Philipp Bayer
From Applied Bioinformatics Group
Research interests
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 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. I'm also a certified and active Software and Data Carpentry instructor and have set up as well as taught at several workshops.
Academic history
| Authors | Title | Publication | Volume | Number | Pages | Year | Publisher |
|---|---|---|---|---|---|---|---|
| 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 | |
| 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 | ||||
| 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 | |
| Yuan, Yuxuan; Bayer, Philipp E; Batley, Jacqueline; Edwards, David; | Improvements in genomic technologies: application to crop genomics | Trends in Biotechnology | 2017 | Elsevier Current Trends | |||
| 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 | ||||
| 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 |
| 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 |
| 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 | ||
| 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 | 2 | 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 | 60814 | 2016 | Cold Spring Harbor Labs Journals | ||
| 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 | |
| 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 | ||
| 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 | |||||
| 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 | |
| Golicz, Agnieszka A; Bayer, Philipp E; Edwards, David; | Skim-based genotyping by sequencing | Plant Genotyping: Methods and Protocols | 257-270 | 2015 | Springer New York | ||
| 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 |
| Greshake, Bastian; Bayer, Philipp; Rausch, Helge; Reda, Julia; | openSNP–personal genomics and the public domain | F1000Research | 4 | 2015 | |||
| 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 |
| 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 |
| 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 |
| 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 | ||
| 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 | |||
| 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 |
Contact
University of Western Australia
Crawley, Australia
Tel: +61 (0)8 6488 4311
email: philipp.bayer@uwa.edu.au
Twitter: @PhilippBayer
Homepage: http://philipp-bayer.net
GitHub: https://github.com/philippbayer/
