Daiki Kumakura

© 2022 Daiki Kumakura.
Design by Utsusemi.

Peer reviewed papers

2020

  • [1] Tanaka M, Kumakura D , Mino S, Doi H, Ogura Y, Hayashi T, et al. Genomic characterization of closely related species in the Rumoiensis clade infers ecogenomic signatures to non-marine environments. Environ Microbiol. 2020 Aug;22(8):3205–17.

2021

  • [2] Kumakura D , Nakaoka S. Exploring Similarity Between Embedding Dimension of Time-Series Data and Flows of an Ecological Population Model. In: Methods of Mathematical Oncology. 2021. Springer Singapore, 69–80.

2022

  • [3] Komatsu Y, Kumakura D , Seto N, Izumi H, Takeda Y, Ohnishi Y, et al. Dynamic Associations of Milk Components With the Infant Gut Microbiome and Fecal Metabolites in a Mother–Infant Model by Microbiome, NMR Metabolomic, and Time-Series Clustering Analyses. Frontiers in Nutrition. 2022;8: 1192.

  • [4] Suzuki K, Abe MS, Kumakura D, Nakaoka S, Fujiwara F, Miyamoto H, Nakaguma T, Okada M, Sakurai K, Shimizu S, Iwata H, Masuya H, Nihei N, Ichihashi Y. 2022. Chemical-Mediated Microbial Interactions Can Reduce the Effectiveness of Time-Series-Based Inference of Ecological Interaction Networks. International journal of environmental research and public health 19:1228.

Conference, Symposium & Seminar

2020

  • [1] Daiki Kumakura, Ryo Yamaguchi, Shinji Nakaoka. Verification of inference of causality method using relative abundance in the Lotka-Volterra equation. JSMB 2020, Japan. September 2020 (oral, japanese)

  • [2] Daiki Kumakura, Ryo Yamaguchi, Shinji Nakaoka. Reconstruction of a vector field using a time-series causal approach. Applied Mathematics Joint Research Conference, Japan. December 2020 (oral, japanese)

2021

  • [3] Shinji Nakaoka, Daiki Kumakura. Application of mathematical science methods for community function analysis and design of soil microbial ecosystems. Soil Microbe × Nutrient Cycling Workshop, Japan. January 2021 (invited, oral, japanese)

  • [4] Daiki Kumakura. Prediction and availability of ecosystem phenomena at the macro level by optimality of embedding dimension. Soil Microbe × Nutrient Cycling Workshop, Japan. January 2021 (poster, japanese)

  • [5] Daiki Kumakura, Ryo Yamaguchi, Shinji Nakaoka. Compositional data applicability of causal estimation methods using CCM. ESJ 68, Japan. March 2021 (oral, japanese)

  • [6] Daiki Kumakura, Ryo Yamaguchi, Shinji Nakaoka. Analysis and validation of microbial growth dynamics with the environment suitability. WAKATE COLOSSEUM FOR BACTERIOLOGY 15th, Japan. August 2021 (oral, japanese)

  • [7] Daiki Kumakura, Ryo Yamaguchi, Shinji Nakaoka. Analysis and validation of microbial growth dynamics with the environment suitability. WAKATE COLOSSEUM FOR BACTERIOLOGY 15th, Japan. August 2021 (poster, japanese)

  • [8] Daiki Kumakura, Ryo Yamaguchi, Shinji Nakaoka. Analysis and validation of microbial growth dynamics with the environment suitability. JSMB 2021, Japan. September 2021 (oral, japanese)

  • [9] Daiki Kumakura, Junya Sunagawa, Takuya Shiramata, Shinji Nakaoka, Masaki Kamakura. Multi-omics analysis of honey bees for searching diseases. JSME2021, Japan. November 2021 (poster, japanese)

  • [10] Junya Sunagawa, Daiki Kumakura, Takuya Shiramata, Shinji Nakaoka, Masaki Kamakura. Virome analysis to explore virus ubiquity in honeybees. JSME2021, Japan. November 2021 (poster, japanese)

  • [11] Daiki Kumakura. Microbial dark matter estimation on time series causality method. NetworkScienceResearch2021, Japan. December 2021 (invited, oral, japanese)

  • [12] Daiki Kumakura. Bacterial growth with subpopulation. Mathematical analysis research for life science workshop 1st, Japan. December 2021 (oral, japanese)

2022

  • [13] Daiki Kumakura, Ryo Yamaguchi, Shinji Nakaoka. Growth dynamics of microbes in consideration of environmental suitability. ESJ 69, Japan. March 2022 (oral, japanese)

  • [14] Daiki Kumakura, Ryo Yamaguchi, Akane Hara, Shinji Nakaoka. Theoretical analysis of microbial dynamics considering functional labor. The 95th Annual Meeting of Japanese Society for Bacteriology, Japan. March 2022 (invited, oral, japanese)

  • [15] Daiki Kumakura. The relationship between host and virus in the natural environments. EVE seminar, Japan. April 2022 (oral, english)

  • [16] Daiki Kumakura. Diversity of Asgardarchaota and Theoretical verification of endosymbiotic theory. iTHEMS biology seminar, Japan. April 2022 (oral, english)

  • [17] T Matsumoto, T Hayakawa, M Ueno, H Kitayama, D Kumakura, H Teramori, I Nakaoka, Y Nechijima, T Hasegawa, K Minagawa, T Yokoyama. The relationship between the behavior of Macaca fuscata and microbes in the Jigokudani-onsen. Japanese Macaque Research Seminar 2022. July 2022 (poster, japanese)

  • [18] Daiki Kumakura. Theoretical analysis of the extinction condition for the plasmid-carrying bacteria. WAKATE COLOSSEUM FOR BACTERIOLOGY 16th, Japan. August 2022 (oral, japanese)

  • [19] Daiki Kumakura. Theoretical analysis of the extinction condition for the plasmid-carrying bacteria. WAKATE COLOSSEUM FOR BACTERIOLOGY 16th, Japan. August 2022 (poster, japanese)

  • [20] Daiki Kumakura, Shinji Nakaoka. Theoretical analysis of microbial co-culture system depending on limiting substrate. JSMB2022, Japan. September 2022 (oral, japanese)

  • [21] Kyoko Kojima, Akiko Takahashi, Eiri Ono, Daiki Kumakura. How can we create a more communicative application chart? JSMB2022, Japan. September 2022 (panelist, seminar, japanese)

  • [22] Daiki Kumakura, Tetsuya J Kobayashi. Hessian Geometric Structure of Equilibrium and Nonequilibrium Chemical Reaction Newtworks. iTHEMS biology seminar, Japan. September 2022 (organizer, oral, english)

  • [23] Daiki Kumakura, Haruka Kitayama, Hiroki Teramori, Takashi Hayakawa, Takuya Matsumoto. Hotspring microbiome diversity with Macaca fuscata entering. JSME2022, Japan. October 2022 (poster, japanese)

  • [24] Hiroki Teramori, Daiki Kumakura, Haruka Kitayama, Takashi Hayakawa, Takuya Matsumoto. Studying the microbiome heterogenity between several hotspring source in the Jigokudani onsen at Nagano prefecture. JSME2022, Japan. October 2022 (poster, japanese)

  • [25] Ishara Uhanie Perera, So Fujiyoshi, Daiki Kumakura, Shinji Nakaoka, Fumito Maruyama. An approach to forecast harmful algal blooms in Chile using emprical dynamic modeling. JSME2022, Japan. October 2022 (oral, english)

  • [26] Daiki Kumakura, Kento Tominaga, Daichi Morimoto, Ryuta Wagatsuma. New Perspectives on Environmental Virology for Everyone. JSME2022, Japan. October 2022 (workshop, japanese)

Review articles and books

2020

  • [1] Shinji Nakaoka, Daiki Kumakura. The role of mathematical sciences in preserving the gut environment. Experimental Medicine. 2020 Nov;38(18):3078-84. (japanese)
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