CURRICULUM VITAE

	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

1. Major transitions in living(-eco) systems evolution
2. Multiscale dynamics in living(-eco) systems
3. Meta-reflective (effect, structure, function) in living(-eco) systems dynamics

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)

1. .zshrc (Updated: 30 June. 2013)
2. .vimrc (Updated: 30 June. 2013)
3. .screenrc (Updated: 22 July. 2013)

1. Hiromi Matsumae, Utsugi Jinbo, Takeru Nakazato, Masaomi Hatakeyama, Takeshi Obayashi, Bioinformatics linking to biodiversity and cultural research, JSBi Bioinformatics Review, 3(2), 88-114, 2022 https://doi.org/10.11234/jsbibr.2022.primer3
2. Kakui H, Tsuchimatsu T, Yamazaki M, Hatakeyama M and Shimizu KK, Pollen Number and Ribosome Gene Expression Altered in a Genome-Editing Mutant of REDUCED POLLEN NUMBER1 Gene. Front. Plant Sci. 12:768584, 2022. https://doi.org/10.3389/fpls.2021.768584
3. Rajashekarreddy Bellam, Prashanth Thankachan, Masaomi Hatakeyama, Netravati Hiremath, Diego Moretti, Nanja Reddy Yellodu, Mathi Thumilan, Ravikumar Ramapura, Shamprasad Phadnis, Beena Bose, Lucy Poveda, Geetha Kalaiah, Michael Zimmermann, Kentaro K. Shimizu, Ralph Schlapbach, Anura Kurpad and Sheshshayee Sreeman Frontiers in Nutrition, A natural low phytic acid finger millet accession significantly improves iron bioavailability in Indian women, Frontiers in Nutrition, 8: 791392, 2021. https://doi.org/10.3389/fnut.2021.791392
4. The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests Kevin Kit Siong Ng, Masaki J. Kobayashi, Jeffrey A. Fawcett, Masaomi Hatakeyama, Timothy Paape, Chin Hong Ng, Choon Cheng Ang, Lee Hong Tnah, Chai Ting Lee, Tomoaki Nishiyama, Jun Sese, Michael J. O'Brien, Dario Copetti, Mohd Noor Mat Isa, Robert Cyril Ong, Mahardika Putra, Iskandar Z. Siregar, Sapto Indrioko, Yoshiko Kosugi, Ayako Izuno, Yuji Isagi, Soon Leong Lee, Kentaro K. Shimizu, Communications Biology, Vol. 4 (1166), 2021. https://doi.org/10.1038/s42003-021-02682-1
5. Gwyneth Halstead-Nussloch1, Tsuyoshi Tanaka, Dario Copetti, Timothy Paape, Fuminori Kobayashi, Masaomi Hatakeyama, Hiroyuki Kanamori, Jianzhong Wu, Martin Mascher, Kanako Kawaura, Kentaro K. Shimizu, and Hirokazu Handa, Multiple Wheat Genomes Reveal Novel Gli-2 Sublocus Location and Variation of Celiac Disease Epitopes in Duplicated alpha-Gliadin Genes, Frontiers in Plant Science, Vol. 12 (715985), 2021. https://doi.org/10.3389/fpls.2021.715985
6. Kentaro K Shimizu, Dario Copetti, Moeko Okada, Thomas Wicker, Toshiaki Tameshige, Masaomi Hatakeyama, et al., De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium Resistance Genes in East Asian Genotypes, Plant Cell Physiol, pcaa152, 2020
7. Sean Walkowiak, Liangliang Gao, ..., Masaomi Hatakeya, ..., et al., Multiple wheat genomes reveal global variation in modern breeding, Nature, 588, pages277-283, 2020
8. Reiko Akiyama, Jianqiang Sun, Masaomi Hatakeyama, Heidi E. L. Lischer, Roman V. Briskine, Angela Hay, Xiangchao Gan, Miltos Tsiantis, Hiroshi Kudoh, Masahiro M. Kanaoka, Jun Sese, Kentaro K. Shimizu, Rie Shimizu-Inatsugi, Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species, New Physiologist, 2020
9. Joel L. Pick, Masaomi Hatakeyama, Kate E. Ihle, Julien Gasparini, Claudy Haussy, Satoshi Ishishita, Yoichi Matsuda, Takashi Yoshimura, Masahiro M. Kanaoka, Rie Shimizu-Inatsugi, Kentaro K. Shimizu, Barbara Tschirren, Artificial selection reveals the role of transcriptional constraints in the maintenance of life history variation, Evolution Letters, 2020
10. Goro Hanya, Janko Tackmann, Akiko Sawada, Wanyi Lee, Sanjeeta Sharma Pokharel, Valdevino Gisele de Castro Maciel, Akito Toge, Kota Kuroki, Ryoma Otsuka, Ryoma Mabuchi, Jie Liu, Masaomi Hatakeyama, Eri Yamasaki, Christian von Mering, Rie Shimizu-Inatsugi, Takashi Hayakawa, Kentaro K. Shimizu, Kazunari Ushida, Fermentation Ability of Gut Microbiota of Wild Japanese Macaques in the Highland and Lowland Yakushima: In Vitro Fermentation Assay and Genetic Analyses, Microbial Ecology, 2020.
11. Michiaki Tsujimoto, Kiwako S Araki, Mie N Honjo, Masaki Yasugi, Atsushi J Nagano, Satoru Akama, Masaomi Hatakeyama, Rie Shimizu-Inatsugi, Jun Sese, Kentaro K Shimizu, Genet assignment and population structure analysis in a clonal forest-floor herb, Cardamine leucantha, using RAD-seq, AoB PLANTS, plz080, 2019
12. Ayako Izuno, Thomas Wicker, Masaomi Hatakeyama, Dario Copetti and Kentaro K. Shimizu, Updated Genome Assembly and Annotation for Metrosideros polymorpha, an Emerging Model Tree Species of Ecological Divergence, G3: GENES, GENOMES, GENETICS November 1, vol. 9 no. 11 3513-3520
13. Tony CY Kuo, Masaomi Hatakeyama, Toshiaki Tameshige, Kentaro K Shimizu, Jun Sese, Homeolog expression quantification methods for allopolyploids, Briefings in Bioinformatics, bby121, 2018,
14. Timothy Paape, Roman V. Briskine, Gwyneth Halstead-Nussloch, Heidi E. L. Lischer, Rie Shimizu-Inatsugi, Masaomi Hatakeyama, Kenta Tanaka, Tomoaki Nishiyama, Renat Sabirov, Jun Sese, Kentaro K. Shimizu, Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica, Nature Communication, Vol.9 (3909), 2018,
15. 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,
16. 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,
17. 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,
18. 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,
19. 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
20. 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
21. 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)
22. 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.
23. 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.
24. 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.
25. 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.
26. 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.
27. Masaomi Hatakeyama, The emergence of new properties in the life system -Attending the 32th annual meeting- (Japanese), VIVA Origino, 2007.
28. Masaomi Hatakeyama, Roland Faller, Coarse Grained Simulation of ABA Triblock Copolymers in Thin Films, Physical Chemistory Chemical Physics, 9 (33), pp.4662-4672, 2007

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

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

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