <br /> Pongamia: I have previously contributed towards the analysis of the Pongamia Pinnata genome in a project led by Peter Gresshoff at the University of Queensland<br /> <br /> <br /> Back to [[Main_Page]]</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Other_legumes&diff=1000 2017-05-27T05:19:42Z

<p>Dave: </p> <hr /> <div>In addition to chickpea, we contribute to a range of legume genome projects including.<br /> <br /> Soybean: We contribute to an international collaboration on soybean genomics with researchers in the US and India<br /> <br /> Pea: We are members of an international consortium to sequence the pea genome, led by INRA, France. <br /> <br /> Pigeonpea: We are working with colleagues at ICRISAT on pigeonpea genomics<br /> <br /> Lentil: We are members of an international consortium to sequence the lentil genome led by Kirstin Bett in Saskatoon, we are sequencing isolated chromosomes (from Jaroslav Dolezel) and undertaking skimGBS to assess contig assembly quality and placement.<br /> <br /> Lupin: I contribute to a lupin genome project at UWA<br /> <br /> Clover: I contribute to a clover genome project at UWA<br /> <br /> Pongamia: I have previously contributed towards the analysis of the Pongamia Pinnata genome in a project led by Peter Gresshoff at the University of Queensland<br /> <br /> <br /> Back to [[Main_Page]]</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=999 2017-05-25T06:53:04Z

<p>Dave: /* Publications */</p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en Google Scholar]<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> <br /> <br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SSR discovery]]<br /> <br /> :[[Genetic map visualisation]]<br /> <br /> <br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> <br /> <br /> ===Knowledge networks===<br /> <br /> :[[QTLNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Metagenomics]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> <br /> [[Kenneth Chan]]<br /> <br /> [[Philipp Bayer]]<br /> <br /> <br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Research Assistants===<br /> <br /> <br /> <br /> ===PhD students===<br /> <br /> <br /> Primary supervisor:<br /> <br /> [[Habib Rijzaani]]<br /> <br /> [[Andy Yuan]]<br /> <br /> [[Armin Scheben]]<br /> <br /> [[Bhavna Hurgobin]]<br /> <br /> [[Jenny (HueyTyng) Lee]]<br /> <br /> [[Juan Montenegro]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> <br /> === Honours students ===<br /> <br /> [[Ricky Hu]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> <br /> [[Oliver Schliebs]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=998 2017-05-25T06:52:30Z

<p>Dave: /* Publications */</p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found on Google Scholar: [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en 'publications']<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> <br /> <br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SSR discovery]]<br /> <br /> :[[Genetic map visualisation]]<br /> <br /> <br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> <br /> <br /> ===Knowledge networks===<br /> <br /> :[[QTLNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Metagenomics]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> <br /> [[Kenneth Chan]]<br /> <br /> [[Philipp Bayer]]<br /> <br /> <br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Research Assistants===<br /> <br /> <br /> <br /> ===PhD students===<br /> <br /> <br /> Primary supervisor:<br /> <br /> [[Habib Rijzaani]]<br /> <br /> [[Andy Yuan]]<br /> <br /> [[Armin Scheben]]<br /> <br /> [[Bhavna Hurgobin]]<br /> <br /> [[Jenny (HueyTyng) Lee]]<br /> <br /> [[Juan Montenegro]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> <br /> === Honours students ===<br /> <br /> [[Ricky Hu]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> <br /> [[Oliver Schliebs]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave https://www.appliedbioinformatics.com.au/Edwards/index.php?title=Main_Page&diff=997 2017-05-25T06:51:20Z

<p>Dave: /* Publications */</p> <hr /> <div>==About the group==<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> We are based at the University of Western Australia's Crawley campus in Perth, Australia.<br /> <br /> ==Publications==<br /> <br /> We publish extensively in major journals. A current list of publications can be found here [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&amp;hl=en 'publications']<br /> <br /> ==Public research projects==<br /> <br /> 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.<br /> <br /> <br /> <br /> <br /> ===[[Genome sequencing]]===<br /> <br /> :[http://www.wheatgenome.info Wheat genome sequencing]<br /> <br /> :[http://www.brassicagenome.net Brassica genome sequencing]<br /> <br /> :[http://www.cicer.info/ Chickpea genome sequencing]<br /> <br /> :[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]<br /> <br /> :[[Metagenomics]]<br /> <br /> :[[TAGdb]]<br /> <br /> ===Transcriptomics===<br /> <br /> :[[A differential kmer analysis pipeline]]<br /> <br /> ===Molecular marker discovery===<br /> <br /> :[[SNP discovery]]<br /> <br /> :[[SSR discovery]]<br /> <br /> :[[Genetic map visualisation]]<br /> <br /> <br /> <br /> ===Genome annotation and visualisation===<br /> <br /> :[[Gene and genome annotation]]<br /> <br /> <br /> ===Knowledge networks===<br /> <br /> :[[QTLNetMiner collaboration with Rothamstead Research]]<br /> <br /> ===Species of interest include:===<br /> <br /> <br /> :[[Brassica]]<br /> <br /> :[[Chickpea]]<br /> <br /> :[[Wheat]]<br /> <br /> :[[Seagrass]]<br /> <br /> :[[Other legumes]]<br /> <br /> :[[Metagenomics]]<br /> <br /> ==Group members==<br /> <br /> <br /> <br /> ===Group leader===<br /> <br /> [[David Edwards]] <br /> <br /> <br /> <br /> ===Postdocs===<br /> <br /> <br /> [[Kenneth Chan]]<br /> <br /> [[Philipp Bayer]]<br /> <br /> <br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===Research Assistants===<br /> <br /> <br /> <br /> ===PhD students===<br /> <br /> <br /> Primary supervisor:<br /> <br /> [[Habib Rijzaani]]<br /> <br /> [[Andy Yuan]]<br /> <br /> [[Armin Scheben]]<br /> <br /> [[Bhavna Hurgobin]]<br /> <br /> [[Jenny (HueyTyng) Lee]]<br /> <br /> [[Juan Montenegro]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Master students ===<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> <br /> === Honours students ===<br /> <br /> [[Ricky Hu]]<br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> === Interns ===<br /> <br /> [[Oliver Schliebs]]<br /> <br /> <br /> Positions available, please contact David Edwards if interested<br /> <br /> ===[[Alumni]]===<br /> <br /> ===Positions available===<br /> <br /> 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.</div>

Dave