Difference between revisions of "Philipp Bayer"

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=== Research interests ===
+
== Research interests ==
  
 
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''.  
  
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.
  
I am also involved in organising and teaching the Bioinformatics courses for Masters students and am an active poster on biostars.org
+
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.
  
=== Academic history ===
+
==Academic history==
 +
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]
  
{| class="wikitable"
+
== Contact ==
! Authors
 
! Title
 
! Publication
 
! Volume
 
! Number
 
! Pages
 
! Year
 
! Publisher
 
|-
 
| '''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
 
|
 
|
 
| 60814
 
| 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
 
|-
 
| 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 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
 
|-
 
|}
 
 
 
=== Contact ===
 
  
 
University of Western Australia
 
University of Western Australia
Line 177: Line 22:
 
email: philipp.bayer@uwa.edu.au
 
email: philipp.bayer@uwa.edu.au
  
Twitter: @philippbayer
+
Twitter: [http://twitter.com/philippbayer @PhilippBayer]
  
Homepage: philipp-bayer.net
+
Homepage: http://philipp-bayer.net
  
 
GitHub: https://github.com/philippbayer/
 
GitHub: https://github.com/philippbayer/

Latest revision as of 06:50, 6 October 2021

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 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.

Academic history

I have published more than 100 publications. For an up-to-date list of my publications, please see my Google Scholar page

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/