Kazufumi Hosoda | Homepage (->Japanese)

Hi! I'm

Kazufumi Hosoda
Associate professor,
Institute for Academic Initiatives (IAI), Osaka University
e-mail: hosoda"at"humanware.osaka-u.ac.jp
-> "Details of a Researcher" page at Osaka-u.

I'm working for a PhD (5yr) educational program as a chair of Education Committee: Humanware Innovation Program (Program for Leading Graduate Schools of Japan Society for the Promotion of Science). If you are interested in the program, please feel free to contact me.

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Research

I'm interested in the dynamics of biological systems. Biological systems are composed of various things that are continuously changing over time with interacting each other. Thus biological systems are high-dimensional and nonlinear dynamic systems, and we are yet to have enough understanding for such systems in any scientific field. Every system has each characteristics but various biological system often show common trends. I want to highlight the common basis for understanding complex biological systems. Therefore, my research includes various fields of science with both experimental and theoretical approaches. It may sound unfocused but I actually focus the basis with keeping my view always naive and flexible.

Specifically...
- Experimental (microbial) ecology and evolution
- Simple theory of biological dynamics
- Application of biological dynamics
- Artificial life by biochemicals

Papers

--- New ---

- 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. PNAS, Early Edition, doi: 10.1073/pnas.1615351114

- 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.

--- Experimental ecology and evolution ---

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- 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.

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- 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.

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- 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.

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- 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.

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- 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 ---

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- 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.


--- Application of biological dynamics ---


- 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.
- 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.

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- 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).


--- Artificial life by biochemicals ---

Link: -> Dr. Matsuura , Associate Professor, Graduate School of Engineering, Osaka university

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- 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. PNAS, Early Edition, doi: 10.1073/pnas.1615351114

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- 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.
- 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.
- 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.
- 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.
- 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.


- 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.
- 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.
- 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.
- 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.

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- 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.

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- 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.

Short bio

1998-2002, School of Engineering, Osaka University (Bachelor, 2002 Mar)
2002-2003, absence (3 month job, 9 month a round-the-world journey)
2003-2005, Graduate school of information science and technology, Osaka University (Master, 2005 Mar)
2005-2008, Graduate School of Frontier Bioscience. Osaka University (Ph.D. 2008 Mar)
2008-2013, Research associate, Graduate school of information science and technology, Osaka University
2013-, Associate professor, Institute for Academic Initiatives, Osaka University