{"id":92,"date":"2021-08-07T03:39:59","date_gmt":"2021-08-06T18:39:59","guid":{"rendered":"http:\/\/localhost\/wordpress\/?page_id=92"},"modified":"2025-11-14T18:28:44","modified_gmt":"2025-11-14T09:28:44","slug":"publications","status":"publish","type":"page","link":"http:\/\/localhost\/wordpress\/en\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">Publications<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">Papers<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n\n\n<li><strong>CGC1, a new reference genome for <em>Caenorhabditis elegans<\/em><\/strong><br>Kazuki Ichikawa, Massa J. Shoura, Karen L. Artiles, Dae-Eun Jeong, Chie Owa, Haruka Kobayashi, Yoshihiko Suzuki, Manami Kanamori, Yu Toyoshima, Yuichi Iino, Ann E. Rougvie, Lamia Wahba, Andrew Z. Fire, Erich M. Schwarz and Shinichi Morishita<br><a href=\"https:\/\/genome.cshlp.org\/content\/35\/8\/1902\">Genome Research, volume 35, pp.1902-1918, (2025)<\/a>.  <a href=\"https:\/\/doi.org\/10.1101\/gr.280274.124\">https:\/\/doi.org\/10.1101\/gr.280274.124<\/a><br><\/li>\n\n\n\n<li><strong>Dissection of Behavioral Components and the Role of Omega\/Delta Turns for the Chemotaxis of <em>C. elegans<\/em><\/strong><br>Karin Suwazono, Koyo Kuze, Ukyo T. Tazawa, Moon Sun Jang, Hirofumi Kunitomo, Yu Toyoshima, Yuichi Iino<br><a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/gtc.70026\">Genes To Cells, volume 30, e70026, (2025)<\/a>.  <a href=\"https:\/\/doi.org\/10.1111\/gtc.70026\">https:\/\/doi.org\/10.1111\/gtc.70026<\/a><br><\/li>\n\n\n\n<li><strong>Ensemble dynamics and information flow deduction from whole-brain imaging data<\/strong><br>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<br><a href=\"https:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1011848\">PLOS Computational Biology, volume 20, e1011848, (2024)<\/a>.  <a href=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1011848\">https:\/\/doi.org\/10.1371\/journal.pcbi.1011848<\/a><br><br><\/li>\n\n\n\n<li><strong>Neuronal sensorimotor integration guiding salt concentration navigation in <em>Caenorhabditis elegans<\/em><\/strong><br>Ayaka Matsumoto, Yu Toyoshima, Chenqi Zhang, Akihiro Isozaki, Keisuke Goda, Yuichi Iino<br><a href=\"https:\/\/www.pnas.org\/doi\/full\/10.1073\/pnas.2310735121\">PNAS, volume 121, e2310735121, (2024)<\/a>.  <a href=\"https:\/\/doi.org\/10.1073\/pnas.2310735121\">https:\/\/doi.org\/10.1073\/pnas.2310735121<\/a><br><br><\/li>\n\n\n\n<li><strong>WormTracer: A precise method for worm posture analysis using temporal continuity<\/strong><br>Koyo Kuze, Ukyo T. Tazawa, Karin Suwazono, Yu Toyoshima, Yuichi Iino<br><a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2023.12.11.571048\">bioRxiv (preprint), (2023)<\/a>.&nbsp;<a href=\"https:\/\/doi.org\/10.1101\/2023.12.11.571048\">https:\/\/doi.org\/10.1101\/2023.12.11.571048<\/a><br><br><\/li>\n\n\n\n<li><strong>WormTensor: a clustering method for time-series whole-brain activity data from <em>C. elegans<\/em><\/strong><br>Koki Tsuyuzaki, Kentaro Yamamoto, Yu Toyoshima, Hirofumi Sato, Manami Kanamori, Takayuki Teramoto, Takeshi Ishihara, Yuichi Iino, Itoshi Nikaido<br><a href=\"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-023-05230-2\">BMC Bioinformatics, volume 24, Article Number 254, (2023).<\/a> <a href=\"https:\/\/doi.org\/10.1186\/s12859-023-05230-2\">https:\/\/doi.org\/10.1186\/s12859-023-05230-2<\/a><br><br><\/li>\n\n\n\n<li><strong>Different modes of stimuli delivery elicit changes in glutamate driven, experience-dependent interneuron response in <i>C. elegans<\/i><\/strong><br>Llian Mabardi, Hirofumi Sato, Yu Toyoshima, Yuichi Iino, Hirofumi Kunitomo<br><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0168010222002644\">Neuroscience Research, volume 186, pages 33-42, (2022).<\/a> <a href=\"https:\/\/doi.org\/10.1016\/j.neures.2022.10.004\">https:\/\/doi.org\/10.1016\/j.neures.2022.10.004<\/a><br><br><\/li>\n\n\n\n<li><strong>Probabilistic generative modeling and reinforcement learning extract the intrinsic features of animal behavior<\/strong><br>Keita Mori, Naohiro Yamauchi, Haoyu Wang, Ken Sato, Yu Toyoshima, Yuichi Iino<br><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0893608021003932\">Neural Networks, volume 145, pages 107-120, (2021).<\/a> <a href=\"https:\/\/doi.org\/10.1016\/j.neunet.2021.10.002\">https:\/\/doi.org\/10.1016\/j.neunet.2021.10.002<\/a><br><br><\/li>\n\n\n\n<li><strong>Neuron ID dataset facilitates neuronal annotation for whole-brain activity imaging of <em>C. elegans<\/em><\/strong><br>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 &amp; Yuichi Iino<br><a rel=\"noreferrer noopener\" href=\"https:\/\/bmcbiol.biomedcentral.com\/articles\/10.1186\/s12915-020-0745-2\" data-type=\"URL\" data-id=\"https:\/\/bmcbiol.biomedcentral.com\/articles\/10.1186\/s12915-020-0745-2\" target=\"_blank\">BMC Biology, volume 18, pages 30, (2020).<\/a> <a rel=\"noreferrer noopener\" href=\"https:\/\/doi.org\/10.1186\/s12915-020-0745-2\" target=\"_blank\">https:\/\/doi.org\/10.1186\/s12915-020-0745-2<\/a><br><br><\/li>\n\n\n\n<li><strong>Multiple sensory neurons mediate starvation-dependent aversive navigation in <em>Caenorhabditis elegans<\/em><\/strong><br>Moon Sun Jang, Yu Toyoshima, Masahiro Tomioka, Hirofumi Kunitomo, Yuichi Iino<br><a rel=\"noreferrer noopener\" href=\"https:\/\/www.pnas.org\/content\/116\/37\/18673\" target=\"_blank\">PNAS, volume 116, pages 18673-18683, (2019)<\/a>. <a rel=\"noreferrer noopener\" href=\"https:\/\/doi.org\/10.1073\/pnas.1821716116\" target=\"_blank\">https:\/\/doi.org\/10.1073\/pnas.1821716116<\/a><br><br><\/li>\n\n\n\n<li><strong>SPF-CellTracker: Tracking multiple cells with strongly-correlated moves using a spatial particle filter<\/strong><br>Osamu Hirose, Shotaro Kawaguchi, Terumasa Tokunaga, Yu Toyoshima, Takayuki Teramoto, Sayuri Kuge, Takeshi Ishihara, Yuichi Iino, Ryo Yoshida<br><a rel=\"noreferrer noopener\" href=\"https:\/\/ieeexplore.ieee.org\/document\/8186251\" target=\"_blank\">IEEE\/ACM Transactions on Computational Biology and Bioinformatics, volume 15, pages 1822-1831, (2017). <\/a><a rel=\"noreferrer noopener\" href=\"https:\/\/doi.org\/10.1109\/TCBB.2017.2782255\" target=\"_blank\">https:\/\/doi.org\/10.1109\/TCBB.2017.2782255<\/a><br><br><\/li>\n\n\n\n<li><strong>Modulation of sensory information processing by a neuroglobin in <em>C. elegans<\/em><\/strong><br>Shigekazu Oda, Yu Toyoshima, Mario de Bono<br><a rel=\"noreferrer noopener\" href=\"https:\/\/www.pnas.org\/content\/114\/23\/E4658\" target=\"_blank\">PNAS, volume 114, pages E4658\u2013E4665, (2017)<\/a>. <a rel=\"noreferrer noopener\" href=\"https:\/\/doi.org\/10.1073\/pnas.1614596114\" target=\"_blank\">https:\/\/doi.org\/10.1073\/pnas.1614596114<\/a><br><br><\/li>\n\n\n\n<li><strong>Accurate Automatic Detection of Densely Distributed Cell Nuclei in 3D Space.<\/strong><br>Yu Toyoshima, Terumasa Tokunaga, Osamu Hirose, Manami Kanamori, Takayuki Teramoto, Moon-Sun Jang, Sayuri Kuge, Takeshi Ishihara, Ryo Yoshida, Yuichi Iino<br><a rel=\"noreferrer noopener\" href=\"https:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1004970\" target=\"_blank\">PLOS Computational Biology, volume 12, pages e1004970, (2016)<\/a>. <a rel=\"noreferrer noopener\" href=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1004970\" target=\"_blank\">https:\/\/doi.org\/10.1371\/journal.pcbi.1004970<\/a><br><br><\/li>\n\n\n\n<li><strong>Glucose Homeostatic Law: Insulin Clearance Predicts the Progression of Glucose Intolerance in Humans<\/strong><br>Kaoru Ohashi, Hisako Komada, Shinsuke Uda, Hiroyuki Kubota, Toshinao Iwaki, Hiroki Fukuzawa, Yasunori Komori, Masashi Fujii, Yu Toyoshima, Kazuhiko Sakaguchi, Wataru Ogawa, Shinya Kuroda<br><a rel=\"noreferrer noopener\" href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0143880\" target=\"_blank\">PLOS One, volume 10, pages e0143880, (2015)<\/a>. <a rel=\"noreferrer noopener\" href=\"https:\/\/doi.org\/10.1371\/journal.pone.0143880\" target=\"_blank\">https:\/\/doi.org\/10.1371\/journal.pone.0143880<\/a><br><br><\/li>\n\n\n\n<li><strong>Reconstruction of Insulin Signal Flow from Phosphoproteome and Metabolome Data<\/strong><br>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<br><a rel=\"noreferrer noopener\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S2211124714005907?via%3Dihub\" target=\"_blank\">Cell Reports, volume 8, pages 1171-1183, (2014)<\/a>. <a rel=\"noreferrer noopener\" href=\"https:\/\/doi.org\/10.1016\/j.celrep.2014.07.021\" target=\"_blank\">https:\/\/doi.org\/10.1016\/j.celrep.2014.07.021<\/a><br><br><\/li>\n\n\n\n<li><strong>Automated detection and tracking of many cells by using 4D live-cell imaging data<\/strong><br>Terumasa Tokunaga, Osamu Hirose, Shotaro Kawaguchi, Yu Toyoshima, Takayuki Teramoto, Hisaki Ikebata, Sayuri Kuge, Takeshi Ishihara, Yuichi Iino, Ryo Yoshida<br><a rel=\"noreferrer noopener\" href=\"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/12\/i43\/385877\" target=\"_blank\">Bioinformatics, volume 30, pages i43-i51, (2014)<\/a>. <a rel=\"noreferrer noopener\" href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btu271\" target=\"_blank\">https:\/\/doi.org\/10.1093\/bioinformatics\/btu271<\/a><br><br><\/li>\n\n\n\n<li><strong>The selective control of glycolysis, gluconeogenesis and glycogenesis by temporal insulin patterns<\/strong><br>Rei Noguchi, Hiroyuki Kubota, Katsuyuki Yugi, Yu Toyoshima, Yasunori Komori, Tomoyoshi Soga, Shinya Kuroda<br><a rel=\"noreferrer noopener\" href=\"https:\/\/www.embopress.org\/doi\/full\/10.1038\/msb.2013.19\" target=\"_blank\">Molecular Systems Biology, volume 9, pages 1-12, (2013)<\/a>. <a rel=\"noreferrer noopener\" href=\"https:\/\/doi.org\/10.1038\/msb.2013.19\" target=\"_blank\">https:\/\/doi.org\/10.1038\/msb.2013.19<\/a><br><br><\/li>\n\n\n\n<li><strong>Temporal Coding of Insulin Action through Multiplexing of the AKT Pathway<\/strong><br>Hiroyuki Kubota, Rei Noguchi, Yu Toyoshima, Yu-ichi Ozaki, Shinsuke Uda, Kanako Watanabe, Wataru Ogawa, Shinya Kuroda<br><a rel=\"noreferrer noopener\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1097276512003401?via%3Dihub\" target=\"_blank\">Molecular Cell, volume 46, pages 820-832, (2012)<\/a>. <a rel=\"noreferrer noopener\" href=\"https:\/\/doi.org\/10.1016\/j.molcel.2012.04.018\" target=\"_blank\">https:\/\/doi.org\/10.1016\/j.molcel.2012.04.018<\/a><br><br><\/li>\n\n\n\n<li><strong>Sensitivity control through attenuation of signal transfer efficiency by negative regulation of cellular signalling<\/strong><br>Yu Toyoshima, Hiroaki Kakuda, Kazuhiro A. Fujita, Shinsuke Uda, and Shinya Kuroda<br><a rel=\"noreferrer noopener\" href=\"https:\/\/www.nature.com\/articles\/ncomms1745\" target=\"_blank\">Nature Communications, volume 3, pages 743, (2012)<\/a>. <a rel=\"noreferrer noopener\" href=\"https:\/\/doi.org\/10.1038\/ncomms1745\" target=\"_blank\">https:\/\/doi.org\/10.1038\/ncomms1745<\/a><br><br><\/li>\n\n\n\n<li><strong>Decoupling of receptor and downstream signals in Akt pathway by its low-pass filter characteristics<\/strong><br>Kazuhiro A. Fujita, Yu Toyoshima, Sinsuke Uda, Yu-ichi Ozaki, Hiroyuki Kubota, Shinya Kuroda<br><a rel=\"noreferrer noopener\" href=\"https:\/\/stke.sciencemag.org\/content\/3\/132\/ra56\" target=\"_blank\">Science Signalling, volume 3, pages ra56, (2010)<\/a>. <a rel=\"noreferrer noopener\" href=\"https:\/\/doi.org\/10.1126\/scisignal.2000810\" target=\"_blank\">https:\/\/doi.org\/10.1126\/scisignal.2000810<\/a><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Publications Papers<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":4,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_locale":"en_US","_original_post":"http:\/\/localhost\/wordpress\/?page_id=39","footnotes":""},"class_list":["post-92","page","type-page","status-publish","hentry","en-US"],"_links":{"self":[{"href":"http:\/\/localhost\/wordpress\/wp-json\/wp\/v2\/pages\/92","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/localhost\/wordpress\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/localhost\/wordpress\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/localhost\/wordpress\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/localhost\/wordpress\/wp-json\/wp\/v2\/comments?post=92"}],"version-history":[{"count":9,"href":"http:\/\/localhost\/wordpress\/wp-json\/wp\/v2\/pages\/92\/revisions"}],"predecessor-version":[{"id":407,"href":"http:\/\/localhost\/wordpress\/wp-json\/wp\/v2\/pages\/92\/revisions\/407"}],"wp:attachment":[{"href":"http:\/\/localhost\/wordpress\/wp-json\/wp\/v2\/media?parent=92"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}