Applied Bioinformatics Group - User contributions [en]

SNParrayDB

2018-02-07T08:30:59Z

ArminPS: /* Using SNParrayDB */

==Introduction==
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.

==Link==
The Crop SNParrayDB can be accessed here: http://snpdb.appliedbioinformatics.com.au:5000/

==Using SNParrayDB==

===Scan a genomic region for SNPs===
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).
[[File:CropSNPdb_Search.png|200px|thumb|right|'''Figure 1''' Overview of the Search page for querying SNPs]]

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).
[[File:Mypic.png|200px|thumb|right|'''Figure 2''' Result of an example search for SNPs between the oilseed rape lines Karat and Marnoo]]

===Bulk download SNPs by chromosome===
Users can download all canola genotypes hosted by the database by chromosome as comma-delimited tabular files (Fig. 3).
[[File:CropSNPdb_Download.png|200px|thumb|right|'''Figure 3''' Download page of Crop SNParrayDB]]

===Submit SNPs===
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.
[[File:CropSNPdb_Submit.png|200px|thumb|right|'''Figure 4''' Submission portal of Crop SNParrayDB]]

===References===
*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.
*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.
*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.
*The Triticeae Toolbox (T3) (http://triticeaetoolbox.org/)

Back to [[Main_Page|main page]]

SNParrayDB

2018-02-07T08:30:35Z

ArminPS: /* Using SNParrayDB */

==Introduction==
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.

==Link==
The Crop SNParrayDB can be accessed here: http://snpdb.appliedbioinformatics.com.au:5000/

==Using SNParrayDB==

===Scan a genomic region for SNPs===
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).
[[File:CropSNPdb_Search.png|200px|thumb|'''Figure 1''' Overview of the Search page for querying SNPs]]

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).
[[File:Mypic.png|200px|thumb|right|'''Figure 2''' Result of an example search for SNPs between the oilseed rape lines Karat and Marnoo]]

===Bulk download SNPs by chromosome===
Users can download all canola genotypes hosted by the database by chromosome as comma-delimited tabular files (Fig. 3).
[[File:CropSNPdb_Download.png|200px|thumb|right|'''Figure 3''' Download page of Crop SNParrayDB]]

===Submit SNPs===
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.
[[File:CropSNPdb_Submit.png|200px|thumb|right|'''Figure 4''' Submission portal of Crop SNParrayDB]]

===References===
*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.
*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.
*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.
*The Triticeae Toolbox (T3) (http://triticeaetoolbox.org/)

Back to [[Main_Page|main page]]

SNParrayDB

2018-02-07T08:29:57Z

ArminPS: /* Using SNParrayDB */

==Introduction==
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.

==Link==
The Crop SNParrayDB can be accessed here: http://snpdb.appliedbioinformatics.com.au:5000/

==Using SNParrayDB==

===Scan a genomic region for SNPs===
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).
[[File:CropSNPdb_Search.png|50px|thumb|right|'''Figure 1''' Overview of the Search page for querying SNPs]]

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).
[[File:Mypic.png|50px|thumb|right|'''Figure 2''' Result of an example search for SNPs between the oilseed rape lines Karat and Marnoo]]

===Bulk download SNPs by chromosome===
Users can download all canola genotypes hosted by the database by chromosome as comma-delimited tabular files (Fig. 3).
[[File:CropSNPdb_Download.png|50px|thumb|right|'''Figure 3''' Download page of Crop SNParrayDB]]

===Submit SNPs===
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.
[[File:CropSNPdb_Submit.png|50px|thumb|right|'''Figure 4''' Submission portal of Crop SNParrayDB]]

===References===
*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.
*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.
*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.
*The Triticeae Toolbox (T3) (http://triticeaetoolbox.org/)

Back to [[Main_Page|main page]]

SNParrayDB

2018-02-07T08:28:36Z

ArminPS: /* Using SNParrayDB */

SNParrayDB

2018-02-07T08:25:53Z

ArminPS: /* Using SNParrayDB */

==Introduction==
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.

==Link==
The Crop SNParrayDB can be accessed here: http://snpdb.appliedbioinformatics.com.au:5000/

==Using SNParrayDB==

===Scan a genomic region for SNPs===
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).
[[File:CropSNPdb_Search.png|200px|thumb|right|'''Figure 1''' Overview of the Search page for querying SNPs]]

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).
[[File:Mypic.png|200px|thumb|right|'''Figure 2''' Result of an example search for SNPs between the canola lines Karat and Marnoo]]

===Bulk download SNPs by chromosome===
[Section in progress]
[[File:CropSNPdb_Download.png|200px|thumb|right|'''Figure 3''' Download page of Crop SNParrayDB]]

===Submit SNPs===
[[File:CropSNPdb_Submit.png|200px|thumb|right|'''Figure 4''' Submission portal of Crop SNParrayDB]]

===References===
*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.
*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.
*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.
*The Triticeae Toolbox (T3) (http://triticeaetoolbox.org/)

Back to [[Main_Page|main page]]

SNParrayDB

2018-02-07T08:25:32Z

ArminPS: /* Using SNParrayDB */

==Introduction==
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.

==Link==
The Crop SNParrayDB can be accessed here: http://snpdb.appliedbioinformatics.com.au:5000/

==Using SNParrayDB==

===Scan a genomic region for SNPs===
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).
[[File:CropSNPdb_Search.png|200px|thumb|right|'''Figure 1''' Overview of the Search page for querying SNPs]]

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).
[[File:Mypic.png|200px|thumb|right|'''Figure 2''' Result of an example search for SNPs between the canola lines Karat and Marnoo]]

===Bulk download SNPs by chromosome===
[Section in progress]
[[File:CropSNPdb_Download.png|200px|thumb|right|'''Figure 3''' Download page of Crop SNParrayDB]]

===Submit SNPs===
[[File:CropSNPdb_Submit.png|200px|thumb|right|'''Figure 4''' Submission portal of Crop SNParrayDB]]

===References===
*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.
*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.
*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.
*The Triticeae Toolbox (T3) (http://triticeaetoolbox.org/)

Back to [[Main_Page|main page]]

File:CropSNPdb Submit.png

2018-02-07T08:22:15Z

ArminPS:

File:CropSNPdb Download.png

2018-02-07T08:21:59Z

ArminPS:

SNParrayDB

2018-02-07T08:21:26Z

ArminPS: /* Scan a genomic region for SNPs */

==Introduction==
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.

==Link==
The Crop SNParrayDB can be accessed here: http://snpdb.appliedbioinformatics.com.au:5000/

==Using SNParrayDB==

===Scan a genomic region for SNPs===
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).
[[File:CropSNPdb_Search.png|200px|thumb|right|'''Figure 1''' Overview of the Search page for querying SNPs]]

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).
[[File:Mypic.png|200px|thumb|right|'''Figure 2''' Result of an example search for SNPs between the canola lines Karat and Marnoo]]

===Bulk download SNPs by chromosome===
[Section in progress]
[[File:CropSNPdb_Download.png|200px|thumb|right|alt text]]

===Submit SNPs===
[[File:CropSNPdb_Submit.png|200px|thumb|right|alt text]]

===References===
*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.
*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.
*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.
*The Triticeae Toolbox (T3) (http://triticeaetoolbox.org/)

Back to [[Main_Page|main page]]

SNParrayDB

2018-02-07T08:19:21Z

ArminPS: /* Using SNParrayDB */

==Introduction==
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.

==Link==
The Crop SNParrayDB can be accessed here: http://snpdb.appliedbioinformatics.com.au:5000/

==Using SNParrayDB==

===Scan a genomic region for SNPs===
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.
[[File:CropSNPdb_Search.png|200px|thumb|right|Overview of the Search page for querying SNPs]]

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.
[[File:Mypic.png|200px|thumb|right|Result of an example search for SNPs between the canola lines Karat and Marnoo]]

===Bulk download SNPs by chromosome===
[Section in progress]
[[File:CropSNPdb_Download.png|200px|thumb|right|alt text]]

===Submit SNPs===
[[File:CropSNPdb_Submit.png|200px|thumb|right|alt text]]

===References===
*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.
*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.
*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.
*The Triticeae Toolbox (T3) (http://triticeaetoolbox.org/)

Back to [[Main_Page|main page]]

File:CropSNPdb Search.png

2018-02-07T08:15:01Z

ArminPS:

SNParrayDB

2018-02-07T08:14:47Z

ArminPS: /* Scan a genomic region for SNPs */

==Introduction==
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.

==Link==
The Crop SNParrayDB can be accessed here: http://snpdb.appliedbioinformatics.com.au:5000/

==Using SNParrayDB==

===Scan a genomic region for SNPs===
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.
[[File:CropSNPdb_Search.png|200px|thumb|right|Overview of the Search page for querying SNPs]]

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.
[[File:CropSNPdb_Result.png|200px|thumb|right|Result of an example search for SNPs between the canola lines Karat and Marnoo]]

===Bulk download SNPs by chromosome===
[Section in progress]
[[File:CropSNPdb_Download.png|200px|thumb|right|alt text]]

===Submit SNPs===
[[File:CropSNPdb_Submit.png|200px|thumb|right|alt text]]

===References===
*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.
*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.
*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.
*The Triticeae Toolbox (T3) (http://triticeaetoolbox.org/)

Back to [[Main_Page|main page]]

SNParrayDB

2018-02-07T08:12:50Z

ArminPS: /* Scan a genomic region for SNPs */

==Introduction==
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.

==Link==
The Crop SNParrayDB can be accessed here: http://snpdb.appliedbioinformatics.com.au:5000/

==Using SNParrayDB==

===Scan a genomic region for SNPs===
An example of a comparative search query between the cultivars Karat and Marnoo for SNPs in a region of chromosome A01 is provided.
[[File:CropSNPdb_Search.png|200px|thumb|right|alt text]]

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.
[[File:CropSNPdb_Result.png|200px|thumb|right|alt text]]

===Bulk download SNPs by chromosome===
[Section in progress]
[[File:CropSNPdb_Download.png|200px|thumb|right|alt text]]

===Submit SNPs===
[[File:CropSNPdb_Submit.png|200px|thumb|right|alt text]]

===References===
*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.
*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.
*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.
*The Triticeae Toolbox (T3) (http://triticeaetoolbox.org/)

Back to [[Main_Page|main page]]

SNParrayDB

2018-02-07T08:10:59Z

ArminPS:

==Introduction==
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.

==Link==
The Crop SNParrayDB can be accessed here: http://snpdb.appliedbioinformatics.com.au:5000/

==Using SNParrayDB==

===Scan a genomic region for SNPs===

[[File:CropSNPdb_Search.png|200px|thumb|right|alt text]]
[[File:CropSNPdb_Result.png|200px|thumb|right|alt text]]

===Bulk download SNPs by chromosome===
[Section in progress]
[[File:CropSNPdb_Download.png|200px|thumb|right|alt text]]

===Submit SNPs===
[[File:CropSNPdb_Submit.png|200px|thumb|right|alt text]]

===References===
*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.
*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.
*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.
*The Triticeae Toolbox (T3) (http://triticeaetoolbox.org/)

Back to [[Main_Page|main page]]

SNParrayDB

2018-02-07T08:10:34Z

ArminPS:

==Introduction==
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.

==Link==
The Crop SNParrayDB can be accessed here: http://snpdb.appliedbioinformatics.com.au:5000/

==Using SNParrayDB==

===Scan a genomic region for SNPs===

[[File:CropSNPdb_Search.png|200px|thumb|left|alt text]]
[[File:CropSNPdb_Result.png|200px|thumb|left|alt text]]

===Bulk download SNPs by chromosome===
[Section in progress]
[[File:CropSNPdb_Download.png|200px|thumb|left|alt text]]

===Submit SNPs===
[[File:CropSNPdb_Submit.png|200px|thumb|left|alt text]]

===References===
*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.
*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.
*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.
*The Triticeae Toolbox (T3) (http://triticeaetoolbox.org/)

Back to [[Main_Page|main page]]

SNParrayDB

2018-02-07T08:01:00Z

ArminPS: /* Links */

SNParrayDB

2018-02-07T08:00:50Z

ArminPS:

SNParrayDB

2018-02-07T08:00:29Z

ArminPS:

SNParrayDB

2018-02-07T07:57:58Z

ArminPS: /* Scan a genomic region for SNPs */

SNParrayDB

2018-02-07T07:56:55Z

ArminPS: /* Using SNParrayDB */

SNParrayDB

2018-02-07T07:56:40Z

ArminPS: /* Scan a genomic region for SNPs */

File:Mypic.png

2018-02-07T07:56:04Z

ArminPS:

SNParrayDB

2018-02-07T07:53:15Z

ArminPS: /* Links */

SNParrayDB

2018-02-07T07:52:37Z

ArminPS: /* References */

SNParrayDB

2018-02-07T07:50:37Z

ArminPS: /* References */

SNParrayDB

2018-02-07T07:50:09Z

ArminPS:

SNParrayDB

2018-01-29T02:33:11Z

ArminPS:

SNParrayDB

2018-01-28T04:45:35Z

ArminPS:

SNParrayDB

2018-01-28T04:44:36Z

ArminPS: /* Using SNParrayDB */

SNParrayDB

2018-01-28T04:43:00Z

ArminPS: /* Introduction */

SNParrayDB

2018-01-28T04:42:21Z

ArminPS:

SNParrayDB

2018-01-28T04:41:32Z

ArminPS: /* Introduction */

SNParrayDB

2018-01-28T04:36:35Z

ArminPS: /* Introduction */

SNParrayDB

2018-01-28T04:13:16Z

ArminPS: Created page with "==Introduction== XXX ===Links=== http://snpdb.appliedbioinformatics.com.au:5000/ Back to main page"

==Introduction==

XXX

===Links===
http://snpdb.appliedbioinformatics.com.au:5000/

Back to [[Main_Page|main page]]

Main Page

2018-01-28T03:43:30Z

ArminPS: /* Molecular marker discovery */

==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]]

:[[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===

[[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.

SnpArrayDB

2018-01-28T03:43:05Z

ArminPS: Created page with "==Crop SNParrayDB== Genetic linkage mapping enables the study of genome organisation and the association of heritable traits with regions of sequenced genomes. Comparative ge..."

==Crop SNParrayDB==

Genetic linkage mapping enables the study of genome organisation and the association of heritable traits with regions of sequenced genomes. Comparative genetic mapping is particularly powerful as it allows translation of information between related genomes and gives an insight into genome evolution. A common tool for the storage, comparison and visualisation of genetic maps is CMap. However, current visualisation in CMap is limited to the comparison of adjacent aligned maps. To overcome this limitation and in collaboration with CMap developers, we have developed CMap3D, a tool to compare multiple genetic maps in three-dimensional space. CMap3D is based on a client/server model ensuring operability with current CMap data repositories. This tool can be applied to any species where genetic map information is available and enables rapid, direct comparison between multiple aligned maps.

The software is a standalone application written in Processing and Java. Binaries are available for Windows, OSX and Linux, and require Sun Microsystems Java Runtime Environment 1.6 or later.
The software is freely available for non-commercial use.

===Publications===

* Duran C, Boskovic Z, Imelfort M, Batley J, Hamilton NA and Edwards D. (2010) CMap3D: A 3D visualisation tool for comparative genetic maps. [http://bioinformatics.oxfordjournals.org/content/26/2/273.short Bioinformatics 26 (2) 273-274]

* Lim GAC, Jewell EG, Li X, Erwin TA, Love C, Spangenberg GC and Edwards D. (2007) CMap: A Comparative Mapping Tool for Brassica. Cruciferae Newsletter 27

===Links===

Back to [[Main_Page|main page]]

Main Page

2018-01-28T03:39:12Z

ArminPS: /* Molecular marker discovery */

==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]]

:[[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===

[[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

2018-01-28T03:38:45Z

ArminPS: /* Molecular marker discovery */

==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]]

:[[Crop 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===

[[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.

Armin Scheben

2016-02-05T01:56:33Z

ArminPS:

== Armin Scheben ==

===Academic achievement: ===

MSc: Evolution, Ecology and Systematics. Ludwig Maximilian University of Munich (Germany)

BSc: Biodiversity and Ecology. Georg-August University Goettingen (Germany)

===Posts held:===

*2016 - present PhD candidate - Applied Bioinformatics - The University of Western Australia, Perth, Australia
*2015 Master Thesis project - Plant Biology Dept - Ludwig Maximilian University of Munich, Germany
Phylogenetics and macroevolution in lower plants
*2014 Research internship - Evolutionary Biology Dept - Ludwig Maximilian University of Munich, Germany
Statistical analysis of variation between 30 housekeeping and stress genes in two populations of wild tomato
*2015 Bachelor Thesis project - Plant Biology Dept - Georg-August University Goettingen, Germany
Hybridization and internal transcribed spacer variation in an apomictic buttercup

===Publications:===
List of publications can be found at [https://www.researchgate.net/profile/Armin_Scheben ResearchGate]

===Summary:===
My primary research goals are directed toward understanding how phylogenetic and genomic processes shape biodiversity in plants.

===Awards and Prizes:===
2016: International Postgraduate Research Scholarship and Australian Postgraduate Award

2015: Graduated in the top 10 per cent, Faculty of Biology, Ludwig Maximilian University of Munich

2015: Young Researcher Award, Faculty of Biology, Ludwig Maximilian University of Munich

2014: Young Researcher Award, Faculty of Biology, Ludwig Maximilian University of Munich

===Contact:===

Armin Patrick Scheben

PhD Candidate

School of Plant Biology

University of Western Australia

Perth, 6009

Australia

armin.scheben@research.uwa.edu.au

Armin Scheben

2016-02-05T01:55:05Z

ArminPS: Created page with "== Armin Scheben == ===Academic achievement: === MSc: Evolution, Ecology and Systematics. Ludwig Maximilian University of Munich (Germany) BSc: Biodiversity and Ecology. Georg..."

== Armin Scheben ==

===Academic achievement: ===

MSc: Evolution, Ecology and Systematics. Ludwig Maximilian University of Munich (Germany)

BSc: Biodiversity and Ecology. Georg-August University Goettingen (Germany)

===Posts held:===

*2016 - present PhD candidate - Applied Bioinformatics - The University of Western Australia, Perth, Australia
*2015 Master Thesis project - Plant Biology Dept - Ludwig Maximilian University of Munich, Germany
Phylogenetics and macroevolution in lower plants
*2014 Research internship - Evolutionary Biology Dept - Ludwig Maximilian University of Munich, Germany
Statistical analysis of variation between 30 housekeeping and stress genes in two populations of wild tomato
*2015 Bachelor Thesis project - Plant Biology Dept - Georg-August University Goettingen, Germany
Hybridization and internal transcribed spacer variation in an apomictic buttercup

===Publications:===
List of publications can be found at [https://www.researchgate.net/profile/Armin_Scheben ResearchGate]

===Summary:===
My primary research goals are directed toward understanding how phylogenetic and genomic processes shape biodiversity in plants.

===Awards and Prizes:===
2016: International Postgraduate Research Scholarship and Australian Postgraduate Award

2015: Graduated in the top 10 per cent, Faculty of Biology, Ludwig Maximilian University of Munich

2015: Young Researcher Award, Faculty of Biology, Ludwig Maximilian University of Munich

2014: Young Researcher Award, Faculty of Biology, Ludwig Maximilian University of Munich

===Contact:===

Armin Patrick Scheben
PhD Candidate
School of Plant Biology
University of Western Australia
Perth, 6009
Australia

armin.scheben@research.uwa.edu.au

Main Page

2016-02-04T04:41:08Z

ArminPS: /* 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]

:[[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]]

:[[Other legumes]]

:[[Metagenomics]]

==Group members==

===Group leader===

[[David Edwards]]

===Postdocs===

[[Kenneth Chan]]

[[Philipp Bayer]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Agnieszka Golicz]]

[[Armin Scheben]]

[[Bhavna Hurgobin]]

[[Kaitao Lai]]

[[Jenny (Huey Tyng) Lee]]

[[Michal Lorenc]]

[[Paula Andrea Martinez]]

[[Juan Montenegro]]

[[Paul Visendi Muhindira]]

[[Pradeep Ruperao]]

Co supervisor:

[[Salman Alamery]]

[[Fabian Inturrsis]]

[[Sarah Loberg]]

[[Dhwani Patel]]

[[Reece Tollenaere]]

[[Manuel Zander]]

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