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.

2023

• [5] Kumakura D., Yamaguchi, R., Hara, A., and Nakaoka, S. (2023) Disentangling the growth curve of microbial culture. J Theor Biol 111597.

2025

• [6] Perera, I. U., Fujiyoshi, S., Kumakura, D., Medel, C., Yarimizu, K., Espinoza-González, O., Guzmán, L., Nakaoka, S., Tucca, F., Jaramillo-Torres, A., Tohsato, Y., Acuña, J. J., Jorquera, M. A., Lee, H., & Maruyama, F. (2025). Causal interactions among phytoplankton and Pseudo-nitzschia species revealed by empirical dynamic modelling. Marine Pollution Bulletin, 211(117432), 117432.

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)

2023

• [27] Daiki Kumakura. Basic of microbial ecology and applicability of your life and research. iTHEMS biology seminar, Japan. January 2023 (Organizer, Oral, English)
• [28] Daiki Kumakura. Microbial diversity with the Japanese monkey entering Jigokudani onsen hotspring. 2022 Jigokudani research meeting, Japan. March 2023 (Oral, Japanese)
• [29] Daiki Kumakura. Investigation of hot spring microbiome at Jigokudani onsen and the microbial vector of Japanese monkey's behavior. Animal behavior joint seminar March 2023 (Oral, Japanese)
• [30] Daiki Kumakura. Theoretical analysis of plasmid fixation condition under antibiotic addition. The 96th Annual Meeting of Japanese Society for Bacteriology March 2023 (Invited, Oral, Japanese)
• [31] Daiki Kumakura, Ryo Yamaguchi. Deciphering speciation processes: a mathematical modeling approach to biodiversity patterns. iTHEMS biology seminar. June 2023 (Organizer, Oral, English)
• [32] Daiki Kumakura. Quantitative analysis of antibiotic bactericidal effect and susceptibility. The 8th CIJK International Conference on Mathematical and Theoretical Biology. Korea. June 2023 (Symposium, Oral, English)
• [33] Daiki Kumakura. Proposing the best treatment for your pathogenic microorganisms. 50th Seminar on Protists, Parasites, and Evolution (PPE seminar). July 2023 (Invited, Oral, Japanese)
• [34] Kumakura D, Morita K, Nishiyama T, Kumata R. 3rd Summer School of Mathematical Biology. August 2023 (Workshop, Japanese)
• [35] Kumakura D, Morita K. Let's Talk Young! Mathematical Biology 2023. JSMB 2023, Japan. September 2023 (Workshop, Japanese)
• [36] Kumakura D. The theoretical condition of antibiotic resistance plasmid with antibiotic. 4th medical and mathematical workshop, Japan. September 2023 (Poster, Japanese)
• [37] Daiki Kumakura, Yoshitomo Kikuchi. How is host-symbiont specificity determined? ---Host’s partner-choice mechanisms and symbiont’s motility. iTHEMS biology seminar, Japan. October 2023 (Organizer, Oral, English)
• [38] Ryohei S, Daiki K, Shinji N. Supervised Machine Learning Classification of Bacterial Vaginosis and Microbial Biomarker Search. The 3rd Society for Gut Design. November 2023 (Oral, Japanese)
• [39] Daiki Kumakura. Coexistence system and invasion conditions of hot spring microbial ecosystems: a fusion of mathematics x experiment. JSME2023, Japan. November 2023 (Workshop, Oral, Japanese)
• [40] Daiki Kumakura, Takara Nishiyama. Application of mathematical models to the COVID-19 cohort study. iTHEMS biology seminar, Japan. December 2023 (Organizer, Oral, English)

2024

• [41] Daiki Kumakura. Construction of a mathematical foundation for the application of phage therapy to bacterial infections. The 1st Chowaka Research Exchange Seminar, Japan. March 2024 (Oral, Japanese)
• [42] Daiki Kumakura. Theoretical analysis of plasmid establishment on repeated treatments. JSMB research meeting, Japan. March 2024 (Oral, Japanese)
• [43] Daiki Kumakura. Investigation of biomarker bacteria for very early diagnosis of bacterial vaginosis. Mathematical microbiome research meeting, Japan. March 2024 (Oral, Japanese)
• [44] Haruka Kitayama, Daiki Kumakura. The research progress of shotgun metagenomics for either the snow monkey entering bath or not. 2023 Jigokudani research meeting, Japan. March 2024 (Oral, Japanese)
• [45] Daiki Kumakura, Haruka Kitayama. A socio-ecological and genomic approach to mixed-species formation of African forest guenons. iTHEMS biology seminar, Japan. April 2024 (Organizer, Oral, English)
• [46] Daiki Kumakura, Shohei Kojima. Finding and understanding disease-causing genetic mutations. iTHEMS biology seminar, Japan. June 2024 (Organizer, Oral, English)
• [47] Daiki Kumakura. Theoretical analysis of extinction conditions of drug-resistant plasmids under repeated administration. iTHEMS NOW & NEXT 2024, Japan. July 2024 (Poster, English)
• [48] Daiki Kumakura. Dry research in microbiology is bioinformatics and mathematical biology. SOKENDAI Seminar, Japan. August 2024 (Invited, Oral, Japanese)
• [49] Kumakura D, Morita K, Nishiyama T, Yoshimura R, Akashi R, Nakano R, Minami S, Isshiki R. 4rd Summer School of Theoretical Biology. September 2024 (Workshop, Japanese)
• [50] Kumakura D, Akashi R, Nishiyama T. Ph.D, what do you do in Japan? Or to GO! ~Let's hear what our seniors have to say about their experiences~. JSMB 2024, Japan. September 2024 (Symposium, Japanese)
• [51] Ryohei Shimizuhata, Daiki Kumakura, Shinji Nakaoka. Analysis of progression patterns of bacterial vaginosis using energy landscape analysis. JSMB 2024, Japan. September 2024 (Oral, Japanese)
• [52] Kumakura D. Understanding and discussing the pathogenesis process and conditions of bacterial vaginosis. 5th medical and mathematical workshop, Japan. September 2024 (Poster, Japanese)
• [53] Daiki Kumakura, Jeffrery Fawcett, Euki Yazaki. Investigation of compositional changes of microbial mats in Jigokudani hot springs, Nagano Prefecture, caused by geographical isolation and environmental conditions. JSME2024. October 2024 (Poster, Japanese)
• [54] Daiki Kumakura, Sayaki Suzuki. Theoretical analysis of High-dose/Refuge strategy for durability of pest control. iTHEMS biology seminar, Japan. November 2024 (Organizer, Oral, English)
• [55] Daiki Kumakura, Ryohei Shimizuhata, Shinji Nakaoka. Elucidating the Process of Bacterial Vaginosis Development Using Pseudotime and State Transitions. The 47th Annual Meeting of the Molecular Biology Society of Japan. November 2024 (Poster, Japanese)

General article and book, interview

2020

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

2023

• [2] Daiki Kumakura. Close-up on Research in Focus “Mathematics Reveals the Wonders of Cleaning Bacteria”. Hokkaido University. December 2023 (URL) (Interview, Japanese)

2024

• [3] Nagai T, Kaneko I, Kumakura D, Iritani R et al. Study Material "One Poster per Family" Connecting "Mathematics" to the World. MEXT & RIKEN iTHEMS et al. March 2024 (URL) (Poster, Japanese)
• [4] T Nagai, T Hatsuda, S Matsuura, R Iritani, N tsuzi, D Kumakura. The commemorative lecture for "Science and Technology Week”. The Liberal Democratic Party of Japan Headquarters. April 2024 (URL) (Oral, Japanese)
• [5] Tomoya Nagai, Naoko Shinozaki, Daiki Kumakura. RIKEN DAY: Let's Talk with Researchers! Let's get to know each other through "Mathematics: One S&T poster for Every Household”! RIKEN. April 2024 (Oral, Japanese)
• [6] Daiki Kumakura. School Strike! ~Cho-Hokudaisei~, IMAREAL. AIR-G'FM Hokkaido. 13th September 2024 (Live radio, Japanese)
• [7] T Nagai, T Shimada, N Shinozaki, D Kumakura et al. Let's use mathematics. RIKEN Wako Open Day. October 2024 (Workshop, Japanese)
• [8] T Nagai, T Shimada, N Shinozaki, D Kumakura et al. Let's use mathematics. RIKEN Kobe Open Day. November 2024 (Workshop, Japanese)
• [9] Daiki Kumakura. Omoshiro Hokudai Lab! Hokkaido University Graduate School Education Reform Promotion Office. November 2024 (X, YouTube, Podcast, Japanese)

Award

2023

• [1] Daiki Kumakura. 52nd Akai Ito Kai (1st in 2023) Grand Prize. September 2023 (Oral, Japanese)