Applied Bioinformatics Group - User contributions [en]

Seagrass Zmu Genome

2018-04-16T03:49:44Z

Jennylee:

This page provides access to ''Zostera muelleri'' genome assembly and annotation data for the paper Lee et al. 2016.
http://www.plantphysiol.org/content/172/1/272.full.pdf+html

Data DOI: 10.4225/23/5ad41a6c77b60

Full records of data is viewable and downloadable here: http://research-repository.uwa.edu.au/en/datasets/zostera-muelleri-seagrass-genome-data(83e77b30-9044-4012-b9c7-b0b97827c989).html

OR as below

The draft assembly can be downloaded from:

:[http://appliedbioinformatics.com.au/download/Zmu_v1_scaffolds.fa.tar.gz Scaffolds]

The predicted genes in proteins, transcripts and CDS can be downloaded from:

:[http://appliedbioinformatics.com.au/download/Zmu_v1_protein.fa.tar.gz Proteins]

:[http://appliedbioinformatics.com.au/download/Zmu_v1_transcript.fa.tar.gz Transcripts]

:[http://appliedbioinformatics.com.au/download/Zmu_v1_cds.fa.tar.gz CDS]

The gene models reported by MAKER in the format of gff can be downloaded from:
:[http://appliedbioinformatics.com.au/download/Zmu_v1_maker.gff.tar.gz Gene_models]

The domains annotation of predicted proteins in the format of gff can be downloaded from:
:[http://appliedbioinformatics.com.au/download/Zmu_v1_interproscan_of_proteins.gff.tar.gz Domains_annotation]

The tab-deliminated text file for orthologous groups between five species can be downloaded from:
:[http://appliedbioinformatics.com.au/download/Zmu_v1_orthomclgroups.txt.tar.gz Orthogroups]

Seagrass Zmu Genome

2018-04-16T03:49:21Z

Jennylee:

Jenny (HueyTyng) Lee

2017-10-28T09:31:50Z

Jennylee: /* Academic history: */

=Academic history:=

2014 PhD candidate, University of Queensland (Thesis submitted in July 2017)

2009 Honours in Biochemistry, University of Adelaide

2006 Bachelor of Science (Biotechnology), University of Adelaide

=Previous experience:=

2013 Bioinformatics Specialist, Genome Institute of Singapore (GIS)

2010 Bioinformatician, Malaysian Genomics Resource Centre (MGRC)

=Publications:=
Full list of publications here https://scholar.google.com/citations?user=doKoR9YAAAAJ&hl=en&oi=ao

=Contact:=

Applied Bioinformatics Group

School of Biological Sciences

University of Western Australia

Perth, 6009

Australia

Email: h.lee12@uq.edu.au or hueytyng.lee@gmail.com
<br>Twitter: @hueytynglee

Jenny (HueyTyng) Lee

2017-10-23T04:12:51Z

Jennylee: /* Previous experience: */

=Academic history:=

2014 PhD candidate, University of Queensland (Thesis submitted July 2017)

2009 Honours in Biochemistry, University of Adelaide

2006 Bachelor of Science (Biotechnology), University of Adelaide

=Previous experience:=

2013 Bioinformatics Specialist, Genome Institute of Singapore (GIS)

2010 Bioinformatician, Malaysian Genomics Resource Centre (MGRC)

=Publications:=
Full list of publications here https://scholar.google.com/citations?user=doKoR9YAAAAJ&hl=en&oi=ao

=Contact:=

Applied Bioinformatics Group

School of Biological Sciences

University of Western Australia

Perth, 6009

Australia

Email: h.lee12@uq.edu.au or hueytyng.lee@gmail.com
<br>Twitter: @hueytynglee

Jenny (HueyTyng) Lee

2017-10-23T04:12:06Z

Jennylee: /* Previous experience: */

=Academic history:=

2014 PhD candidate, University of Queensland (Thesis submitted July 2017)

2009 Honours in Biochemistry, University of Adelaide

2006 Bachelor of Science (Biotechnology), University of Adelaide

=Previous experience:=

2013::Bioinformatics Specialist, Genome Institute of Singapore (GIS)

2010-2012:Bioinformatician, Malaysian Genomics Resource Centre (MGRC)

=Publications:=
Full list of publications here https://scholar.google.com/citations?user=doKoR9YAAAAJ&hl=en&oi=ao

=Contact:=

Applied Bioinformatics Group

School of Biological Sciences

University of Western Australia

Perth, 6009

Australia

Email: h.lee12@uq.edu.au or hueytyng.lee@gmail.com
<br>Twitter: @hueytynglee

Jenny (HueyTyng) Lee

2017-10-23T04:10:54Z

Jennylee: /* Previous experience: */

=Academic history:=

2014 PhD candidate, University of Queensland (Thesis submitted July 2017)

2009 Honours in Biochemistry, University of Adelaide

2006 Bachelor of Science (Biotechnology), University of Adelaide

=Previous experience:=

2013 Bioinformatics Specialist, Genome Institute of Singapore (GIS)

2010-2012 Bioinformatician, Malaysian Genomics Resource Centre (MGRC)

=Publications:=
Full list of publications here https://scholar.google.com/citations?user=doKoR9YAAAAJ&hl=en&oi=ao

=Contact:=

Applied Bioinformatics Group

School of Biological Sciences

University of Western Australia

Perth, 6009

Australia

Email: h.lee12@uq.edu.au or hueytyng.lee@gmail.com
<br>Twitter: @hueytynglee

Main Page

2017-10-18T06:19:22Z

Jennylee: /* 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]]

:[[SSR discovery]]

:[[Genetic map visualisation]]

===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===

[[Kenneth Chan]]

[[Philipp Bayer]]

[[Jenny (HueyTyng) Lee]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Habib Rijzaani]]

[[Andy Yuan]]

[[Armin Scheben]]

[[Bhavna Hurgobin]]

[[Juan Montenegro]]

[[Seyedehmahsa Mousaviderazmahalleh (Mahsa Mousavi)]]

[[Ricky Hu]]

[[Clementine Merce]]

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

2017-10-18T06:19:04Z

Jennylee: /* Public research projects */

Main Page

2017-10-18T06:18:57Z

Jennylee: /* Public research projects */

Jenny (HueyTyng) Lee

2017-10-18T05:52:17Z

Jennylee: /* Contact: */

Jenny (HueyTyng) Lee

2017-10-14T05:17:36Z

Jennylee: /* Contact: */

=Academic history:=

2014 PhD candidate, University of Queensland (Thesis submitted July 2017)

2009 Honours in Biochemistry, University of Adelaide

2006 Bachelor of Science (Biotechnology), University of Adelaide

=Previous experience:=

2013 Bioinformatics Specialist, Genome Institute of Singapore (GIS)

2010 Bioinformatician, Malaysian Genomics Resource Centre (MGRC)

=Publications:=
Full list of publications here https://scholar.google.com/citations?user=doKoR9YAAAAJ&hl=en&oi=ao

=Contact:=

Email: h.lee12@uq.edu.au or hueytyng.lee@gmail.com

Applied Bioinformatics Group

School of Biological Sciences

University of Western Australia

Perth, 6009

Australia

Jenny (HueyTyng) Lee

2017-10-14T05:17:15Z

Jennylee: /* Contact: */

=Academic history:=

2014 PhD candidate, University of Queensland (Thesis submitted July 2017)

2009 Honours in Biochemistry, University of Adelaide

2006 Bachelor of Science (Biotechnology), University of Adelaide

=Previous experience:=

2013 Bioinformatics Specialist, Genome Institute of Singapore (GIS)

2010 Bioinformatician, Malaysian Genomics Resource Centre (MGRC)

=Publications:=
Full list of publications here https://scholar.google.com/citations?user=doKoR9YAAAAJ&hl=en&oi=ao

=Contact:=

Email: h.lee12@uq.edu.au

hueytyng.lee@gmail.com

Applied Bioinformatics Group

School of Biological Sciences

University of Western Australia

Perth, 6009

Australia

Jenny (HueyTyng) Lee

2017-10-14T05:15:38Z

Jennylee: /* Academic history: */

=Academic history:=

2014 PhD candidate, University of Queensland (Thesis submitted July 2017)

2009 Honours in Biochemistry, University of Adelaide

2006 Bachelor of Science (Biotechnology), University of Adelaide

=Previous experience:=

2013 Bioinformatics Specialist, Genome Institute of Singapore (GIS)

2010 Bioinformatician, Malaysian Genomics Resource Centre (MGRC)

=Publications:=
Full list of publications here https://scholar.google.com/citations?user=doKoR9YAAAAJ&hl=en&oi=ao

=Contact:=

h.lee12@uq.edu.au

hueytyng.lee@gmail.com

Applied Bioinformatics Group

School of Plant Biology

University of Western Australia

Perth, WA, 6009

Australia

Jenny (HueyTyng) Lee

2017-06-06T06:27:36Z

Jennylee: /* Publications: */

=Academic history:=

2014 PhD candidate, University of Queensland

2009 Honours in Biochemistry, University of Adelaide

2006 Bachelor of Science (Biotechnology), University of Adelaide

=Previous experience:=

2013 Bioinformatics Specialist, Genome Institute of Singapore (GIS)

2010 Bioinformatician, Malaysian Genomics Resource Centre (MGRC)

=Publications:=
Full list of publications here https://scholar.google.com/citations?user=doKoR9YAAAAJ&hl=en&oi=ao

=Contact:=

h.lee12@uq.edu.au

hueytyng.lee@gmail.com

Applied Bioinformatics Group

School of Plant Biology

University of Western Australia

Perth, WA, 6009

Australia

Seagrass Zmu Genome

2017-05-30T02:33:56Z

Jennylee:

This page provides access to ''Zostera muelleri'' genome assembly and annotation data for the paper Lee et al. 2016.
http://www.plantphysiol.org/content/172/1/272.full.pdf+html

The draft assembly can be downloaded from:

:[http://appliedbioinformatics.com.au/download/Zmu_v1_scaffolds.fa.tar.gz Scaffolds]

The predicted genes in proteins, transcripts and CDS can be downloaded from:

:[http://appliedbioinformatics.com.au/download/Zmu_v1_protein.fa.tar.gz Proteins]

:[http://appliedbioinformatics.com.au/download/Zmu_v1_transcript.fa.tar.gz Transcripts]

:[http://appliedbioinformatics.com.au/download/Zmu_v1_cds.fa.tar.gz CDS]

The gene models reported by MAKER in the format of gff can be downloaded from:
:[http://appliedbioinformatics.com.au/download/Zmu_v1_maker.gff.tar.gz Gene_models]

The domains annotation of predicted proteins in the format of gff can be downloaded from:
:[http://appliedbioinformatics.com.au/download/Zmu_v1_interproscan_of_proteins.gff.tar.gz Domains_annotation]

The tab-deliminated text file for orthologous groups between five species can be downloaded from:
:[http://appliedbioinformatics.com.au/download/Zmu_v1_orthomclgroups.txt.tar.gz Orthogroups]

Jenny (HueyTyng) Lee

2017-01-15T19:39:23Z

Jennylee: /* Contact: */

=Academic history:=

2014 PhD candidate, University of Queensland

2009 Honours in Biochemistry, University of Adelaide

2006 Bachelor of Science (Biotechnology), University of Adelaide

=Previous experience:=

2013 Bioinformatics Specialist, Genome Institute of Singapore (GIS)

2010 Bioinformatician, Malaysian Genomics Resource Centre (MGRC)

=Publications:=
Full list of publications here http://orcid.org/0000-0001-8561-3161

=Contact:=

h.lee12@uq.edu.au

hueytyng.lee@gmail.com

Applied Bioinformatics Group

School of Plant Biology

University of Western Australia

Perth, WA, 6009

Australia

Jenny (Huey Tyng) Lee

2016-08-09T05:25:27Z

Jennylee: Redirected page to Jenny (HueyTyng) Lee

#Redirect [[Jenny (HueyTyng) Lee]]

Jenny (HueyTyng) Lee

2016-08-09T05:24:44Z

Jennylee: Created page with "=Academic history:= 2014 PhD candidate, University of Queensland 2009 Honours in Biochemistry, University of Adelaide 2006 Bachelor of Science (Biotechnology), University of ..."

=Academic history:=

2014 PhD candidate, University of Queensland

2009 Honours in Biochemistry, University of Adelaide

2006 Bachelor of Science (Biotechnology), University of Adelaide

=Previous experience:=

2013 Bioinformatics Specialist, Genome Institute of Singapore (GIS)

2010 Bioinformatician, Malaysian Genomics Resource Centre (MGRC)

=Contact:=

h.lee12@uq.edu.au

hueytyng.lee@gmail.com

Applied Bioinformatics Group

School of Plant Biology

University of Western Australia

Perth, WA, 6009

Australia

Main Page

2016-08-05T05:39:05Z

Jennylee: /* 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 here [[publications_DE|'publications']]

==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]]

:[[SSR discovery]]

:[[Genetic map visualisation]]

===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===

[[Kenneth Chan]]

[[Philipp Bayer]]

[[Pradeep Ruperao]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Agnieszka Golicz]]

[[Andy Yuan]]

[[Armin Scheben]]

[[Bhavna Hurgobin]]

[[Jenny (HueyTyng) Lee]]

[[Paula Andrea Martinez]]

[[Juan Montenegro]]

[[Paul Visendi Muhindira]]

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.

Jenny (Huey Tyng) Lee

2016-08-05T05:38:48Z

Jennylee:

=Academic history:=

2014 PhD candidate, University of Queensland

2009 Honours in Biochemistry, University of Adelaide

2006 Bachelor of Science (Biotechnology), University of Adelaide

=Previous experience:=

2013 Bioinformatics Specialist, Genome Institute of Singapore (GIS)

2010 Bioinformatician, Malaysian Genomics Resource Centre (MGRC)

=Contact:=

h.lee12@uq.edu.au

hueytyng.lee@gmail.com

Applied Bioinformatics Group

School of Plant Biology

University of Western Australia

Perth, WA, 6009

Australia

Jenny (Huey Tyng) Lee

2016-07-29T06:22:00Z

Jennylee:

=Academic history:=

2014 PhD candidate, University of Queensland

2009 Honours in Biochemistry, University of Adelaide

2006 Bachelor of Science (Biotechnology), University of Adelaide

=Previous experience:=

2013 Bioinformatics Specialist, Genome Institute of Singapore (GIS)

2010 Bioinformatician, Malaysian Genomics Research Centre (MGRC)

=Contact:=

h.lee12@uq.edu.au

hueytyng.lee@gmail.com

Applied Bioinformatics Group

School of Plant Biology

University of Western Australia

Perth, WA, 6009

Australia

Jenny (Huey Tyng) Lee

2016-07-29T06:21:37Z

Jennylee:

Academic history:

2014 PhD candidate, University of Queensland

2009 Honours in Biochemistry, University of Adelaide

2006 Bachelor of Science (Biotechnology), University of Adelaide

Previous experience:

2013 Bioinformatics Specialist, Genome Institute of Singapore (GIS)

2010 Bioinformatician, Malaysian Genomics Research Centre (MGRC)

Contact:

h.lee12@uq.edu.au

hueytyng.lee@gmail.com

Applied Bioinformatics Group

School of Plant Biology

University of Western Australia

Perth, WA, 6009

Australia

Jenny (Huey Tyng) Lee

2016-07-29T06:21:15Z

Jennylee: Created page with "Academic history: 2014 PhD candidate, University of Queensland 2009 Honours in Biochemistry, University of Adelaide 2006 Bachelor of Science (Biotechnology), University of Adel..."

Academic history:

2014 PhD candidate, University of Queensland
2009 Honours in Biochemistry, University of Adelaide
2006 Bachelor of Science (Biotechnology), University of Adelaide

Previous experience:

2013 Bioinformatics Specialist, Genome Institute of Singapore (GIS)
2010 Bioinformatician, Malaysian Genomics Research Centre (MGRC)

Contact:

h.lee12@uq.edu.au
hueytyng.lee@gmail.com

Applied Bioinformatics Group
School of Plant Biology
University of Western Australia
Perth, WA, 6009
Australia

Main Page

2016-07-29T06:11:28Z

Jennylee: /* 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 here [[publications_DE|'publications']]

==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]]

:[[SSR discovery]]

:[[Genetic map visualisation]]

===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===

[[Kenneth Chan]]

[[Philipp Bayer]]

[[Pradeep Ruperao]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Agnieszka Golicz]]

[[Andy Yuan]]

[[Armin Scheben]]

[[Bhavna Hurgobin]]

[[Jenny (Huey Tyng) Lee]]

[[Paula Andrea Martinez]]

[[Juan Montenegro]]

[[Paul Visendi Muhindira]]

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.

Seagrass

2016-07-29T06:11:03Z

Jennylee: Redirected page to Seagrass Zmu Genome

#REDIRECT [[Seagrass Zmu Genome]]

Main Page

2016-07-29T06:10:31Z

Jennylee: /* Species of interest include: */

==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 here [[publications_DE|'publications']]

==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]]

:[[SSR discovery]]

:[[Genetic map visualisation]]

===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===

[[Kenneth Chan]]

[[Philipp Bayer]]

[[Pradeep Ruperao]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Agnieszka Golicz]]

[[Andy Yuan]]

[[Armin Scheben]]

[[Bhavna Hurgobin]]

[[Jenny (Huey Tyng) Lee]]

[[Paula Andrea Martinez]]

[[Juan Montenegro]]

[[Paul Visendi Muhindira]]

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

2016-07-29T06:10:07Z

Jennylee: /* Species of interest include: */

==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 here [[publications_DE|'publications']]

==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]]

:[[SSR discovery]]

:[[Genetic map visualisation]]

===Genome annotation and visualisation===

:[[Gene and genome annotation]]

===Knowledge networks===

:[[QTLNetMiner collaboration with Rothamstead Research]]

===Species of interest include:===

:[[Brassica]]

:[[Chickpea]]

:[[Wheat]]

:[[Seagrass Zmu Genome]]

:[[Other legumes]]

:[[Metagenomics]]

==Group members==

===Group leader===

[[David Edwards]]

===Postdocs===

[[Kenneth Chan]]

[[Philipp Bayer]]

[[Pradeep Ruperao]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Agnieszka Golicz]]

[[Andy Yuan]]

[[Armin Scheben]]

[[Bhavna Hurgobin]]

[[Jenny (Huey Tyng) Lee]]

[[Paula Andrea Martinez]]

[[Juan Montenegro]]

[[Paul Visendi Muhindira]]

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

2016-07-29T06:09:45Z

Jennylee: /* 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 here [[publications_DE|'publications']]

==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]]

:[[SSR discovery]]

:[[Genetic map visualisation]]

===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===

[[Kenneth Chan]]

[[Philipp Bayer]]

[[Pradeep Ruperao]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Agnieszka Golicz]]

[[Andy Yuan]]

[[Armin Scheben]]

[[Bhavna Hurgobin]]

[[Jenny (Huey Tyng) Lee]]

[[Paula Andrea Martinez]]

[[Juan Montenegro]]

[[Paul Visendi Muhindira]]

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.

Seagrass Zmu Genome

2016-07-29T06:06:38Z

Jennylee: Redirected page to Seagrass Zmu Genome

#REDIRECT [[Seagrass Zmu Genome]]

Seagrass Zmu Genome

2016-05-04T03:51:53Z

Jennylee:

This page provides access to ''Zostera muelleri'' genome assembly and annotation data for the paper Lee et al. 2016.

The draft assembly can be downloaded from:

:[http://appliedbioinformatics.com.au/download/Zmu_v1_scaffolds.fa.tar.gz Scaffolds]

The predicted genes in proteins, transcripts and CDS can be downloaded from:

:[http://appliedbioinformatics.com.au/download/Zmu_v1_protein.fa.tar.gz Proteins]

:[http://appliedbioinformatics.com.au/download/Zmu_v1_transcript.fa.tar.gz Transcripts]

:[http://appliedbioinformatics.com.au/download/Zmu_v1_cds.fa.tar.gz CDS]

The gene models reported by MAKER in the format of gff can be downloaded from:
:[http://appliedbioinformatics.com.au/download/Zmu_v1_maker.gff.tar.gz Gene_models]

The domains annotation of predicted proteins in the format of gff can be downloaded from:
:[http://appliedbioinformatics.com.au/download/Zmu_v1_interproscan_of_proteins.gff.tar.gz Domains_annotation]

The tab-deliminated text file for orthologous groups between five species can be downloaded from:
:[http://appliedbioinformatics.com.au/download/Zmu_v1_orthomclgroups.txt.tar.gz Orthogroups]

Seagrass Zmu Genome

2016-04-21T08:18:33Z

Jennylee:

This page provides access to ''Zostera muelleri'' genome assembly and annotation data for the paper Lee et al. 2016.

The draft assembly can be downloaded from:

:[http://appliedbioinformatics.com.au/download/Zmu_v1_scaffolds.fa.tar.gz Scaffolds]

The predicted genes in proteins, transcripts and CDS can be downloaded from:

:[http://appliedbioinformatics.com.au/download/Zmu_v1_protein.fa.tar.gz Proteins]

:[http://appliedbioinformatics.com.au/download/Zmu_v1_transcript.fa.tar.gz Transcripts]

:[http://appliedbioinformatics.com.au/download/Zmu_v1_cds.fa.tar.gz CDS]

The gene models reported by MAKER in the format of gff can be downloaded from:
:[http://appliedbioinformatics.com.au/download/Zmu_v1_maker.gff.tar.gz Gene_models]

The domains annotation of predicted proteins in the format of gff can be downloaded from:
:[http://appliedbioinformatics.com.au/download/Zmu_v1_interproscan_of_proteins.gff.tar.gz Domains_annotation]

The tab-deliminated text file for orthologous groups between five species can be downloaded from
:[http://appliedbioinformatics.com.au/download/Zmu_orthogroups.txt.tar.gz Orthogroups]

Seagrass Zmu Genome

2016-04-18T06:42:19Z

Jennylee:

This page provides access to ''Zostera muelleri'' genome assembly and annotation data for the paper Lee et al. 2016.

The draft assembly can be downloaded from:

:[http://appliedbioinformatics.com.au/download/Zmu_assembly.fa.tar.gz Scaffolds]

The predicted genes in proteins, transcripts and CDS can be downloaded from:

:[http://appliedbioinformatics.com.au/download/Zmu_protein.fa.tar.gz Proteins]

:[http://appliedbioinformatics.com.au/download/Zmu_transcript.fa.tar.gz Transcripts]

:[http://appliedbioinformatics.com.au/download/Zmu_cds.fa.tar.gz CDS]

The gene models reported by MAKER in the format of gff can be downloaded from:
:[http://appliedbioinformatics.com.au/download/Zmu_maker.gff3.tar.gz Gene_models]

The domains annotation of predicted proteins in the format of gff can be downloaded from:
:[http://appliedbioinformatics.com.au/download/Zmu_iprs.gff3.tar.gz Domains_annotation]

The tab-deliminated text file for orthologous groups between five species can be downloaded from
:[http://appliedbioinformatics.com.au/download/Zmu_orthogroups.txt.tar.gz Orthogroups]

Seagrass Zmu Genome

2016-04-18T02:31:16Z

Jennylee:

This page provides access to ''Zostera muelleri'' genome assembly and annotation data for the paper Lee et al. 2016.

The draft assembly can be downloaded from:

:[http://appliedbioinformatics.com.au/download/Zmu_assembly.fa.tar.gz Scaffolds]

The predicted genes in proteins, transcripts and CDS can be downloaded from:

:[http://appliedbioinformatics.com.au/download/Zmu_protein.fa.tar.gz Proteins]

:[http://appliedbioinformatics.com.au/download/Zmu_transcript.fa.tar.gz Transcripts]

:[http://appliedbioinformatics.com.au/download/Zmu_cds.fa.tar.gz CDS]

The gene models reported by MAKER in the format of gff can be downloaded from:
:[http://appliedbioinformatics.com.au/download/Zmu.gff3.tar.gz Gene_models]

The tab-deliminated text file for orthologous groups between five species can be downloaded from
:[http://appliedbioinformatics.com.au/download/Zmu_orthogroups.txt.tar.gz Orthogroups]

Seagrass Zmu Genome

2016-04-18T02:29:07Z

Jennylee:

Seagrass Zmu Genome

2016-04-18T02:26:58Z

Jennylee:

Seagrass Zmu Genome

2016-04-18T02:26:43Z

Jennylee:

This page provides access to ''Zostera muelleri'' genome assembly and annotation data for the paper Lee et al. 2016.

The draft assembly can be downloaded from:

::[http://appliedbioinformatics.com.au/download/Zmu_assembly.fa.tar.gz Scaffolds]

The predicted genes in proteins, transcripts and CDS can be downloaded from:

::[http://appliedbioinformatics.com.au/download/Zmu_protein.fa.tar.gz Proteins]

::[http://appliedbioinformatics.com.au/download/Zmu_transcript.fa.tar.gz Transcripts]

::[http://appliedbioinformatics.com.au/download/Zmu_cds.fa.tar.gz CDS]

Seagrass Zmu Genome

2016-04-18T02:21:37Z

Jennylee:

This page provides access to ''Zostera muelleri'' genome assembly and annotation data for the paper Lee et al. 2016.

Assembly:

Scaffolds [http://appliedbioinformatics.com.au/download/Zmu_assembly.fa.tar.gz Zmu_assembly.fa.tar.gz]

Annotation:

Proteins [http://appliedbioinformatics.com.au/download/Zmu_protein.fa.tar.gz Zmu_protein.fa.tar.gz]

Transcripts [http://appliedbioinformatics.com.au/download/Zmu_transcript.fa.tar.gz Zmu_transcript.fa.tar.gz]

CDS [http://appliedbioinformatics.com.au/download/Zmu_cds.fa.tar.gz Zmu_cds.fa.tar.gz]

Seagrass Zmu Genome

2016-04-18T02:20:34Z

Jennylee:

Seagrass Zmu Genome

2016-04-18T02:20:20Z

Jennylee:

Seagrass Zmu Genome

2016-04-18T02:20:12Z

Jennylee:

Seagrass Zmu Genome

2016-04-18T02:19:59Z

Jennylee:

This page provides access to ''Zostera muelleri'' genome assembly and annotation data for the paper Lee et al. 2016.

Assembly:
Scaffolds [http://appliedbioinformatics.com.au/download/Zmu_assembly.fa.tar.gz Zmu_assembly.fa.tar.gz]

Annotation:
Proteins [http://appliedbioinformatics.com.au/download/Zmu_protein.fa.tar.gz Zmu_protein.fa.tar.gz]
Transcripts [http://appliedbioinformatics.com.au/download/Zmu_transcript.fa.tar.gz Zmu_transcript.fa.tar.gz]
CDS [http://appliedbioinformatics.com.au/download/Zmu_cds.fa.tar.gz Zmu_cds.fa.tar.gz]

Seagrass Zmu Genome

2016-04-18T02:12:41Z

Jennylee: Created page with "This page provides access to ''Zostera muelleri'' genome assembly and annotation data."

This page provides access to ''Zostera muelleri'' genome assembly and annotation data.

User talk:Jennylee

2016-04-18T02:07:32Z

Jennylee: Blanked the page

User talk:Jennylee

2016-04-18T02:07:20Z

Jennylee: Created page with "''Zostera muelleri'' genome"

[[''Zostera muelleri'' genome]]

Applied Bioinformatics Group - User contributions [en]

Seagrass Zmu Genome

Seagrass Zmu Genome

Jenny (HueyTyng) Lee

Jenny (HueyTyng) Lee

Jenny (HueyTyng) Lee

Jenny (HueyTyng) Lee

Main Page

Main Page

Main Page

Jenny (HueyTyng) Lee

Jenny (HueyTyng) Lee

Jenny (HueyTyng) Lee

Jenny (HueyTyng) Lee

Jenny (HueyTyng) Lee

Seagrass Zmu Genome

Jenny (HueyTyng) Lee

Jenny (Huey Tyng) Lee

Jenny (HueyTyng) Lee

Main Page

Jenny (Huey Tyng) Lee

Jenny (Huey Tyng) Lee

Jenny (Huey Tyng) Lee

Jenny (Huey Tyng) Lee

Main Page

Seagrass

Main Page

Main Page

Main Page

Seagrass Zmu Genome​

Seagrass Zmu Genome

Seagrass Zmu Genome

Seagrass Zmu Genome

Seagrass Zmu Genome

Seagrass Zmu Genome

Seagrass Zmu Genome

Seagrass Zmu Genome

Seagrass Zmu Genome

Seagrass Zmu Genome

Seagrass Zmu Genome

Seagrass Zmu Genome

Seagrass Zmu Genome

Seagrass Zmu Genome

User talk:Jennylee

User talk:Jennylee

Seagrass Zmu Genome