Masaomi Hatakeyama

Link to Research Group page (Prof. Dr. Kentaro K. Shimizu)

Research Interests

Bioinformatics of molecular genomics and genetics: de novo genome assembly and transcriptomics analysis, population genetics analysis of polyploid species, and software development.


Education and Professional Positions

2012 - present Postdoctoral researcher, Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland
2012 - present Informatics specialist, Functional Genomic Center Zurich, Switzerland
2011 - 2012 Postdoctoral researcher, Institute of Plant Biology, University of Zurich, Switzerland
2010 - 2012 Web application developer, ywesee GmbH, Switzerland
2008 - 2009 Visiting Researcher, Material Fundamental Research Div., Toyota Central Research and Development Laboratories, Inc., Japan
1998 - 2002 Vocational Trainer, Polytechnic Center Hyogo, Employment and Human Resources Development Organization of Japan, Japan

Selected Publications

  • Hatakeyama M., Aluri S., Balachadran MT., Sivarajan SR., Patrignani A., Grüter S., Poveda L., Shimizu-Inatsugi R., Baeten J., Francoijs K-J., Nataraja KN., Reddy YAN., Phadnis S., Ravikumar RL., Schlapbach R., Sreeman SM., Shimizu KK. (2017). Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop. DNA Research:Epub ahead of print. DOI: 10.1093/dnares/dsx036
  • Paape T., Hatakeyama M., Shimizu-Inatsugi R., Cereghetti T., Onda Y., Kenta T., Sese J., Shimizu KK. (2016). Conserved but attenuated parental gene expression in allopolyploids: constitutive zinc hyperaccumulation in the allotetraploid Arabidopsis kamchatica. Mol Biol Evol. 2016 Jul 12. pii: msw141. DOI: 10.1093/molbev/msw141
  • Hatakeyama M., Opitz L., Russo G., Qi W., Schlapbach R., Rehrauer H. (2016). SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis. BMC bioinformatics, 17(1), 228. DOI: 10.1186/s12859-016-1104-8
  • Kubo K., Paape T., Hatakeyama M., Entani T., Takara A., Kajihara K., Tsukahara M., Shimizu-Inatsugi R., Shimizu K.K., Takayama S. (2015). Gene duplication and genetic exchange drive the evolution of S-RNase-based self-incompatibility in Petunia. Nature Plants, 1:14005. DOI: 10.1038/nplants.2014.5