Researcher's Information - National Institute for Agro-Environmental Sciences, NIAES

April 1, 2015

Name:

Nobuhiro MINAKA

Affiliation:

Ecosystem Informatics Division

Position

Senior Researcher

Degree:

Ph.D

Education:

Bachelor of Agronomy: The University of Tokyo, 1980
Master of Agronomy: The University of Tokyo, 1982
Ph.D.(Doctor of Agronomy): The University of Tokyo, 1985

Research Activities:

1. Mathematical phylogenetics: Theoretical foundations of phylogenetic systematics from the standpoint of partial-order theory; Mathematical theory of most parsimonious reconstruction of hypothetical ancestral character states; The formal system of tree diagrams (cladogram, phylogram, and phylogenetic tree) in pattern cladistics.
2. Visualizing phylogeny and evolutionary infographics: Iconology of phylogenetic diagrams (chain, tree, and networks); Infographic representations of large phylogenetic structures in, biology, stemmatics, linguistics, and other historiographic sciences.
3. Computational phylogenetics: Developing algorithms and softwares for computing phylogenetic trees from large datasets (> 20,000 OTUs)
4. History and philosophy of systematics: Historical transformation of biological systematics among other related sciences; Sociological networks in contemporary systematics communties and their impact.

Honors and Awards:

• Society Award 1993, the Biogeographical Society of Japan
• Education and Outreach Award 2003, The Society of Evolutionary Studies, Japan

Contact:

Phone: +81-29-838-8224
Email: minaka [at] affrc.go.jp
Website: http://www.naro.affrc.go.jp/archive/niaes/minaka/

Recent Publications (2005—):

Refereed Papers

• Yuki Mitsui, Michihiko Shimomura, Kenji Komatsu, Nobukazu Namiki, Mari Shibata-Hatta, Misaki Imai, Yuichi Katayose, Yoshiyuki Mukai, Hiroyuki Kanamori, Kanako Kurita, Tsutomu Kagami, Akihito Wakatsuki, Hajime Ohyanagi, Hiroshi Ikawa, Nobuhiro Minaka, Kunihiro Nakagawa, Yu Shiwa and Takuji Sasaki: The radish genome and comprehensive gene expression profile of tuberous root formation and development. Scientific Reports, 5: 10835; doi: 10.1038/srep10835 (2015)
• Nobuhiro Minaka: Tree and network in systematics, philology, and linguistics – Structural model selection in phylogeny reconstruction. Senri Ethnological Studies, National Museum of Ethnology, Osaka. [in press] (2015)
• Hisakazu Matsumura, Hiroshi Kitajima, Shinji Akada, Jun Abe, Nobuhiro Minaka, Ryoji Takahashi: Molecular cloning and linkage mapping of cryptochrome multigene family in soybean. The Plant Genome, 2(3): 271-281 (2009.11)
• Majid OLIA, Wasim AHMAD, Masaaki ARAKI and Nobuhiro MINAKA: Molecular characterisation of some species of Mylonchulus (Nematoda: Mononchida) from Japan and comments on the status of Paramylonchulus and Pakmylonchulus. Nematology, 11(3): 337-342. （2009.5）
• Majid Olia, Wasim Ahmad, Masaaki Araki, Nobuhiro Minaka, Hirosuke Oba and Hiroaki Okada：Actus salvadoricus Baqri and Jairajpuri (Monochida: Mylonchulidae) from Japan with comment on the phylogenetic position of the genus Actus based on 18S rDNA sequences. Japanese Journal of Nematology, 38(2):57-69. (2008.12)
• Takahashi, R., H. Matsumura, S. Watanabe, K. Harada, M. Senda, S. Akada, S. Kawasaki, E. Doubouzet and N. Minaka:Molecular linkage mapping and phylogeny of chalcone synthase multigene family in soybeen. Theoretical and Applied Genetics, 110: 1203-1209. (2005.3)

Book Chapters

• Nobuhiro Minaka: Chain, tree, and network – The development of phylogenetic systematics in the context of genealogical visualization and information graphics. In: David M. Williams, Quentin D. Wheeler, and Michael Schmitt (eds.), The Future of Phylogenetic Systematics – The Legacy of Willi Hennig. Cambridge University Press, Cambridge [in press] (2015)

Abstracts

• Minaka, N.:ACCTRAN is better than DELTRAN: Basic properties of ancestral character-state reconstruction [abstract]. Hennig XXXII: The 32th Annual Meeting of the Willi Hennig Society, 3-7 August 2013, Rostock, Germany, Abstracts p. 98(2013.8)
• Minaka, N.:Tree and network in systematics, philology, and linguistics – Structural model selection in phylogeny reconstruction [abstract]. The international symposium: Linguistic Relationships – Methodological Advances in Reconstructing the Past. 9-10 February 2013, National Museum of Ethnology, Osaka. (2013.2)
• Minaka, N.:The Gromov transform of phylogenetic diversity index and its statistical confidence test [abstract]. The International Biometric Conference, 26-31 August 2012, Kobe, Japan. Abstracts for the XXVIth International Biometric Conference, 26-31 August, 2012, Kobe, Japan. International Biometric Society（2012.8）
• Minaka, N.:Historical reasoning and abductive inference in phylogenetic reconstruction [abstract]. Hennig XXX, Sao Jose do Rio Preto, Sao Paulo, Brazil. Abstracts, p. 96. (2011.7-8)
• Minaka, N., T. Suemura, and K. Machii: Measuring phylogenetic diversity on cladograms: a new index based on the Gromov transform with reference to the root. [abstract] Cladistics, 26(2): 218. (2010.4)
• Minaka, N., T. Suemura, K. Okano, N. Sugiura, H. Yamamoto, K. Machii:Ancestral character-state reconstruction and its applications using BALANCE, an integrated software for calculating large phylogenies under the maximum parsimony criterion. [Abstract]. Cladistics, 24(1): 98-99. (2008.2)