(Last Update: 18 Sep. 2017)


M. Hatakeyama, Ph.D.
Short Name: Masa
Date of birth: 10 Dec. 1974
Place of birth: Japan
Present address: Zurich, Switzerland
Email: 6D6173616F6D692E686174616B6579616D6140676D61696C2E636F6D
GnuPG Public Key:masa_pubkey.asc

Reseach interests
  1. Major transitions in living(-eco) systems evolution
  2. Multiscale dynamics in living(-eco) systems
  3. Self-referential (effect, structure, function) in living(-eco) systems dynamics

Documents (old)
  1. Constructive Approach (Japanese, updated: 20 May. 2012)
  2. Minimum Nomic (English, Japanese, updated: 22 Jan. 2007)
  3. Textile wiki template (pdf, 16 Aug. 2017)

Shells (old)
  1. .zshrc (Updated: 30 June. 2013)
  2. .vimrc (Updated: 30 June. 2013)
  3. .screenrc (Updated: 22 July. 2013)
Ph.D. (2008)Hash Lab., Knowledge Science, Japan Advanced Institute of Science and Technology(JAIST)
Doctoral Thesis: Constructive study of proto-cell membrane using coarse-grained molecuar model and abstract chemical reaction system model (Japanese)
M.S. (2004)Knowledge Science, Japan Advanced Institute of Science and Technology (JAIST)
B.E. (1998)Infomation Engineering, Polytechnic University

  1. Masaomi Hatakeyama, Sirisha Aluri, Mathi Thumilan Balachadran, Sajeevan Radha Sivarajan, Andrea Patrignani, Simon Grueter, Lucy Poveda, Rie Shimizu-Inatsugi, John Baeten, Kees-Jan Francoijs, Karaba N. Nataraja, Yellodu A. Nanja Reddy, Shamprasad Phadnis, Ramapura L. Ravikumar ,Ralph Schlapbach, Sheshshayee M. Sreeman and Kentaro K. Shimizu, Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop, DNA Research, dsx036, 2017,
  2. Ayako Izuno, Kanehiro Kitayama, Yusuke Onoda, Yuki Tsujii, Masaomi Hatakeyama, Atsushi J. Nagano, Mie N. Honjo, Rie Shimizu-Inatsugi, Hiroshi Kudoh, Kentaro K. Shimizu and Yuji Isagi, The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae), Molecular Ecology, 2017,
  3. Timothy Paape, Masaomi Hatakeyama, Rie Shimizu-Inatsugi, Teo Cereghetti, Yoshihiko Onda, Tanaka Kenta, Jun Sese and Kentaro K. Shimizu, Conserved but attenuated parental gene expression in allopolyploids: constitutive zinc hyperaccumulation in the allotetraploid Arabidopsis kamchatica, Molecular Biology and Evolution, 2016,
  4. Masaomi Hatakeyama, Lennart Opitz, Giancarlo Russo, Weihong Qi, Ralph Schlapbach and Hubert Rehrauer, SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis, BMC Bioinformatics, 17:228, 2016,
  5. Ayako Izuno, Masaomi Hatakeyama, Tomoaki Nishiyama, Ichiro Tamaki, Rie Shimizu-Inatsugi, Ryuta Sasaki, Kentaro K. Shimizu, Yuji Isagi, Genome sequencing of Metrosideros polymorpha (Myrtaceae), a dominant species in various habitats in the Hawaiian Islands with remarkable phenotypic variations, Journal of Plant Research, Online first, 2016, pp.1-10
  6. Ken-ichi Kubo, Timothy Paape, Masaomi Hatakeyama, Tetsuyuki Entani, Akie Takara, Kie Kajihara, Mai Tsukahara, Rie Shimizu-Inatsugi, Kentaro K. Shimizu & Seiji Takayama, Gene duplication and genetic exchange drive the evolution of S-RNase-based self-incompatibility in Petunia, Nature Plants, Vol. 1, 2015, pp.1-9
  7. Masaomi Hatakeyama, Tomoyuki Kinjo and Shi-aki Hyodo, Topological Modeling of Hydrogen Bond Network of Water Cluster and Proton Hopping in Hydrated Polyelectrolyte Membrane, Molecular Simulation, Vol. 37 (1), 2011, pp.53-61. (Japanese Abstract)
  8. Fumio Oosawa ( Editors: Takayuki Ariga, Yasunobu Igarashi, Takehiko Inaba, Keiichi Okazaki, Masako Kondou, Yuuichi Togashi, Mieko Tamura, Youichi Toriya, Rumi Negishi, Masaomi Hatakeyama ), Lecture on statistics : Prof. Fumio Oosawa (Japanese), Young Researchers Society for Biophysics, 2009.
  9. Jayeeta Ghosh, Masaomi Hatakeyama, Petra Traeskelin, Chenyue Xing and Roland Faller, Molecular Modeling in confined polymer and biomembrane systems, Songklanakarin Journal of Science Technology, 31(2), pp.167-173, 2009.
  10. Ken-ichi Ishii, Tsutomu Hamada, Masaomi Hatakeyama, Takeshi Nagasaki and Masahiro Takagi, Reversible Control of Exo- and Endo-Budding Transitions in a Photosensitive Lipid Membrane, ChemBioChem,Vol.10, pp.251-256, 2009.
  11. Masaomi Hatakeyama and Takashi Hashimoto , Minimum Nomic, a Tool for studying Rule Dynamics, Journal of Artificial Life and Robotics,Vol. 13 (2), pp. 500-503, 2009.
  12. Masaomi Hatakeyama and Takashi Hashimoto, The Diversification of Proto-Cell driven by Membrane Permselectivity, Journal of Artificial Life and Robotics,Vol. 13 (1), pp. 194-198, 2008.
  13. Masaomi Hatakeyama, The emergence of new properties in the life system -Attending the 32th annual meeting- (Japanese), VIVA Origino, 2007.
  14. Masaomi Hatakeyama, Roland Faller, Coarse Grained Simulation of ABA Triblock Copolymers in Thin Films, Physical Chemistory Chemical Physics, 9 (33), pp.4662-4672, 2007

Work Experience
Mar. 2012 to Present
Researcher (Post doctor 2012-2017, Over assistant 2017-)
Evolutionary and Ecological Genomics (Shimizu Lab.), Institute of Evolutionary Biology and Environmental Studies, University of Zurich
Mar. 2012 to Present
Bioinformatician (Administrator)
Functional Genomics Center Zurich, University of Zurich
Jan. 2011 to Mar. 2012
Researcher (Post doctor)
Evolutionary Functional Genomics (Shimizu Lab.), Institute of Plant Biology, University of Zurich
May. 2010 to Mar. 2012
Ruby Programmer
ywesee GmbH, Zurich, Switzerland
Apr. 2008 to Aug. 2009
Visiting Researcher
Computational Physics Lab., Material Fundamental Research Div.
Toyota Central Research and Development Laboratories, Inc.
Sep. 2004 toAug. 2005
Visiting Researcher
Soft-Condensed Matter Simulation Group, Dep. of Chemical Engineering and Materials Science
University of California, Davis (UCD)
Oct. 2003 to Mar. 2004
Junior College Lecturer
Teaching entry level numerical analysis with C-Language.
Polytechnic College Ishikawa, Employment and Human
Resources Development Organization of Japan.
Apr. 1998 to Mar. 2002
Vocational Trainer
Job training of information processing to unemployed persons.
Polytechnic Center Hyogo, Employment and Human
Resources Development Organization of Japan.

  1. The Best Student Award at JAIST in 2008
  2. Young Author Award at International Symposium on Artificial Life and Robotics(AROB 13th) in 2008

Favorite Words
  1. One by One
  2. Keep Going
  3. Sessatakuma

The last word
  1. Yuigon (Japanese, updated: 10 Dec. 2012)