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KAZUFUMI HOSODA

   
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 * Japanese

 * Experience
 * Research
 * Publications
 * Miscellaneous

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© 2023 Kazufumi Hosoda
# Thx Saetl.net for template


WELCOME TO KAZUFUMI HOSODA HOMEPAGE


WHAT IS SELF, WHAT IS HUMAN, AND WHAT IS LIFE?


REGULAR WORK

Principal Investigator, CiNet, NICT [Link]
# CiNet: Center for Information and Neural Networks
# NICT: National Institute of Information and Communications Technology


SIDE JOBS

Professor, Graduate School of Health Sciences, Kobe university [Link] Visiting
Professor, Graduate School of Frontier Biosciences, Osaka University [Link]
Visiting Scientist, Furusawa team, RIKEN BDR (Artificial ecosystems) [Link]
Owner, Ansanga lab (Business for education and research) [Link]


EXPERIENCE

1998-2002 Osaka University (Bachelor, 2002 Mar) 2002-2003 absence (a
round-the-world journey) 2003-2005 Osaka University (Master, 2005 Mar) 2005-2008
Osaka University (Ph.D. 2008 Mar) 2008-2013 Assistant professor, Osaka
University 2013-2021 Associate professor, Osaka University 2021-2021 Researcher,
Riken BDR 2021-NOW Principal investigator, NICT CiNet
(2019-NOW) Owner, Ansanga lab (2021-NOW) Visiting Scientist, RIKEN (2022-NOW)
Professor, Kobe university


RESEARCH

Brain dynamics and its application Experimental (microbial) ecology and
evolution Simple theory of biological dynamics Application of biological
dynamics Artificial life by biochemicals


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.


MISCELLANEOUS


--- INVITED TALKS (INTERNATIONAL) ---

"A high-throughput synthetic microbial ecosystem: stochastic community dynamics,
inter-ecosystem interactions, predictions and controls", Symposium of Ecological
Society of Japan Kanto Branch, Online, 2021, Jul. 21 "Perspectives on ecosystems
as biofluids", Biofluids 2021, Online, 2021, Jul. 5-7 "Introduction: Microbes go
to work", Gordon Research Conference (Microbial Population Biology), Proctor
Academy (Andover, NH), July 19-24, 2015 "Toward a paradigm shift having fun with
complex living systems.", The 10th SOKENDAI Life Science Retreat, Shizuoka,
Japan, 2013, Dec. 30-31 "Phenotypic Plasticity for the Establishment of
Symbiosis." The 7th Okazaki Biology Conference (Shizuoka, Japan), Jan. 11-14,
2010


--- AWARDS ---

Best Crowd Award, KICSS 2022, Kyoto, Japan, 2022 Nov．23-25 Evolution in Action,
Artificial Life XIII, Michigan, USA, 2012 July．19-22