Publications (KUBO Takuya)

Original articles (refereed)

(submitted)
  1. Matsuda, I., Nakabayashi, M., Otani, Y., Wai, Y., Tuuga, A., Wong, A., Kubo, T. 2018. Comparison of Plant Diversity and Phenology of Riverine and Mangrove Forests with Those of the Dryland Forest in Sabah, Borneo, Malaysia. In K. Nowak, A. Barnett, & I. Matsuda (Eds.), Primates in Flooded Habitats: Ecology and Conservation (pp. 15-28). Cambridge: Cambridge University Press.
  2. Assessment of Impulsivity in Adolescent Mice: A New Training Procedure for a 3-Choice Serial Reaction Time Task. Yu Ohmura, Takuya Kubo, Mitsuhiro Yoshioka, Takayuki Yoshida, Hitomi Sasamori. Behavioural Brain Research. (Received 10 September 2017; Received in revised form 26 December 2017; Accepted 15 January 2018) https://doi.org/10.1016/j.bbr.2018.01.014 https://doi.org/10.1016/j.bbr.2018.01.014
  3. Yoko Matsumura and Takuya Kubo. Eversion and withdrawal of an intromittent organ before sexual maturation prepares male beetles for copulation. Royal Society Open Science. (Received December 13, 2016, Accepted July 10, 2017, Published online August 9, 2017) https://doi.org/10.1098/rsos.161029 [HUSCAP repository]
  4. Kiwako S. Araki, Takuya Kubo, and Hiroshi Kudoh. 2017. Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population. (Received: January 13, 2016; Accepted: May 8, 2017; Published: May 22, 2017) https://doi.org/10.1371/journal.pone.0178145 PONE-D-16-01229R2
  5. Ohno, Yuko; Ogiyama, Yuki; Kubota, Yoshino; Kubo, Takuya; Ishii, Kojiro. 2015. Acentric chromosome ends are prone to fusion with functional chromosome ends through a homology-directed rearrangement. Nucleic Acids Research. http://dx.doi.org/10.1093/nar/gkv997 10.1093/nar/gkv997 (NAR-02297-X-2015.R1, Received: 26 January 2015/Revised: 22 September 2015/Accepted: 23 September 2015)
  6. Takao Araya, Takuya Kubo, Nicolaus von Wiren, and Hideki Takahashi. 2015. Statistical modeling of nitrogen-dependent modulation of root system architecture in Arabidopsis thaliana. Journal of Integrative Plant Biology. http://dx.doi.org/10.1111/jipb.12433 10.1111/jipb.12433 (Received: 14 July2015/Revised: 28 September 2015/Accepted: 2 November 2015)
  7. Eri Nabeshima, Takuya Kubo, Koh Yasue, Tsutom Hiura, and Ryo Funada. 2015. Long-term changes in earlywood width and radial growth of Quercus crispula under climate change. Trees 29(4): 1273-1281. http://dx.doi.org/10.1007/s00468-015-1206-3 10.1007/s00468-015-1206-3 (Received: 11 November 2014/Revised: 8 April 2015/Accepted: 9 April 2015)
  8. Yoshiko Iida, Lourens Poorter, Frank J. Sterck, Abd Rahman Kassim, Matthew D. Potts, Takuya Kubo, and Takashi Kohyama. 2014. Linking size-dependent growth and mortality with architectural traits across 145 co-occurring tropical tree species. Ecology 95(2): 353-363. http://dx.doi.org/10.1890/11-2173.1 (Received: December 3, 2011; Revised: February 27, 2013; Accepted: April 1, 2013)
  9. Iida, Y. , Poorter, L., Sterck, F., Kassim, A. R., Kubo, T., Potts, M. D. and Kohyama, T. S. 2012. Wood density explains architectural differentiation across 145 co-occurring tropical tree species. Functional Ecology 26 (1): 274-282. http://dx.doi.org/10.1111/j.1365-2435.2011.01921.x (received at 2011-06-10; accepted at 2011-09-09)
  10. Rie Miyata, Takuya Kubo, Eri Nabeshima,Takashi S. Kohyama. 2011. Common allometric response of open-grown leader shoots to tree height in co-occurring deciduous broad-leaved trees. Annals of Botany 108 (7): 1279-1286. http://dx.doi.org/10.1093/aob/mcr228 (received at 2011-05-27; accepted at 2011-07-07)
  11. Yoshiko Iida, Takashi S. Kohyama, Takuya Kubo, Abd Rahman Kassim, Lourens Poorter, Frank Sterck and Matthew D. Potts. 2011. Tree architecture and life-history strategies across 200 co-occurring tropical tree species. Functional Ecology 25 (6): 1260-1268. http://dx.doi.org/10.1111/j.1365-2435.2011.01884.x (received at 2010-08-19; accepted at 2011-05-27)
  12. Ikki Matsuda, Takuya Kubo, Augustine Tuuga, and Seigo Higashi. 2010. A Bayesian analysis of the temporal change of local density of proboscis monkeys: implications for environmental effects on a fission-fusion society. American Journal of Physical Anthropology 142: 235-245. http://dx.doi.org/10.1002/ajpa.21218 (accepted at 2009-09-25)
  13. Chiho Kamiyama, Shimpei Oikawa, Takuya Kubo, Kouki Hikosaka. 2010. Light interception in species with different functional groups coexisting in moorland plant communities. Oecologia 164(3): 591-599. http://dx.doi.org/10.1007/s00442-010-1674-5 (accepted at 2010-05-19)
  14. Satoshi Miyazaki, Takahiro Murakami, Takuya Kubo, Noriko Azuma, Seigo Higashi and Toru Miura. 2010. Ergatoid queen development in the ant Myrmecina nipponica: Modular and heterochronic regulation of caste differentiation. Proceedings of the Royal Society B 277 (1690): 1953-1961. http://dx.doi.org/10.1098/rspb.2010.0142 (errata) (accepted at 2010-02-10)
  15. Eri Nabeshima, Takuya Kubo and Tsutom Hiura. 2010. Variation in tree diameter growth in response to the weather conditions and tree size in deciduous broad-leaved trees. Forest Ecology and Management 259: 1055-1066. http://dx.doi.org/10.1016/j.foreco.2009.12.012 (accepted at 2009-12-15)
  16. Mori Y, Nagamitsu T, Kubo T. 2009. Clonal growth and its effects on male and female reproductive success in Prunus ssiori (Rosaceae). Population Ecology 51:175-186. http://dx.doi.org/10.1007/s10144-008-0099-z
  17. Shimizu A and Kubo T. 2009. Relationship between thallus size and apothecium density in two alpine umbilicate lichens. The Lichenologist 41:285-297 http://dx.doi.org/10.1017/S0024282909007762
  18. Chunlan Lian, Susumu Goto, Takuya Kubo, Yasuo Takahashi, Masahiko Nakagawa and Taizo Hogetsu. 2008. Nuclear and chloroplast microsatellite analysis of Abies sachalinensis regeneration on fallen logs in a sub-boreal forest in Hokkaido, Japan. Molecular Ecology 17: 2948-2962. http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-294X.2008.03802.x
  19. Kubo, T., Kobayashi, T., Kato, K., Nishimura, S., Uemura, S., Ono, K., Sumida, A., Hara, T. 2008. Estimating the three-dimensional structure of canopy foliage based on the light measurements in a Betula ermanii stand. Agricultural and Forest Meteorology 148: 1293-1304. Draft http://dx.doi.org/10.1016/j.agrformet.2008.03.008
  20. Kubo, T. and Kobayashi, T. 2007. Modelling of stem biomass accumulation in Pinus densiflora seedlings exposed to aqueous-phase OH radicals generating mist. Ecological Modelling 200: 467-474. Draft http://dx.doi.org/10.1016/j.ecolmodel.2006.08.014
  21. Kubo, T and Kohyama, T. 2005. Abies population dynamics simulated using a functional-structural tree model. Ecological Research 20:255-269. Draft http://www.springerlink.com/content/q080g42245753725/ (also included in Forest Ecosystems and Environments, edited by T. Kohyama)
  22. Kohyama, T., Kubo, T. and Macklin, E. 2005. Effect of temporal autocorrelation on apparent growth rate variation in forest tree census data and an alternative distribution function of tree growth rate. Ecological Research. 20: 11-15.
  23. Uraguchi, A. and Kubo, T. 2005. Responses to light in individual growth and reproduction of two Acer species and their long-term consequences. Ecological Research 20:177-187. (6th Ecological Research Award, 2006-03-26) http://www.springerlink.com/content/wuje9hu420fg6acq/
  24. Kohyama, T., Suzuki, E., Partomihardjo, T., Yamada, T., and Kubo, T. 2003. Tree species differentiation in growth, recruitment and allometry in relation to maximum height in a Bornean mixed dipterocarp forest. J. Ecol., 91:797-806.
  25. Kubo, T. 2002. Individual-based Model of Forest Dynamics. in Ecological Studies 158:167-183. ``Diversity and Interaction in a Temperate Fosret Community: Ogawa Forest Reserve of Japan'' (Nakashizuka and Matsumoto eds.) Springer-Verlag, Tokyo.
  26. Kubo, T., T. Kohyama, M.D. Potts and P.S. Ashton. 2000. Mortality rate estimation, when inter-census intervals vary. J. Trop. Ecol., 16, 753-756.
  27. Nanami, S., H. Kawaguchi and T. Kubo. 2000. Community dynamic models of two dioecious tree species. Ecological Research 15: 159-164.
  28. Kubo, T. and H. Ida. 1998. Sustainability of an isolated beech-dwarf bamboo stand: analysis of forest dynamics with individual based model. Ecol. Modelling 111: 223-235.
  29. Katori, M., Kizaki, S., Terui, Y. and Kubo, T. 1998. Forest dynamics with canopy gap expansion and stochastic Ising model. Fractals 6: 81-86.
  30. Klinkhamer, P.G.L., T. Kubo and Y. Iwasa. 1997. Herbivores and the evolution of the semelparous perennial life-history of plants. J. evol. Biol. 10: 529-550.
  31. Iwasa, Y. and T. Kubo. 1997. Optimal size of storage for recovery after unpredictable disturbances. Evol. Ecol. 11: 41-65.
  32. Kubo, T., Y. Iwasa, and N. Furumoto. 1996. Forest spatial dynamics with gap expansion: total gap area and gap size distribution. J. theor. Biol. 180: 229-246.
  33. Kubo, T. and Y. Iwasa, 1996. Phenological pattern of tree regeneration in a model for forest species diversity. Theor. Pop. Biol. 49:90-117.
  34. van Dam, N., T.J. de Jong, Y. Iwasa and T. Kubo, 1996. Optimal distribution of pyrrolizidine alkaloids in rosette plants of Cynoglossum officinale L.: are plants smart investors? Funct. Ecol. 10: 128-136.
  35. Kubo, T and Y. Iwasa, 1995. Inferring the rates of branching and extinction from molecular phylogenies. Evolution 49: 694-704.

解説記事   (一部の原稿ファイルは各「サポートペイジ」や北大図書館 HUSCAP site でも入手できます)

  1. 久保拓弥. 2018. 階層モデルで「個性」をとらえる. ベイズモデリングの世界 23-35 (伊庭幸人 編集) 刊行日 2018-01-17. 岩波書店.
  2. 久保拓弥. 2016.「特集 生態学における統計モデリング」について. 統計数理 64 (1): 1-2
  3. 中川震一・久保拓弥．2016. 生態学・進化生物学のメタ解析のための統計モデル. 統計数理 64 (1): 123-137
  4. 久保拓弥. 2015. 階層ベイズ 最初の一歩 --- JAGS を使って. Iwanami Data Science 1: 19-38 (2015 年 10 月; 査読) ISBN 978-4-00-029851-3 C3340. 岩波書店. (サポートペイジ)
  5. 久保拓弥. 2010. 私の研究:「ゆーい差」なヒトたち． 北大図書館 HUSCAP レター 17: 1-2 (PDF ファイル; HTML ファイル)
  6. 久保拓弥. 2009. 「アリのケンカ」の統計モデリング. 蟻 32: 47-66 (2009 年 12 月)
  7. 久保拓弥. 2009. 最近のベイズ理論の進展と応用 [I] 階層ベイズモデルの基礎. 電子情報通信学会誌 92 (10): 881-885 (2009 年 10 月) (サポートペイジ)
  8. 久保拓弥. 2009. 簡単な例題で理解する空間統計モデル (特集: 始めよう! ベイズ推定によるデータ解析). 日本生態学会誌 59 (2): 187-196 (2009 年 7 月号; 査読) (サポートペイジ)
  9. 久保拓弥, 竹中明夫, 粕谷英一. 2008. R で改善する生態学のデータ解析. 日本生態学会誌 58: 219-224 (2008 年 11 月号) (サポートペイジ)
  10. 久保拓弥. 2007. 階層モデルで「個性」をとらえる. 数学セミナー 46 (11): 16-22 (2007 年 11 月号, 通巻 554) (サポートペイジ)
  11. 久保拓弥, 粕谷英一. 2006. 「個体差」の統計モデリング. 日本生態学会誌 56: 181-190 (2006 年 8 月号) (サポートペイジ)
  12. 久保拓弥 2003. 樹木・森林生態学「よく出る」誤用統計学の基本わざ． 生物科学 54: 188-192 (2003 年 3 月号)． (原稿)
  13. 久保拓弥 2001. 長期観測データを解明する森林シミュレイター． 科学 71: 86-91 (2001 年 1 月号)． (HTML 版; PDF 版 in HUSCAP)
  14. 久保拓弥 1996.ギャップダイナミックスの格子モデル (特集: 森林系研究の展望：シュートからグローバルチェンジまで). 日本生態学会誌 46:53-56.
  15. 久保拓弥・巌佐庸・原田祐子. 1994. 植物集団の栄枯盛衰を格子モデルで調べる． 遺伝 48:26-31.

書籍

  1. 久保拓弥 (翻訳: 李鍾賛). 2017. R 활용 통계모델링 입문 (R 活用統計モデリング入門). ISBN 9791130302560. 303 ペイジ． 박영사 (バクヨウンサ) 出版社． 2017 年 9 月 15 日．
  2. 久保拓弥. 2012. データ解析のための統計モデリング入門: 一般化線形モデル・階層ベイズモデル・MCMC (シリーズ 確率と情報の科学，編集: 甘利俊一，麻生英樹，伊庭幸人). 岩波書店. 272 ペイジ． 978-4-000069731 (9784000069731). 2012 年 5 月 18 日. (サポートペイジ)
  3. Paul Murrell. 2009. Rグラフィックス - Rで思いどおりのグラフを作図するために - (翻訳: 久保拓弥). 共立出版. 344 ペイジ. ISBN 978-4-320-01905-8 (9784320019058). 2009 年 10 月 25 日. (サポートペイジ)
  4. 久保拓弥 1997. 森林動態の格子モデル．『数理生態学』（分担執筆）． 共立出版．

Oral Presentation

  1. Kubo, T. 2007-10-25. Modeling forest stands: PipeTree simulator and Gibbs canopy model. Phenotypic plasticity in response to environmental changes: Scaling from the molecular to ecosystem levels. Nikko Sougou Kaikan, Tochigi, Japan. (files)
  2. Kubo, T. and T. Kohyama. 2001-09-29. Population-level processes of overcrowded subalpine fir stands, reconstructed from a shoot-based simulator of tree architecture. Third International Workshop on Functional-Structural Tree and Stand Models. Quebec, Canada.
  3. その他の 日本語による講演など (PDF file)