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| − | === Research interests ===
| + | == Research interests == |
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| | Pan-genomics, Graph databases & knowledge networks, genotyping by sequencing, genome assembly assessment, genome assembly improvement | | Pan-genomics, Graph databases & knowledge networks, genotyping by sequencing, genome assembly assessment, genome assembly improvement |
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| | 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 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''. |
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| − | 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 now work as a DECRA fellow in the same group focusing on the mechanisms of gene birth and gene death via 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. |
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| − | I am also involved in organising and teaching the Bioinformatics courses for Masters students and am an active poster on biostars.org. I'm also a certified and active Software and Data Carpentry instructor and have set up as well as taught at several workshops. | + | I am also involved in organising and teaching the Bioinformatics courses SCIE4002 and SCIE5003 for Masters students at UWA (MSc Biotechnology, MSc Bioinformatics) and am an active poster on biostars.org. I'm also a certified and active Software and Data Carpentry instructor and have set up as well as taught at several workshops. |
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| | ==Academic history== | | ==Academic history== |
| − | {| class="wikitable"
| + | I have published more than 100 publications. For an up-to-date list of my publications, please see my [https://scholar.google.com/citations?user=GOL15xQAAAAJ&hl=en Google Scholar page] |
| − | ! Authors || Title || Publication || Volume || Number || Pages || Year || Publisher
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| − | | 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 || 15 || 3 || 318-330 || 2017 ||
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| − | | Kaur, Parwinder; Bayer, Philipp E; Milec, Zbyněk; Vrána, Jan; Yuan, Yuxuan; Appels, Rudi; Edwards, David; Batley, Jacqueline; Nichols, Phillip; Erskine, William; || An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance || Plant biotechnology journal || || || || 2017 ||
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| − | | Montenegro, Juan D; Golicz, Agnieszka A; Bayer, Philipp E; Hurgobin, Bhavna; Lee, HueyTyng; Chan, Chon‐Kit Kenneth; Visendi, Paul; Lai, Kaitao; Doležel, Jaroslav; Batley, Jacqueline; || The pangenome of hexaploid bread wheat || The Plant Journal || 90 || 5 || 1007-1013 || 2017 ||
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| − | | Yuan, Yuxuan; Bayer, Philipp E; Batley, Jacqueline; Edwards, David; || Improvements in genomic technologies: application to crop genomics || Trends in Biotechnology || || || || 2017 || Elsevier Current Trends
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| − | | Bayer, Philipp E; Hurgobin, Bhavna; Golicz, Agnieszka A; Chan, Chon‐Kit Kenneth; Yuan, Yuxuan; Lee, HueyTyng; Renton, Michael; Meng, Jinling; Li, Ruiyuan; Long, Yan; || Assembly and comparison of two closely related Brassica napus genomes || Plant biotechnology journal || || || || 2017 ||
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| − | | Yuan, Yuxuan; Bayer, Philipp E; Lee, Huey-Tyng; Edwards, David; || runBNG: a software package for BioNano genomic analysis on the command line || Bioinformatics || 33 || 19 || 3107-3109 || 2017 || Oxford University Press
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| − | | Yuan, Yuxuan; Bayer, Philipp E; Scheben, Armin; Chan, Chon-Kit Kenneth; Edwards, David; || BioNanoAnalyst: a visualisation tool to assess genome assembly quality using BioNano data || BMC bioinformatics || 18 || 1 || 323 || 2017 || BioMed Central
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| − | | Kaur, Parwinder; Appels, Rudi; Bayer, Philipp E; Keeble-Gagnere, Gabriel; Wang, Jiankang; Hirakawa, Hideki; Shirasawa, Kenta; Vercoe, Philip; Stefanova, Katia; Durmic, Zoey; || Climate clever clovers: New paradigm to reduce the environmental footprint of ruminants by breeding low methanogenic forages utilizing haplotype variation || Frontiers in Plant Science || 8 || || || 2017 || Frontiers Media SA
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| − | | 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
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| − | | 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
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| − | | 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 || 2 || 2016 || BioMed Central
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| − | | Bayer, Philipp Emanuel; || Genomics of Salinity || Plant Genomics and Climate Change || || || 179-194 || 2016 || Springer New York
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| − | | 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
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| − | | 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 || || || 60814 || 2016 || Cold Spring Harbor Labs Journals
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| − | | 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 || || 13390 || 2016 || Nature Publishing Group
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| − | | Gacek, Katarzyna; Bayer, Philipp E; 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 || || || 2016 || Frontiers Media SA
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| − | | Lee, HueyTyng; Golicz, Agnieszka A; Bayer, Philipp E; 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 || || || || || 2016 ||
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| − | | Lai, Kaitao; Lorenc, Michał T; Lee, Hong Ching; Berkman, Paul J; Bayer, Philipp Emanuel; Visendi, Paul; Ruperao, Pradeep; Fitzgerald, Timothy L; Zander, Manuel; Chan, Chon‐Kit Kenneth; || Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat || Plant biotechnology journal || 13 || 1 || 97-104 || 2015 ||
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| − | | Golicz, Agnieszka A; Bayer, Philipp E; Edwards, David; || Skim-based genotyping by sequencing || Plant Genotyping: Methods and Protocols || || || 257-270 || 2015 || Springer New York
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| − | | 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
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| − | | Greshake, Bastian; Bayer, Philipp; Rausch, Helge; Reda, Julia; || openSNP–personal genomics and the public domain || F1000Research || 4 || || || 2015 ||
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| − | | Greshake, Bastian; Bayer, Philipp E; Rausch, Helge; Reda, Julia; || openSNP–a crowdsourced web resource for personal genomics || PLoS One || 9 || 3 || e89204 || 2014 || Public Library of Science
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| − | | Mason, Annaliese S; Batley, Jacqueline; Bayer, Philipp Emanuel; Hayward, Alice; Cowling, Wallace A; Nelson, Matthew N; || High‐resolution molecular karyotyping uncovers pairing between ancestrally related Brassica chromosomes || New Phytologist || 202 || 3 || 964-974 || 2014 || Wiley Online Library
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| − | | Chalhoub, Boulos; Denoeud, France; Liu, Shengyi; Parkin, Isobel AP; Tang, Haibao; Wang, Xiyin; Chiquet, Julien; Belcram, Harry; Tong, Chaobo; Samans, Birgit; || Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome || Science || 345 || 6199 || 950-953 || 2014 || American Association for the Advancement of Science
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| − | | Dattolo, Emanuela; Gu, Jenny; Bayer, Philipp E; Mazzuca, Silvia; Serra, Ilia A; Spadafora, Antonia; Bernardo, Letizia; Natali, Lucia; Cavallini, Andrea; Procaccini, Gabriele; || Acclimation to different depths by the marine angiosperm Posidonia oceanica: transcriptomic and proteomic profiles || Frontiers in plant science || 4 || || || 2013 || Frontiers Media SA
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| − | | Golicz, Agnieszka A; Bayer, Philipp E; Martinez, Paula A; Lai, Kaitao; Lorenc, Michal T; Alamery, Salman; Hayward, A; Tollenaere, Reece; Batley, Jacqueline; Edwards, David; || Characterising diversity in the Brassica genomes || VI International Symposium on Brassicas and XVIII Crucifer Genetics Workshop 1005 || || || 33-47 || 2012 ||
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| − | | Alamery, Salman; Tirnaz, Soodeh; Bayer, Philipp; Tollenaere, Reece; Chalhoub, Boulos; Edwards, David; Batley, Jacqueline; || Genome wide identification and comparative analysis of NBS-LRR resistance genes in Brassica napus || || || || || ||
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| − | | + | == Contact == |
| − | === Contact ===
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| | University of Western Australia | | University of Western Australia |
Pan-genomics, Graph databases & knowledge networks, genotyping by sequencing, 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 DECRA fellow in the same group focusing on the mechanisms of gene birth and gene death via 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 SCIE4002 and SCIE5003 for Masters students at UWA (MSc Biotechnology, MSc Bioinformatics) and am an active poster on biostars.org. I'm also a certified and active Software and Data Carpentry instructor and have set up as well as taught at several workshops.
I have published more than 100 publications. For an up-to-date list of my publications, please see my Google Scholar page
