Difference between revisions of "Philipp Bayer"
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Graph databases & knowledge networks, genotyping by sequencing, BioNano optical mapping, genome assembly assessment, genome assembly improvement | Graph databases & knowledge networks, genotyping by sequencing, BioNano optical mapping, genome assembly assessment, genome assembly improvement | ||
| − | I started to focus on bioinformatics during my BSc Biology in Germany, where I worked on the evolution of HIV/SIV and heat shock resistance in sea-grasses (''Zostera marina'' and ''Posidonia oceanica''). I then came to Australia to work on my IT skills, which culminated in a Master IT with a short stint doing SQL consulting for a web design company. At the same time I co-founded and worked on openSNP.org, an open repository for human genotyping datasets from customers of direct-to-consumer genotyping companies like 23andMe. I did my PhD at the University of Queensland in the Edwards group developing a novel low-coverage genotyping by sequencing pipeline, and used the pipeline to assess genome assembly quality in ''Brassica napus'' and ''Cicer arietinum''. I now work as a post-doc in the same group focusing on knowledge networks, | + | I started to focus on bioinformatics during my BSc Biology in Germany, where I worked on the evolution of HIV/SIV and heat shock resistance in sea-grasses (''Zostera marina'' and ''Posidonia oceanica''). I then came to Australia to work on my IT skills, which culminated in a Master IT with a short stint doing SQL consulting for a web design company. At the same time I co-founded and worked on openSNP.org, an open repository for human genotyping datasets from customers of direct-to-consumer genotyping companies like 23andMe. I did my PhD at the University of Queensland in the Edwards group developing a novel low-coverage genotyping by sequencing pipeline, and used the pipeline to assess genome assembly quality in ''Brassica napus'' and ''Cicer arietinum''. I now work as a post-doc in the same group focusing on knowledge networks, the assembly, annotation and analysis of pan-genomes of several crop species (currently mostly legumes and Brassicas), genome-wide association studies, population genetics, and more. I am also involved in organising and teaching the Bioinformatics courses for Masters students and am an active poster on biostars.org |
=== Academic history === | === Academic history === | ||
| + | |||
| + | "Bayer, Philipp E; Ruperao, Pradeep; Mason, Annaliese S; Stiller, Jiri; Chan, Chon-Kit Kenneth; Hayashi, Satomi; Long, Yan; Meng, Jinling; Sutton, Tim; Visendi, Paul; "",High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus,Theoretical and Applied Genetics,128,6,1039-1047,2015,Springer Berlin Heidelberg | ||
| + | |||
| + | ""Bayer, Philipp Emanuel; "",""Skim-Based Genotyping by Sequencing Using a Double Haploid Population to Call SNPs, Infer Gene Conversions, and Improve Genome Assemblies"",Plant Bioinformatics: Methods and Protocols,,,285-292,2016,Springer New York | ||
| + | |||
| + | ""Mason, Annaliese S; Rousseau-Gueutin, Mathieu; Morice, Jérôme; Bayer, Philipp E; Besharat, Naghmeh; Cousin, Anouska; Pradhan, Aneeta; Parkin, Isobel AP; Chèvre, Anne-Marie; Batley, Jacqueline; "",Centromere locations in brassica A and C genomes revealed through half-tetrad analysis,Genetics,202,2,513-523,2016,Genetics | ||
| + | |||
| + | ""Visendi, Paul; Berkman, Paul J; Hayashi, Satomi; Golicz, Agnieszka A; Bayer, Philipp E; Ruperao, Pradeep; Hurgobin, Bhavna; Montenegro, Juan; Chan, Chon-Kit Kenneth; Staňková, Helena; "",An efficient approach to BAC based assembly of complex genomes,Plant methods,12,1,1,2016,BioMed Central | ||
| + | |||
| + | ""Bayer, Philipp Emanuel; "",Genomics of Salinity,Plant Genomics and Climate Change,,,179-194,2016,Springer New York | ||
| + | |||
| + | ""Lee, HueyTyng; Golicz, Agnieszka A; Bayer, Philipp; Jiao, Yuannian; Tang, Haibao; Paterson, Andrew H; Sablok, Gaurav; Krishnaraj, Rahul R; Chan, Chon-Kit Kenneth; Batley, Jacqueline; "",The genome of a southern hemisphere seagrass species (Zostera muelleri),Plant Physiology,,,pp. 00868.2016,2016,American Society of Plant Biologists | ||
| + | |||
| + | ""Barash, Mark; Bayer, Philipp E; van Daal, Angela; "",Candidate gene scan for Single Nucleotide Polymorphisms involved in the determination of normal variability in human craniofacial morphology,bioRxiv,,,060814,2016,Cold Spring Harbor Labs Journals | ||
| + | |||
| + | ""Hane, James K; Ming, Yao; Kamphuis, Lars G; Nelson, Matthew N; Garg, Gagan; Atkins, Craig A; Bayer, Philipp E; Bravo, Armando; Bringans, Scott; Cannon, Steven; "",""A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant–microbe interactions and legume evolution"",Plant Biotechnology Journal,,,,2016, | ||
| + | |||
| + | ""Golicz, Agnieszka A; Bayer, Philipp E; Barker, Guy C; Edger, Patrick P; Kim, HyeRan; Martinez, Paula A; Chan, Chon Kit Kenneth; Severn-Ellis, Anita; McCombie, W Richard; Parkin, Isobel AP; "",The pangenome of an agronomically important crop plant Brassica oleracea,Nature Communications,7,,,2016,Nature Publishing Group | ||
| + | |||
| + | ""Gacek, Katarzyna; Bayer, Philipp; Bartkowiak-Broda, Iwona; Szala, Laurencja; Bocianowski, Jan; Edwards, David; Batley, Jacqueline; "",Genome-wide association study of genetic control of seed fatty acid biosynthesis in Brassica napus,Frontiers in Plant Science,7,,2062,2016,Frontiers | ||
| + | " | ||
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email: philipp.bayer@uwa.edu.au | email: philipp.bayer@uwa.edu.au | ||
| + | |||
| + | Twitter: @philippbayer | ||
| + | |||
| + | Homepage: philipp-bayer.net | ||
| + | |||
| + | GitHub: https://github.com/philippbayer/ | ||
Revision as of 15:36, 15 January 2017
Research interests
Graph databases & knowledge networks, genotyping by sequencing, BioNano optical mapping, genome assembly assessment, genome assembly improvement
I started to focus on bioinformatics during my BSc Biology in Germany, where I worked on the evolution of HIV/SIV and heat shock resistance in sea-grasses (Zostera marina and Posidonia oceanica). I then came to Australia to work on my IT skills, which culminated in a Master IT with a short stint doing SQL consulting for a web design company. At the same time I co-founded and worked on openSNP.org, an open repository for human genotyping datasets from customers of direct-to-consumer genotyping companies like 23andMe. I did my PhD at the University of Queensland in the Edwards group developing a novel low-coverage genotyping by sequencing pipeline, and used the pipeline to assess genome assembly quality in Brassica napus and Cicer arietinum. I now work as a post-doc in the same group focusing on knowledge networks, the assembly, annotation and analysis of pan-genomes of several crop species (currently mostly legumes and Brassicas), genome-wide association studies, population genetics, and more. I am also involved in organising and teaching the Bioinformatics courses for Masters students and am an active poster on biostars.org
Academic history
"Bayer, Philipp E; Ruperao, Pradeep; Mason, Annaliese S; Stiller, Jiri; Chan, Chon-Kit Kenneth; Hayashi, Satomi; Long, Yan; Meng, Jinling; Sutton, Tim; Visendi, Paul; "",High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus,Theoretical and Applied Genetics,128,6,1039-1047,2015,Springer Berlin Heidelberg
""Bayer, Philipp Emanuel; "",""Skim-Based Genotyping by Sequencing Using a Double Haploid Population to Call SNPs, Infer Gene Conversions, and Improve Genome Assemblies"",Plant Bioinformatics: Methods and Protocols,,,285-292,2016,Springer New York
""Mason, Annaliese S; Rousseau-Gueutin, Mathieu; Morice, Jérôme; Bayer, Philipp E; Besharat, Naghmeh; Cousin, Anouska; Pradhan, Aneeta; Parkin, Isobel AP; Chèvre, Anne-Marie; Batley, Jacqueline; "",Centromere locations in brassica A and C genomes revealed through half-tetrad analysis,Genetics,202,2,513-523,2016,Genetics
""Visendi, Paul; Berkman, Paul J; Hayashi, Satomi; Golicz, Agnieszka A; Bayer, Philipp E; Ruperao, Pradeep; Hurgobin, Bhavna; Montenegro, Juan; Chan, Chon-Kit Kenneth; Staňková, Helena; "",An efficient approach to BAC based assembly of complex genomes,Plant methods,12,1,1,2016,BioMed Central
""Bayer, Philipp Emanuel; "",Genomics of Salinity,Plant Genomics and Climate Change,,,179-194,2016,Springer New York
""Lee, HueyTyng; Golicz, Agnieszka A; Bayer, Philipp; Jiao, Yuannian; Tang, Haibao; Paterson, Andrew H; Sablok, Gaurav; Krishnaraj, Rahul R; Chan, Chon-Kit Kenneth; Batley, Jacqueline; "",The genome of a southern hemisphere seagrass species (Zostera muelleri),Plant Physiology,,,pp. 00868.2016,2016,American Society of Plant Biologists
""Barash, Mark; Bayer, Philipp E; van Daal, Angela; "",Candidate gene scan for Single Nucleotide Polymorphisms involved in the determination of normal variability in human craniofacial morphology,bioRxiv,,,060814,2016,Cold Spring Harbor Labs Journals
""Hane, James K; Ming, Yao; Kamphuis, Lars G; Nelson, Matthew N; Garg, Gagan; Atkins, Craig A; Bayer, Philipp E; Bravo, Armando; Bringans, Scott; Cannon, Steven; "",""A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant–microbe interactions and legume evolution"",Plant Biotechnology Journal,,,,2016,
""Golicz, Agnieszka A; Bayer, Philipp E; Barker, Guy C; Edger, Patrick P; Kim, HyeRan; Martinez, Paula A; Chan, Chon Kit Kenneth; Severn-Ellis, Anita; McCombie, W Richard; Parkin, Isobel AP; "",The pangenome of an agronomically important crop plant Brassica oleracea,Nature Communications,7,,,2016,Nature Publishing Group
""Gacek, Katarzyna; Bayer, Philipp; Bartkowiak-Broda, Iwona; Szala, Laurencja; Bocianowski, Jan; Edwards, David; Batley, Jacqueline; "",Genome-wide association study of genetic control of seed fatty acid biosynthesis in Brassica napus,Frontiers in Plant Science,7,,2062,2016,Frontiers "
Contact
University of Western Australia
Crawley, Australia
Tel: +61 (0)8 6488 4311
email: philipp.bayer@uwa.edu.au
Twitter: @philippbayer
Homepage: philipp-bayer.net
GitHub: https://github.com/philippbayer/
