Name:

MINAKA Nobuhiro, Ph.D.


Affiliation:

  1. Leader: Statistical Modeling Unit, Institute for Agro-Environmental Sciences, NARO, Tsukuba
  2. Professor: Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo
  3. Adjunct Professor: Department of Agricultural Science, Tokyo University of Agriculture, Atsugi

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:

  • 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.
  • Computational phylogenetics: Developing algorithms and softwares for computing phylogenetic trees from large datasets (> 20,000 OTUs)
  • 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.
  • 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://leeswijzer.org/ [in Japanese]


Publications

Refereed Papers

  1. 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) html | pdf
  2. 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) abstract | pdf
  3. 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)abstract | pdf
  4. 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)
  5. 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) abstract
  6. Fujiwara, S., M. Kawachi, N. Minaka, I. Inouye and M. Tsuzuki: Molecular phylogeny of the Prymnesiophyta based on the rbcL gene and sequence variation in the spacer region of the RuBisCO operon. Journal of Phycology, 37: 121-129. (2001.5)
  7. Kanematsu, S., N. Minaka, T. Kobauashi, A. Kudo and Y. Ohtsu:Molecular Phylogenetic Analysis on Ribosomal DNA Internal Transcribed Spacer Regions and Comparison of Fertility in Phomopsis Isolates from Fruit Trees. Journal of General Plant Pathology 66(3): 191-201 (2000.8)
  8. Morinaka, S., N. Minaka, M. Sekiguchi, E. Erniwati, S.N. Prijono, I.K. Ginarsa and T. Hidaka: Molecular phylogeny of birdwing butterflies of the tribe Troidini (Lepidoptera: Papilionidae) - using all species of the genus Ornithoptera. Biogeography, 2: 103-111. [2000.10]
  9. Reyment, R.A. and N. Minaka:A note on reiterated phenotypes in species of Neogastroplites (Ammonoidea, Cenomanian, Cretaceous). Cretaceous Research, 21: 173-175. (2000.7)
  10. Sameshima, S., E. Hasegawa, O. Kitade, N. Minaka and T. Matsumoto:Phylogenetic comparison of endosymbionts with their host ants based on molecular evidence. Zoological Science, 16: 993-1000. (1999.12)
  11. Fujita, N., A. Kubo, P.B. Francisco, M. Nakakita, K. Harada, N. Minaka and Y. Nakamura:Purification, characterization and cDNA structure of isoamylase from developing endosperm of rice. Planta, 208: 283-293.(1999.4)
  12. Masuchi, Y., A. Sugai, N. Minaka, Y.H. Itoh, T. Itoh, I. Karube:Isoprenoid synthesis gene for geranylgeranyl diphosphate synthase from a hyperthermophile, Pyrococcus sp. strain OT3. Journal of Marine Biotechnology, 6(4): 201-205 (1998.10)
  13. Shimamoto, I., P. Vazquez, S. Sonoda, N. Minaka and M. Nishiguchi: Nucleotide sequence analysis of the 3' terminal region of a wasabi strain of tomato mosaic vieus (TMV-W) genomic RNA: subgrouping of crucifer tobamoviruses. Archive of Virology, 143: 1801-1813 (1998.10)
  14. Toriyama, S., T. Kimishima, M. Takahashi, T. Shimizu, N. Minaka and K. Akutsu:The complete nucleotide sequence of the rice grassy stunt virus genome and genomic comparisons with viruses of the genus Tenuivirus. Journal of General Virology, 79: 2051-2058 (1998.8)
  15. Minaka, N.:Classification and phylogeny: cognitive taxonomy and inferential phylogenetics. Actinomycetologica, 10(2): S1-S2 (1996.12)
  16. Chikuni, K., N. Minaka and H. Ikenaga. 1996. Molecular phylogeny of the Passeriformes, based on the cytochrome b sequences. Journal of Yamashina Institute for Ornithology, 28(1): 1-8 (1996.3)
  17. Hanazawa, M., H. Narushima and N. Minaka: Generating most parsimonious reconstructions on a tree: a generalization of the Farris-Swofford-Maddison method. Discrete Applied Mathematics, 56:245-265 (1995.3) html | pdf
  18. Fujiwara, S., M. Sawada, J. Someya, N. Minaka, M. Kawachi and I. Inouye:Molecular phylogenetic analysis of rbcL in the Prymnesiophyta. Journal of Phycology, 30: 863-871. (1994.12)
  19. Minaka, N.:Algebraic properties of the most parsimonious reconstructions of the hypothetical ancestors on a given tree. Forma, 8(2):277-296. (1993.12) abstract
  20. Minaka, N.: Cladistics and biogeographic methods: cladograms, components, and parsimony. Bulletin of the Biogeographical Society of Japan, 48(2), 1-27. (1993.12) [In Japanese with English abstract]
  21. Minaka, N.: Vicariance in historical biogeography : Analytical problems in reconstructing area cladograms. Acta Phytotaxonomica et Geobotanica, 44(2):151-184 (1993.12) [In Japanese with English abstract] pdf
  22. Minaka, N.: Parsimony, phylogeny and discrete mathematics: Combinatorial problems in phylogenetic systematics. Journal of the Natural History Museum and Institute,Chiba, 2(2): 83-98. (1993.3) [In Japanese with English summary]
  23. Fujiwara, S., H. Iwahashi, J. Someya, S. Nishikawa and N. Minaka:Structure and cotranscription of the plastid-encoded rbcL and rbcS genes of the marine haptophyte, Pleurochrysis carterae. Journal of Phycology, 29: 347-355.(1993.6)
  24. Minaka, N. : Cladograms and reticulated structures: a proposal for graphic representation of cladistic structures. Bulletin of the Biogeographical Society of Japan, 45:1-10. (1990.12)
  25. Minaka, N. : Order and causality: logical and biological implications of cladistic strtuctures. Bulletin of the Biogeographical Society of Japan, 43:79-85. (1988.12)
  26. Minaka, N.: Branching diagrams in cladistics:their definitions and implications for biogeographic analyses. Bulletin of the Biogeographical Society of Japan, 42:65-78. (1987.12)

Book Chapters

  1. Nobuhiro Minaka: Chain, tree, and network – The development of phylogenetic systematics in the context of genealogical visualization and information graphics. Pp. 410-430 in: David M. Williams, Michael Schmitt, and Quentin D. Wheeler (eds.), The Future of Phylogenetic Systematics – The Legacy of Willi Hennig. Cambridge University Press, Cambridge (2016)
  2. Nobuhiro Minaka: Tree and network in systematics, philology, and linguistics – Structural model selection in phylogeny reconstruction. In: Ritsuko Kikusawa and Lawrence A. Reid (eds.), Let’s Talk about Trees: Tackling Problems in Representing Phylogenetic Relationships among Languages. Senri Ethnological Studies. National Museum of Ethnology, Ōsaka. [in press] (2016)

Abstracts

  1. 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)
  2. 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)
  3. 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)
  4. 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)
  5. Minaka, N.: The roots of cultural phyogenetics and the universal tree-thinking. Oral presentation. Workshop: Phylogenetic methods and thinking in cultural evolutionary studies. 12th Annual Meeting of the Society for Evolutionary Studies Japan, Tokyo, Abstracts, p. 87.(2010.8)
  6. Nobuhiro Minaka, Takashi Suemura, and Kouki Machii:Phylogenetic diversity index and the Gromov transform: Statistical confidence test based on bootstrapping triplets of terminal taxa. Oral presentation at Hennig XXIX, Honolulu, Hawaii, USA. Abstract, p. 15. (2010.5)
  7. 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)
  8. Noriyoshi Nanbo and Nobuhiro Minaka: Automatic shape identification and discrimination with examples of morphological characters of pest insects. Abstracts of the First International Symposium on Biological Shape Analysis, 3-5 June, 2009, Tsukuba, p. 23 (2009.6)
  9. Minaka, N.: Introduction - Once again, what is a species?. Oral presentation in the symposium "Systematic Biology and the Species Problem" at ISHPSSB Off-year Workshop, Takigawa Memorial Hall, Kobe Univeristy, Kobe. Abstract, p.13. (2008.11)
  10. 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. Oral presentation at Hennig XXVII, San Javier de Tucuman, Argentina. Abstract, pp. 35-36. (2008.10)
  11. Minaka, N.: Measuring phylogenetic diversity - some statistical and computational problems. Symposium: Phylogenetic approaches to community ecology, 55th Annual Meeting of the Ecological Society of Japan, Fukuoka, Abstracts, p.133 (2008.3)
  12. 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)
  13. Minaka, N.:Historical reasoning and abductive inference in phylogenetic reconstruction. Nishinomiya-Yukawa International and Interdisciplinary Symposium 2007〈What is Life? The Next 100 Years of Yukawa's Dream〉, Kyoto. Abstract, p.3 (2007.10)
  14. Nobuhiro Minaka, Takashi Suemura, and Kunihiro Okano:How to search for novel bioresources using cladogram : Examples from molecular phylogenetic studies of mycrocystin-degradating and ethanol-producing bacteria. Poster presented at the 26th Annual Meeting of the Willi Hennig Society held at New Orleans, USA, 28 June - 2 July, 2006. Abstract, p. 13. (2007.6-7)
  15. Nobuhiro Minaka, Takashi Suemura, Kunihiro Okano, Norio Sugiura, Haruo Yamamoto, Kouki Machii : Ancestral character-state reconstruction and its applications using BALANCE, an integrated software for calculating large phylogenies under the maximum parsimony criterion. Paper presented at the 25th Annual Meeting of the Willi Hennig Society held at Oaxaca, Mexico, August 14-17, 2006. Abstract, p. 7. (2006.8)
  16. Maoka, T. and N. Minaka: The phylogeny of the tea ceremony procedure. Oral presentation at the 2004 International Conference on O-CHA (Tea) Culture and Science, 1-3 November 2004, Shizuoka. (2004.11)
  17. Minaka, N., T. Suemura, T. Asano, H. Yamamoto and K. Machii: BOGEN: An improved software for estimating larger Steiner trees in phylogenetics [abstract]. Cladistics, 20(6): 601. (2004.12)
  18. Minaka, N., T. Suemura, T. Asano, H. Yamamoto and K. Machii: BOGEN: A faster parsimony program for computing larger phylogenetic trees [abstract]. Cladistics, 20(1): 89. (2004.2)
  19. Minaka, N., H. Yamamoto, T. Asano, T. Suemura and K. Machii: BOGEN: A faster parsimony program for building larger trees in phylogenetic systematics. Paper presented at the Joint International Forum on Biodiversity Information - Building Capacity in Asia and Oceania, 4-10 October 2003, Tsukuba, Japan. Programme and Abstracts, p.63 (2003.10)
  20. Minaka, N., H. Yamamoto, T. Asano, T. Suemura and K. Machii: A more efficient heuristic algorithm for the large phylogenetic Steiner problem [abstract]. Cladistics, 19: 157.(2003.5)
  21. Minaka, N.:Quantitative comparison of parsimoniously reconstructed ancestral character-states in a cladogram [abstract]. Cladistics, 18(2): 227 (2002.10)
  22. Minaka, N.:Quantitative comparison and visualization of ancestral character-states parsimoniously reconstructed on a phylogenetic tree: A geometric morphometric method. Talk at Symposium 2: Philosophical Issues in Phylogenetic Inference (organized by Daniel Faith). ICSEB VI: Sixth International Congress of Systematic and Evolutionary Biology, Patras, Greece, 9-16 September 2002. Abstracts, p.34. (2002.9)
  23. Minaka, N.:Stepmatrix weighting in phylogenetics: Random-tree estimation and its properties. Talk at the XIXth Meeting of the Willi Hennig Society, Leiden, 28 May - 2 June 2000. Programme and Abstracts, pp.32-34. (2000.5)
  24. Maeda, M. and N. Minaka: Evolutionary and structural estimation of ligand binding domains of steroid hormone receptors. Keystone Symposium 2000: C5. Macromolecular Assemblies at Work: Application of Physics, Chemistry and Mathematics to Biology, Abstracts (2000.3)
  25. Minaka, N.:Ancestral character-state reconstructions on trees and semilattices. Oral presentation at The German-Japanese Seminar on the Methods of Reconstructing Evolutionary History of Genes (National Institute of Genetics, Mishima), Abstracts, p.17. (2000.3)
  26. Minaka, N.:Cladistics: an intellectual lineage which is constantly evolving and diverging in contemporally systematic biology. Oral presentation atthe Special Seminar on Marine Molecular Biology (Ocean Research Institute, Tokyo), Abstract. (2000.2)
  27. Minaka, N.:Stepmatrix character-state weighting in phylogeny reconstruction: a new method for estimating weights using random cladograms. Poster presentation at The International Symposium on Diversity of Fishes (National Science Museum, Tokyo), Program and Abstract, P-2 (no pagination). (2000.3)
  28. Minaka, N.: Estimating stepmatrix using randomly sampled trees. Poster presentation at the Hennig XVIII Göttingen, Abstract, p.39. (1999.9)
  29. Nakamura, Y., N. Fujita, A. Kubo, P.B. Francisco, Jr., A. Nishi, K. Yamashita, H. Satoh and N. Minaka: Structural analysis of enzymes which determine the fine structure of amylopectin in rice. International Conference on Assilate Transport and partitioning (15-20 August 1999, Newcastle), Scientific Programme and Abstracts, p.143. (1999.8)
  30. Minaka, N.: Cladistics: towards the reconstruction of phylogeny - historical approach to evolutionary biology. International Science School for High School Students (22-29 July 1999). Graduate School of Science, University of Tokyo, pp.17-34. (1999.7)
  31. Minaka, N. : Character-state reconstruction problem in there-item analysis. Paper presented in Willi Hennig Society 17th Meeting (Brazil: Sao Paulo). Program and abstracts, p.56 (1998.9)
  32. Minaka, N.:Trees and ancestors: problems of reconstructing hypothetical ancestors. Symposium: "The systematic hierarchy: discovered, imposed orinherent?" Fifth International Congress of Systematic and Evolutionary Biology (Budapest, Hungary), Abstracts: 206 (1996.8)
  33. Minaka, N.:Most parsimonious reconstructions of internal node states of a phylogenetic tree. IFCS-96: Fifth Conference of the International Federation of Classification Societies (Kobe), Abstracts, vol.2: 306-309 (1996.3)
  34. Minaka, N., H. Narushima and M. Hanazawa:Reconstructing the hypothetical character states on a given phylogenetic tree under the Wagner parsimony: A generalization. Biometric Bulletin, 11(1):10-11.(1994.2)
  35. Minaka, N., H. Narushima and M. Hanazawa:Reconstructing the hypothetical character states on a given cladogram under the Wagner parsimony: a generalization of the Swofford-Maddison method. The XV International Botanical Congress, Abstracts, p.243 (1993.8-9)
  36. Fujiwara, S., M. Sawada, N. Minaka, M. Kawachi, I. Inouye and J. Someya: Rubisco genes in the Haptophyta. International Phycology Forum, Tsukuba, Abstracts (1993.8)
  37. Fujiwara, S., M. Sawada, N. Minaka, M. Kawachi, I. Inouye and J. Someya: Rubisco genes of Prymnesiophyta. Abstracts of the International Symposium on the Biology of the Prymnesiophyta, Plymouth. p.8 (1993.3-4.)
  38. Hanazawa, M., H. Narushima and N. Minaka: A method for generating all most parsimonous reconstructions of a given tree : a problem originated in cladistics. Abstracts of the Fifth Franco-Japanese Days on Combinatorics and Optimization. [no pagination] (1992.10)
  39. Fujiwara, S., N. Minaka, H. Iwahashi, J. Someya and S. Nishikawa: Genes for the large and small subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase constitute an operon on the plastosome of the marine haptophyte Pleurocrysis carterae. Photosynthetic Research, 34:178. (1992.10.)
  40. Fujiwara, S., N. Minaka, H. Iwahashi, J. Someya and S. Nishikawa: Genes for the large and small subunits of riburose-1,5-bisphosphate carboxylase/oxygenase constitute an operon on the plastosome of the marine haptophyte Pleurochrysis carterae. The 9th Int. Congr. Photosynthesis (1992.9)
  41. Minaka, N.: Theoretical cladistics and phylogeny reconstruction : Multiple solutions under the principle of parsimony. Abstracts of the 29th International Geological Congress, Kyoto, p.346 (1992.8)
  42. Minaka, N. : Natural classification of environments: A phylogenetic approach to biogeography. Presented at the Tsukuba Center for Institutes, Tsukuba. (1991.10)

Last Modified: 4 July 2016 by MINAKA Nobuhiro