Applied Bioinformatics Group - User contributions [en]

Image based high-throughput phenotyping of crops using neural networks

2020-04-26T09:06:45Z

Monica: Created page with " == Introduction == Deep learning is a rapidly evolving technique with the ability to automatically extract features and analyse complex multi-dimensional datasets with high..."

== Introduction ==

Deep learning is a rapidly evolving technique with the ability to automatically extract features and analyse complex multi-dimensional datasets with high scalability to big data. It can be applied to a wide variety of plant phenotyping tasks, such as the identification of abiotic stress signs caused by climate fluctuations, helping improve crop monitoring and breeding aspects. Climate change has affected the yield of several major crops worldwide, for example as temperature rises, wheat yield is expected to reduce 5-6% per 1 °C of temperature increase. These environmental changes will cause significant abiotic stress to crops causing yield and quality decline, urging crop breeders to develop better adapted varieties in order to withstand the abiotic stresses. In this project, I will develop a model capable to identify abiotic stress in crops under field condition, using computer vision and deep learning.

== Significance ==

The model will have application for crop breeders and growers. It will enable high-throughput phenotyping (HTP) of field multispectral images, collected by Unmaned Aerial Vehicles. The model will support crop breeders to automatically phenotype the varieties under trial, assisting the identification of climate-resilient varieties. Farmers can also potentially implement the model to monitor the crops development, allowing for better informed financial planning and overall management of the farm.

== Aims ==

Develop a model capable to estimate the mean yield per variety based on multispectral image and weather data.

Main Page

2020-04-26T09:06:04Z

Monica: /* =Machine learning in Plant Biology */

==About the group==

The applied bioinformatics group was founded in 2007 at the University of Queensland and moved to the University of Western Australia in January 2015. Since this time, the group has established itself as a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation.

The group receives funding from the [http://www.uwa.edu.au/ University of Western Australia], the [http://www.arc.gov.au/ Australian Research Council], the [http://www.grdc.com.au/ Grains Research and Development Corporation] and several industry partners to undertake applied bioinformatics research in genetics and genomics.

The group is led by Professor [[David Edwards]] and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and [[publications_DE|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:Dave.Edwards@uwa.edu.au David Edwards] for further information.

We are based at the University of Western Australia's Crawley campus in Perth, Australia.

==Publications==

We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&hl=en Google Scholar]

==Public research projects==

The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups.

===[[Genome sequencing]]===

:[http://www.wheatgenome.info Wheat genome sequencing]

:[http://www.brassicagenome.net Brassica genome sequencing]

:[http://www.cicer.info/ Chickpea genome sequencing]

:[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]

:[[Metagenomics]]

:[[TAGdb]]

===Transcriptomics===

:[[A differential kmer analysis pipeline]]

===Molecular marker discovery===

:[[SNP discovery]]

:[[SNParrayDB]]

===Genome annotation and visualisation===

:[[Gene and genome annotation]]
:[http://daisychain.appliedbioinformatics.com.au Daisychain]

===Machine learning in Plant Biology===
:[[Image based high-throughput phenotyping of crops using neural networks]]

===Knowledge networks===

:[[QTLNetMiner collaboration with Rothamstead Research]]

===Species of interest include:===

:[[Brassica]]

:[[Chickpea]]

:[[Wheat]]

:[[Seagrass]]

:[[Other legumes]]

:[[Metagenomics]]

===Publicly available data sets:===

:[[Sample data]]

==Group members==

===Group leader===

[[David Edwards]]

===Postdocs===

[[Philipp Bayer]]

[[Jacob Petereit]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

[[Habib Rijzaani]]

[[Ricky Hu]]

[[Clementine Merce]]

[[Monica Danilevicz]]

[[Robyn Anderson]]

[[Cassandria Tay Fernandez]]

[[Jacob Marsh]]

Positions available, please contact David Edwards if interested

=== Master students ===
[[Xuesong Wang]]

[[Dimity Smith]]

[[Ruolan Zhao]]

Positions available, please contact David Edwards if interested

=== Honours students ===

Positions available, please contact David Edwards if interested

=== Interns ===
[[Callum Corkill]]

[[Gareth Tay Fernandez]]

Positions available, please contact David Edwards if interested

===[[Alumni]]===

===Positions available===

There are current positions available at all levels including Postdoc, PhD students and Interns. Candidates should have a good understanding of one or more areas of Computing, Software development, Complex data analysis, Bioinformatics or Genomics. For consideration, please forward your cv and cover letter to Dave.Edwards@uwa.edu.au.

Main Page

2020-04-26T09:05:01Z

Monica: /* Public research projects */

==About the group==

The applied bioinformatics group was founded in 2007 at the University of Queensland and moved to the University of Western Australia in January 2015. Since this time, the group has established itself as a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation.

The group receives funding from the [http://www.uwa.edu.au/ University of Western Australia], the [http://www.arc.gov.au/ Australian Research Council], the [http://www.grdc.com.au/ Grains Research and Development Corporation] and several industry partners to undertake applied bioinformatics research in genetics and genomics.

The group is led by Professor [[David Edwards]] and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and [[publications_DE|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:Dave.Edwards@uwa.edu.au David Edwards] for further information.

We are based at the University of Western Australia's Crawley campus in Perth, Australia.

==Publications==

We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&hl=en Google Scholar]

==Public research projects==

The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups.

===[[Genome sequencing]]===

:[http://www.wheatgenome.info Wheat genome sequencing]

:[http://www.brassicagenome.net Brassica genome sequencing]

:[http://www.cicer.info/ Chickpea genome sequencing]

:[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]

:[[Metagenomics]]

:[[TAGdb]]

===Transcriptomics===

:[[A differential kmer analysis pipeline]]

===Molecular marker discovery===

:[[SNP discovery]]

:[[SNParrayDB]]

===Genome annotation and visualisation===

:[[Gene and genome annotation]]
:[http://daisychain.appliedbioinformatics.com.au Daisychain]

====Machine learning in Plant Biology===
:[[Image based high-throughput phenotyping of crops using neural networks]]

===Knowledge networks===

:[[QTLNetMiner collaboration with Rothamstead Research]]

===Species of interest include:===

:[[Brassica]]

:[[Chickpea]]

:[[Wheat]]

:[[Seagrass]]

:[[Other legumes]]

:[[Metagenomics]]

===Publicly available data sets:===

:[[Sample data]]

==Group members==

===Group leader===

[[David Edwards]]

===Postdocs===

[[Philipp Bayer]]

[[Jacob Petereit]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

[[Habib Rijzaani]]

[[Ricky Hu]]

[[Clementine Merce]]

[[Monica Danilevicz]]

[[Robyn Anderson]]

[[Cassandria Tay Fernandez]]

[[Jacob Marsh]]

Positions available, please contact David Edwards if interested

=== Master students ===
[[Xuesong Wang]]

[[Dimity Smith]]

[[Ruolan Zhao]]

Positions available, please contact David Edwards if interested

=== Honours students ===

Positions available, please contact David Edwards if interested

=== Interns ===
[[Callum Corkill]]

[[Gareth Tay Fernandez]]

Positions available, please contact David Edwards if interested

===[[Alumni]]===

===Positions available===

There are current positions available at all levels including Postdoc, PhD students and Interns. Candidates should have a good understanding of one or more areas of Computing, Software development, Complex data analysis, Bioinformatics or Genomics. For consideration, please forward your cv and cover letter to Dave.Edwards@uwa.edu.au.

Xuesong Wang

2020-03-09T06:15:30Z

Monica: Created page with "== Project == Investigation of wheat Pangenome == Academic achievements == 2018-present. Master of biotechnology. University of Western Australia (Australia) 2009-2013, Bach..."

== Project ==
Investigation of wheat Pangenome

== Academic achievements ==
2018-present. Master of biotechnology. University of Western Australia (Australia)
2009-2013, Bachelor of Plant protection. Hebei Agricultural University (China)

== Research area ==

Wheat pangenome

== Contact ==
22367148@student.uwa.edu.au

Robyn Anderson

2020-02-03T07:43:25Z

Monica: Created page with " I joined the Applied Bioinformatics group in 2018 during my masters program, and have now started my PhD within the group. My PhD project focuses on Deep Learning application..."

I joined the Applied Bioinformatics group in 2018 during my masters program, and have now started my PhD within the group. My PhD project focuses on Deep Learning applications within genomes, and I’m interested in how techniques from other disciplines can be applied to biological questions. I have taught university courses in biochemistry, genetics and bioinformatics for three years, worked for the WA Museum and volunteered for the Perth Science Festival in a diverse set of roles.

==Academic Achievements==

2019 PhD candidate at the University of Western Australia (expected completion 2022)

2016-2018 Masters of Biotechnology (Genetics and Genomics), awarded with Distinction at the University of Western Australia

2013-2015 Bachelor of Science (Genetics and Biochemistry and Molecular Biology) at the University of Western Australia

==Research Area ==

Applications of Deep Learning with genomic datasets

Genome Assembly

Bioinformatics

==Publication List==

Method for Genome-Wide Association Study: A Soybean Example

R Anderson, CT Fernandez, Y Yuan, AA Golicz, D Edwards, PE Bayer

Legume Genomics, 147-158

Genome‐Wide Association Studies in Plants

R Anderson, D Edwards, J Batley, PE Bayer

eLS, 1-7

==Contact==

robyn.anderson@research.uwa.edu.au

Monica Danilevicz

2020-02-03T02:46:30Z

Monica:

Hi,

My name is Monica, I am a PhD student at University of Western Australia and a Forrest Research Foundation scholar [http://www.forrestresearch.org.au/].
My work focus on developing prediction and classification machine learning models to address plant science problems.
Previously, I completed my Bachelor and Master's degree in Brazil at Universidade Federal do Rio de Janeiro, looking into the interaction of crops (mostly maize and sugarcane) with beneficial bacteria when subjected to water deficit stress. There I worked mostly with bioinformatics, doing some RNA-seq analysis, and looking into the expression of microRNAs and long non-coding RNAs, which I still find a very interesting subject :)

== Areas of Interest ==

Plant Biology, Plant Genetics, Machine learning, Deep neural networks, Bioinformatics, Data Science, Plant Phenotyping.

== Academic History ==

'''2019 to present''' 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.

'''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”.

'''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”.

== Publications ==

Current record of publication is available at [https://scholar.google.com.au/citations?user=SIPvegsAAAAJ&hl=en&oi=ao]

== Contact ==

monica.danilevicz@research.uwa.edu.au

Monica Danilevicz

2020-02-03T02:44:03Z

Monica: Created page with " Hi, My name is Monica, I am a PhD student at University of Western Australia and a Forrest Research Foundation scholar [http://www.forrestresearch.org.au/]. My work focus o..."

Sample data

2019-07-01T07:37:24Z

Monica: Created page with "These sample sequence data is available to perform the methodology described at <link for publication>. Follow the link to download the tar file [https://mega.nz/#!CsF3xA7Z!R..."

These sample sequence data is available to perform the methodology described at <link for publication>.

Follow the link to download the tar file [https://mega.nz/#!CsF3xA7Z!RuxI7Ap_eJe4OaQr_oEOs_K0YIepDQxhDM4VhMI-26A].

Main Page

2019-07-01T07:31:54Z

Monica: /* Public research projects */

==About the group==

The applied bioinformatics group was founded in 2007 at the University of Queensland and moved to the University of Western Australia in January 2015. Since this time, the group has established itself as a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation.

The group receives funding from the [http://www.uwa.edu.au/ University of Western Australia], the [http://www.arc.gov.au/ Australian Research Council], the [http://www.grdc.com.au/ Grains Research and Development Corporation] and several industry partners to undertake applied bioinformatics research in genetics and genomics.

The group is led by Professor [[David Edwards]] and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and [[publications_DE|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:Dave.Edwards@uwa.edu.au David Edwards] for further information.

We are based at the University of Western Australia's Crawley campus in Perth, Australia.

==Publications==

We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&hl=en Google Scholar]

==Public research projects==

The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups.

===[[Genome sequencing]]===

:[http://www.wheatgenome.info Wheat genome sequencing]

:[http://www.brassicagenome.net Brassica genome sequencing]

:[http://www.cicer.info/ Chickpea genome sequencing]

:[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]

:[[Metagenomics]]

:[[TAGdb]]

===Transcriptomics===

:[[A differential kmer analysis pipeline]]

===Molecular marker discovery===

:[[SNP discovery]]

:[[SNParrayDB]]

===Genome annotation and visualisation===

:[[Gene and genome annotation]]

===Knowledge networks===

:[[QTLNetMiner collaboration with Rothamstead Research]]

===Species of interest include:===

:[[Brassica]]

:[[Chickpea]]

:[[Wheat]]

:[[Seagrass]]

:[[Other legumes]]

:[[Metagenomics]]

===Publicly available data sets:===

:[[Sample data]]

==Group members==

===Group leader===

[[David Edwards]]

===Postdocs===

[[Philipp Bayer]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Habib Rijzaani]]

[[Andy Yuan]]

[[Armin Scheben]]

[[Ricky Hu]]

[[Clementine Merce]]

[[Monica Danilevicz]]

Positions available, please contact David Edwards if interested

=== Master students ===

Positions available, please contact David Edwards if interested

=== Honours students ===

Positions available, please contact David Edwards if interested

=== Interns ===

Positions available, please contact David Edwards if interested

===[[Alumni]]===

===Positions available===

There are current positions available at all levels including Postdoc, PhD students and Interns. Candidates should have a good understanding of one or more areas of Computing, Software development, Complex data analysis, Bioinformatics or Genomics. For consideration, please forward your cv and cover letter to Dave.Edwards@uwa.edu.au.

Main Page

2019-07-01T07:26:11Z

Monica: /* PhD students */

==About the group==

The applied bioinformatics group was founded in 2007 at the University of Queensland and moved to the University of Western Australia in January 2015. Since this time, the group has established itself as a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation.

The group receives funding from the [http://www.uwa.edu.au/ University of Western Australia], the [http://www.arc.gov.au/ Australian Research Council], the [http://www.grdc.com.au/ Grains Research and Development Corporation] and several industry partners to undertake applied bioinformatics research in genetics and genomics.

The group is led by Professor [[David Edwards]] and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and [[publications_DE|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:Dave.Edwards@uwa.edu.au David Edwards] for further information.

We are based at the University of Western Australia's Crawley campus in Perth, Australia.

==Publications==

We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&hl=en Google Scholar]

==Public research projects==

The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups.

===[[Genome sequencing]]===

:[http://www.wheatgenome.info Wheat genome sequencing]

:[http://www.brassicagenome.net Brassica genome sequencing]

:[http://www.cicer.info/ Chickpea genome sequencing]

:[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]

:[[Metagenomics]]

:[[TAGdb]]

===Transcriptomics===

:[[A differential kmer analysis pipeline]]

===Molecular marker discovery===

:[[SNP discovery]]

:[[SNParrayDB]]

===Genome annotation and visualisation===

:[[Gene and genome annotation]]

===Knowledge networks===

:[[QTLNetMiner collaboration with Rothamstead Research]]

===Species of interest include:===

:[[Brassica]]

:[[Chickpea]]

:[[Wheat]]

:[[Seagrass]]

:[[Other legumes]]

:[[Metagenomics]]

==Group members==

===Group leader===

[[David Edwards]]

===Postdocs===

[[Philipp Bayer]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Habib Rijzaani]]

[[Andy Yuan]]

[[Armin Scheben]]

[[Ricky Hu]]

[[Clementine Merce]]

[[Monica Danilevicz]]

Positions available, please contact David Edwards if interested

=== Master students ===

Positions available, please contact David Edwards if interested

=== Honours students ===

Positions available, please contact David Edwards if interested

=== Interns ===

Positions available, please contact David Edwards if interested

===[[Alumni]]===

===Positions available===

There are current positions available at all levels including Postdoc, PhD students and Interns. Candidates should have a good understanding of one or more areas of Computing, Software development, Complex data analysis, Bioinformatics or Genomics. For consideration, please forward your cv and cover letter to Dave.Edwards@uwa.edu.au.