Philipp Bayer

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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/