Publications
--- Brain, AI, ICT, Interdisciplinary ---
Kazufumi Hosoda, Keigo Nishida, Shigeto Seno, Tomohiro Mashita, Hideki Kashioka and Izumi Ohzawa (2024). "A single fast Hebbian-like process enabling one-shot class addition in deep neural networks without backbone modification." Frontiers in Neuroscience 18.
Kosuke Tomimatsu, Takeru Fujii, Ryoma Bise, Kazufumi Hosoda, Yosuke Taniguchi, Hiroshi Ochiai, Hiroaki Ohishi, Kanta Ando, Ryoma Minami, Kaori Tanaka, Taro Tachibana, Seiichi Mori, Akihito Harada, Kazumitsu Maehara, Masao Nagasaki, Seiichi Uchida, Hiroshi Kimura, Masashi Narita, Yasuyuki Ohkawa (2024). "Precise immunofluorescence canceling for highly multiplexed imaging to capture specific cell states." Nature Communications 15: 3657
Kazufumi Hosoda, Shigeto Seno and Tsutomu Murata (2023). "Simulating Reaction Time for Eureka Effect in Visual Object Recognition Using Artificial Neural Network." IIAI Letters on Informatics and Interdisciplinary Research 3. 60, (KICSS 2022 Best Crowd Award)
Hiroaki Ohishi, Soya Shinkai, Hitoshi Owada, Takeru Fujii, Kazufumi Hosoda, Shuichi Onami, Takashi Yamamoto, Yasuyuki Ohkawa and Hiroshi Ochiai (2023). "Transcription-coupled changes in higher-order genomic structure and transcription hub viscosity prolong enhancer-promoter connectivity." bioRxiv: 2023.2011. 2027.568629.
Fu, C., Dissanayake, T., Hosoda, K., Maekawa, T., Ishiguro, H., (2020) Similarity of Speech Emotion in Different Languages Revealed by a Neural Network with Attention, 2020 IEEE 14th International Conference on Semantic Computing (ICSC), San Diego, CA, USA, 2020, pp. 381-386
Shibai, A., Arimoto, T., Yoshinaga, T., Tsuchizawa, Y., Khureltulga, D., Brown, Z.P., Kakizuka, T., Hosoda, K., (2018). Attraction of posture and motion-trajectory elements of conspecific biological motion in medaka fish. Scientific Reports 8, p8589
Nakamura, T., Tominaga, T., Watanabe, M., Thammasan, N., Urai, K., Nakamura, Y., Hosoda, K., Hara, T., Hijikata, Y., (2017), Investigation on Dynamics of Group Decision Making with Collaborative Web Search. In Proceedings of 2017 IEEE/WIC/ACM International Conference on Web Intelligence.
Kiyokawa, K., Hatanaka, M., Hosoda, K., Okada, M., Shigeta, H., Ishihara, Y., Ooshita, F., Kakugawa, H., Kurihara, S., and Moriyama, K., (2012), Owens Luis - A context-aware multi-modal smart office chair in an ambient environment. Paper presented at: Virtual Reality (VR), 2012 IEEE (Costa Mesa, CA, USA).
Shigeta, H., Nakase, J., Tsunematsu, Y., Kiyokawa, K., Hatanaka, M., Hosoda, K., Okada, M., Ishihara, Y., Ooshita, F., Kakugawa, H., et al., (2012), Implementation of a smart office system in an ambient environment. Paper presented at: Virtual Reality (VR), 2012 IEEE (Costa Mesa, CA, USA).
--- Experimental ecology and evolution ---
Kazufumi Hosoda, Shigeto Seno, Naomi Murakami, Hideo Matsuda, Yutaka Osada, Rikuto Kamiura and Michio Kondoh (2024). "Synthetic model ecosystem of 12 cryopreservable microbial species allowing for a noninvasive approach." Biosystems: 105087.
Kazufumi Hosoda, Shigeto Seno, Rikuto Kamiura, Naomi Murakami and Michio Kondoh (2023). "Biodiversity and Constrained Information Dynamics in Ecosystems: A Framework for Living Systems." Entropy 25(12): 1624. (Feature Paper)
Yuki Azuma, Saburo Tsuru, Masumi Habuchi, Risa Takami, Sotaro Takano, Kayo Yamamoto and Kazufumi Hosoda (2023). "Synthetic symbiosis between a cyanobacterium and a ciliate toward novel chloroplast-like endosymbiosis." Scientific Reports 13(1): 6104.
Kazufumi Hosoda, Shigeto Seno, Naomi Murakami, Hideo Matsuda, Yutaka Osada, Michio Kondoh, "A model ecosystem of twelve cryopreservable microbial species allowing for a non-invasive approach", bioRxiv, 2020.10.23.351742, (2020)
Hosoda, K., Tsuda, S., Kadowaki, K., Nakamura, Y., Nakano, T., Ishii, K., (2016), Population-reaction model and microbial experimental ecosystems for understanding hierarchical dynamics of ecosystems. Biosystems 140, 28-34.
Hosoda, K., Ono, N., Suzuki, S., and Yomo, T., (2014), Transcriptome Analysis of a Microbial Coculture in which the Cell Populations Are Separated by a Membrane. In Engineering and Analyzing Multicellular Systems, L. Sun, and W. Shou, eds., (Springer New York), pp. 151-164.
Hosoda, K., Habuchi, M., Suzuki, S., Miyazaki, M., Takikawa, G., Sakurai, T., Kashiwagi, A., Sueyoshi, M., Matsumoto, Y., Kiuchi, A., et al., (2014), Adaptation of a Cyanobacterium to a Biochemically Rich Environment in Experimental Evolution as an Initial Step toward a Chloroplast-Like State. Plos One 9.
Kubo, I., Hosoda, K., Suzuki, S., Yamamoto, K., Kihara, K., Mori, K., and Yomo, T., (2013), Construction of bacteria-eukaryote synthetic mutualism. Biosystems 113, 66-71.
Kumano, I., Hosoda, K., Suzuki, H., Hirata, K., and Yomo, T., (2012), Hydrodynamic trapping of Tetrahymena thermophila for the long-term monitoring of cell behaviors. Lab on a chip 12, 3451-3457.
Hosoda, K., Suzuki, S., Yamauchi, Y., Shiroguchi, Y., Kashiwagi, A., Ono, N., Mori, K., and Yomo, T., (2011), Cooperative adaptation to establishment of a synthetic bacterial mutualism. PLoS One 6, e17105.
Hosoda, K., and Yomo, T., (2011), Designing symbiosis. Bioeng Bugs 2, 338-341.
Kihara, K., Mori, K., Suzuki, S., Hosoda, K., Yamada, A., Matsuyama, S., Kashiwagi, A., and Yomo, T., (2011), Probabilistic transition from unstable predator-prey interaction to stable coexistence of Dictyostelium discoideum and Escherichia coli. Biosystems 103, 342-347.
Hosoda, K., Mori, K., Shiroguchi, Y., Yamauchi, Y., Kashiwagi, A., and Yomo, T., (2008), Synthetic ecosystem of Escherichia coli for discovery of novel cooperative and self-adaptive algorithms. Paper presented at: Bioinspired Models of Network, Information, and Computing Systems (BIONETICS) 2008 (ICST).
--- Simple theory of biological dynamics ---
Hosoda, K., Matsuura, T., Suzuki, H., and Yomo, T., (2011), Origin of lognormal-like distributions with a common width in a growth and division process. Physical Review E 83, 031118.
--- Artificial life by biochemicals ---
Link: -> Dr. Matsuura
, Professor, Tokyo Institute of Technology
Matsuura, T., Hosoda, K., Shimizu, Y., (2018). Robustness of a Reconstituted Escherichia coli Protein Translation System Analyzed by Computational Modeling. ACS Synthetic Biology 7, pp1964-1972
Matsuura, T., Tanimura, N., Hosoda, K., Yomo, T., Shimizu, Y., (2017), Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling. Proceedings of the National Academy of Sciences (PNAS): 114: E1336-E1344.
Okaie, Y., Nakano, T., Hara, T., Obuchi, T., Hosoda, K., Hiraoka, Y., Nishio, S., (2014), Cooperative Target Tracking by a Mobile Bionanosensor Network., IEEE Transactions on Nanobioscience, 13(3), p 267-277
Nakano, T., Hosoda, K., Nakamura, Y., and Ishii, K., (2013), A biologically-inspired intrabody nanonetwork: design considerations. In Proceedings of the 8th International Conference on Body Area Networks (Boston, Massachusetts: ICST (Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering)), pp. 484-487.
Matsuura, T., Hosoda, K., Kazuta, Y., Ichihashi, N., Suzuki, H., and Yomo, T., (2012), Effects of compartment size on the kinetics of intracompartmental multimeric protein synthesis. ACS synthetic biology 1, 431-437.
Hirata, K., Ichii, T., Suzuki, H., Matsuura, T., Hosoda, K., and Yomo, T., (2012), Fractal-shaped microchannel design for a kinetic analysis of biochemical reaction in a delay line. Microfluid Nanofluid 13, 273-278.
Matsuura, T., Hosoda, K., Ichihashi, N., Kazuta, Y., and Yomo, T., (2011), Kinetic Analysis of {beta}-Galactosidase and {beta}-Glucuronidase Tetramerization Coupled with Protein Translation. J Biol Chem 286, 22028-22034.
Sunami, T., Hosoda, K., Suzuki, H., Matsuura, T., and Yomo, T., (2010), Cellular compartment model for exploring the effect of the lipidic membrane on the kinetics of encapsulated biochemical reactions. Langmuir 26, 8544-8551.
Ichihashi, N., Matsuura, T., Hosoda, K., and Yomo, T., (2010), Identification of two forms of Q{beta} replicase with different thermal stabilities but identical RNA replication activity. J Biol Chem 285, 37210-37217.
Urabe, H., Ichihashi, N., Matsuura, T., Hosoda, K., Kazuta, Y., Kita, H., and Yomo, T., (2010), Compartmentalization in a water-in-oil emulsion repressed the spontaneous amplification of RNA by Q beta replicase. Biochemistry 49, 1809-1813.
Ichihashi, N., Kita, H., Hosoda, K., Sunami, T., Tsukada, K., Matsuura, T., and Yomo, T., (2009), Requirements for Efficient Replication of Genetic Information in a Translation-Coupled Replication System. Origins Life Evol B 39, 317-318.
Sunami, T., Kita, H., Hosoda, K., Matsuura, T., Suzuki, H., and Yomo, T., (2009), Chapter 2 - Detection and analysis of protein synthesis and RNA replication in giant liposomes. Methods Enzymol 464, 19-30.
Ichihashi, N., Matsuura, T., Kita, H., Hosoda, K., Sunami, T., Tsukada, K., and Yomo, T., (2008), Importance of translation-replication balance for efficient replication by the self-encoded replicase. Chembiochem 9, 3023-3028.
Kita, H., Matsuura, T., Sunami, T., Hosoda, K., Ichihashi, N., Tsukada, K., Urabe, I., and Yomo, T., (2008), Replication of genetic information with self-encoded replicase in liposomes. Chembiochem 9, 2403-2410.
Hosoda, K., Sunami, T., Kazuta, Y., Matsuura, T., Suzuki, H., and Yomo, T., (2008), Quantitative study of the structure of multilamellar giant liposomes as a container of protein synthesis reaction. Langmuir 24, 13540-13548.
Hosoda, K., Matsuura, T., Kita, H., Ichihashi, N., Tsukada, K., Urabe, I., and Yomo, T., (2008), A novel sequence-specific RNA quantification method using nicking endonuclease, dual-labeled fluorescent DNA probe, and conformation-interchangeable oligo-DNA. Rna 14, 584-592.
Hosoda, K., Matsuura, T., Kita, H., Ichihashi, N., Tsukada, K., and Yomo, T., (2007), Kinetic analysis of the entire RNA amplification process by Qbeta replicase. J Biol Chem 282, 15516-15527.
