Publications

Papers

• Ensemble dynamics and information flow deduction from whole-brain imaging data
  Yu Toyoshima, Hirofumi Sato, Daiki Nagata, Manami Kanamori, Moon Sun Jang, Koyo Kuze, Suzu Oe, Takayuki Teramoto, Yuishi Iwasaki, Ryo Yoshida, Takeshi Ishihara, Yuichi Iino
  PLOS Computational Biology, volume 20, e1011848, (2024). https://doi.org/10.1371/journal.pcbi.1011848
  
  
• Neuronal sensorimotor integration guiding salt concentration navigation in Caenorhabditis elegans
  Ayaka Matsumoto, Yu Toyoshima, Chenqi Zhang, Akihiro Isozaki, Keisuke Goda, Yuichi Iino
  PNAS, volume 121, e2310735121, (2024). https://doi.org/10.1073/pnas.2310735121
  
  
• WormTracer: A precise method for worm posture analysis using temporal continuity
  Koyo Kuze, Ukyo T. Tazawa, Karin Suwazono, Yu Toyoshima, Yuichi Iino
  bioRxiv (preprint), (2023). https://doi.org/10.1101/2023.12.11.571048
  
  
• WormTensor: a clustering method for time-series whole-brain activity data from C. elegans
  Koki Tsuyuzaki, Kentaro Yamamoto, Yu Toyoshima, Hirofumi Sato, Manami Kanamori, Takayuki Teramoto, Takeshi Ishihara, Yuichi Iino, Itoshi Nikaido
  BMC Bioinformatics, volume 24, Article Number 254, (2023). https://doi.org/10.1186/s12859-023-05230-2
  
  
• Different modes of stimuli delivery elicit changes in glutamate driven, experience-dependent interneuron response in C. elegans
  Llian Mabardi, Hirofumi Sato, Yu Toyoshima, Yuichi Iino, Hirofumi Kunitomo
  Neuroscience Research, volume 186, pages 33-42, (2022). https://doi.org/10.1016/j.neures.2022.10.004
  
  
• Probabilistic generative modeling and reinforcement learning extract the intrinsic features of animal behavior
  Keita Mori, Naohiro Yamauchi, Haoyu Wang, Ken Sato, Yu Toyoshima, Yuichi Iino
  Neural Networks, volume 145, pages 107-120, (2021). https://doi.org/10.1016/j.neunet.2021.10.002
  
  
• Neuron ID dataset facilitates neuronal annotation for whole-brain activity imaging of C. elegans
  Yu Toyoshima, Stephen Wu, Manami Kanamori, Hirofumi Sato, Moon Sun Jang, Suzu Oe, Yuko Murakami, Takayuki Teramoto, Chanhyun Park, Yuishi Iwasaki, Takeshi Ishihara, Ryo Yoshida & Yuichi Iino
  BMC Biology, volume 18, pages 30, (2020). https://doi.org/10.1186/s12915-020-0745-2
  
  
• Multiple sensory neurons mediate starvation-dependent aversive navigation in Caenorhabditis elegans
  Moon Sun Jang, Yu Toyoshima, Masahiro Tomioka, Hirofumi Kunitomo, Yuichi Iino
  PNAS, volume 116, pages 18673-18683, (2019). https://doi.org/10.1073/pnas.1821716116
  
  
• SPF-CellTracker: Tracking multiple cells with strongly-correlated moves using a spatial particle filter
  Osamu Hirose, Shotaro Kawaguchi, Terumasa Tokunaga, Yu Toyoshima, Takayuki Teramoto, Sayuri Kuge, Takeshi Ishihara, Yuichi Iino, Ryo Yoshida
  IEEE/ACM Transactions on Computational Biology and Bioinformatics, volume 15, pages 1822-1831, (2017). https://doi.org/10.1109/TCBB.2017.2782255
  
  
• Modulation of sensory information processing by a neuroglobin in C. elegans
  Shigekazu Oda, Yu Toyoshima, Mario de Bono
  PNAS, volume 114, pages E4658–E4665, (2017). https://doi.org/10.1073/pnas.1614596114
  
  
• Accurate Automatic Detection of Densely Distributed Cell Nuclei in 3D Space.
  Yu Toyoshima, Terumasa Tokunaga, Osamu Hirose, Manami Kanamori, Takayuki Teramoto, Moon-Sun Jang, Sayuri Kuge, Takeshi Ishihara, Ryo Yoshida, Yuichi Iino
  PLOS Computational Biology, volume 12, pages e1004970, (2016). https://doi.org/10.1371/journal.pcbi.1004970
  
  
• Glucose Homeostatic Law: Insulin Clearance Predicts the Progression of Glucose Intolerance in Humans
  Kaoru Ohashi, Hisako Komada, Shinsuke Uda, Hiroyuki Kubota, Toshinao Iwaki, Hiroki Fukuzawa, Yasunori Komori, Masashi Fujii, Yu Toyoshima, Kazuhiko Sakaguchi, Wataru Ogawa, Shinya Kuroda
  PLOS One, volume 10, pages e0143880, (2015). https://doi.org/10.1371/journal.pone.0143880
  
  
• Reconstruction of Insulin Signal Flow from Phosphoproteome and Metabolome Data
  Katsuyuki Yugi, Hiroyuki Kubota, Yu Toyoshima, Rei Noguchi, Kentaro Kawata, Yasunori Komori, Shinsuke Uda, Katsuyuki Kunida, Yoko Tomizawa, Yosuke Funato, Hiroaki Miki, Masaki Matsumoto, Keiichi I. Nakayama, Kasumi Kashikura, Keiko Endo, Kazutaka Ikeda, Tomoyoshi Soga, Shinya Kuroda
  Cell Reports, volume 8, pages 1171-1183, (2014). https://doi.org/10.1016/j.celrep.2014.07.021
  
  
• Automated detection and tracking of many cells by using 4D live-cell imaging data
  Terumasa Tokunaga, Osamu Hirose, Shotaro Kawaguchi, Yu Toyoshima, Takayuki Teramoto, Hisaki Ikebata, Sayuri Kuge, Takeshi Ishihara, Yuichi Iino, Ryo Yoshida
  Bioinformatics, volume 30, pages i43-i51, (2014). https://doi.org/10.1093/bioinformatics/btu271
  
  
• The selective control of glycolysis, gluconeogenesis and glycogenesis by temporal insulin patterns
  Rei Noguchi, Hiroyuki Kubota, Katsuyuki Yugi, Yu Toyoshima, Yasunori Komori, Tomoyoshi Soga, Shinya Kuroda
  Molecular Systems Biology, volume 9, pages 1-12, (2013). https://doi.org/10.1038/msb.2013.19
  
  
• Temporal Coding of Insulin Action through Multiplexing of the AKT Pathway
  Hiroyuki Kubota, Rei Noguchi, Yu Toyoshima, Yu-ichi Ozaki, Shinsuke Uda, Kanako Watanabe, Wataru Ogawa, Shinya Kuroda
  Molecular Cell, volume 46, pages 820-832, (2012). https://doi.org/10.1016/j.molcel.2012.04.018
  
  
• Sensitivity control through attenuation of signal transfer efficiency by negative regulation of cellular signalling
  Yu Toyoshima, Hiroaki Kakuda, Kazuhiro A. Fujita, Shinsuke Uda, and Shinya Kuroda
  Nature Communications, volume 3, pages 743, (2012). https://doi.org/10.1038/ncomms1745
  
  
• Decoupling of receptor and downstream signals in Akt pathway by its low-pass filter characteristics
  Kazuhiro A. Fujita, Yu Toyoshima, Sinsuke Uda, Yu-ichi Ozaki, Hiroyuki Kubota, Shinya Kuroda
  Science Signalling, volume 3, pages ra56, (2010). https://doi.org/10.1126/scisignal.2000810