Publications

International Journals (English)

• Yamaguchi HQ, Ode KL, Ueda HR. "A design principle for posttranslational chaotic oscillators" iScience, 2021, 15;24(1):101946. doi: 10.1016/j.isci.2020.101946
• Ode KL, Shi S, Katori M, Mitsui K, Takanashi S, Oguchi R, Aoki D, Ueda HR. "A jerk-based algorithm ACCEL for the accurate classification of sleep-wake states from arm acceleration" iScience, 2021, 25(2):103727. doi: 10.1016/j.isci.2021.103727
• Yamada T, Shi S, Ueda HR. "A design principle of spindle oscillations in mammalian sleep." iScience, 25(3):103873. doi: 10.1016/j.isci.2022.103873.
• Katori M, Shi S, Ode KL, Tomita Y, Ueda HR. "103,200 acceleration dataset in UK Biobank revealed a landscape of human sleep phenotypes" Proc Natl Acad Sci U S A. 2022 Mar 22;119(12):e2116729119. doi: 10.1073/pnas.2116729119.
• Glaser AK, Bishop KW, Barner LA, Susaki EA, Kubota SI, Gao G, Serafin RB, Balaram P, Turschak E, Nicovich PR, Lai H, Lucas LAG, Yi Y, Nichols EK, Huang H, Reder NP, Wilson JJ, Sivakumar R, Shamskhou E, Stoltzfus CR, Wei X, Hempton AK, Pende M, Murawala P, Dodt HU, Imaizumi T, Shendure J, Beliveau BJ, Gerner MY, Xin L, Zhao H, True LD, Reid RC, Chandrashekar J, Ueda HR, Svoboda K, Liu JTC. "A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues". Nat Methods. 2022 May;19(5):613-619. doi: 10.1038/s41592-022-01468-5.
• Nojima S, Ishida S, Terayama K, Matsumoto K, Matsui T, Tahara S, Ohshima K, Kiyokawa H, Kido K, Ukon K, Yoshida SY, Mitani TT, Doki Y, Mizushima T, Okuno Y, Susaki EA, Ueda HR, Morii E. "A Novel Three-Dimensional Imaging System Based on Polysaccharide Staining for Accurate Histopathological Diagnosis of Inflammatory Bowel Diseases" Cell Mol Gastroenterol Hepatol. 2022;14(4):905-924. doi: 10.1016/j.jcmgh.2022.07.001.
• Takahashi K, Abe K, Kubota SI, Fukatsu N, Morishita Y, Yoshimatsu Y, Hirakawa S, Kubota Y, Watabe T, Ehata S, Ueda HR, Shimamura T, Miyazono K. "An analysis modality for vascular structures combining tissue-clearing technology and topological data analysis" Nat Commun. 2022 Sep 12;13(1):5239. doi: 10.1038/s41467-022-32848-2.
• Tone D, Ode KL, Zhang Q, Fujishima H, Yamada RG, Nagashima Y, Matsumoto K, Wen Z, Yoshida SY, Mitani TT, Arisato Y, Ohno RI, Ukai-Tadenuma M, Yoshida Garçon J, Kaneko M, Shi S, Ukai H, Miyamichi K, Okada T, Sumiyama K, Kiyonari H, Ueda HR. "Distinct phosphorylation states of mammalian CaMKIIβ control the induction and maintenance of sleep" PLoS Biol. 2022 Oct 4;20(10):e3001813. doi: 10.1371/journal.pbio.3001813.
• Millius A, Yamada RG, Fujishima H, Maeda K, Standley DM, Sumiyama K, Perrin D, Ueda HR. "Circadian ribosome profiling reveals a role for the Period2 upstream open reading frame in sleep." Proc Natl Acad Sci U S A. 2023 Oct 3;120(40):e2214636120. doi: 10.1073/pnas.2214636120.
• Mitani TT, Susaki EA, Matsumoto K, Ueda HR. "Realization of cellomics to dive into the whole-body or whole-organ cell cloud" Nat Methods. 2024 Jul;21(7):1138-1142. doi: 10.1038/s41592-024-02307-5.
• Kon K, Ode KL, Mano T, Fujishima H, Takahashi RR, Tone D, Shimizu C, Shiono S, Yada S, Matsuzawa K, Yoshida SY, Yoshida Garçon J, Kaneko M, Shinohara Y, Yamada RG, Shi S, Miyamichi K, Sumiyama K, Kiyonari H, Susaki EA, Ueda HR. "Cortical parvalbumin neurons are responsible for homeostatic sleep rebound through CaMKII activation" Nat Commun. 2024 Jul 18;15(1):6054. doi: 10.1038/s41467-024-50168-5.
• Yamada RG, Matsuzawa K, Ode KL, Ueda HR. "An automated sleep staging tool based on simple statistical features of mice electroencephalography (EEG) and electromyography (EMG) data" Eur J Neurosci. 2024 Oct;60(7):5467-5486. doi: 10.1111/ejn.16465. Epub 2024 Jul 28.
• Wang Y, Cao S, Tone D, Fujishima H, Yamada RG, Ohno RI, Shi S, Matsuzawa K, Yada S, Kaneko M, Sakamoto H, Onishi T, Ukai-Tadenuma M, Ukai H, Hanashima C, Hirose K, Kiyonari H, Sumiyama K, Ode KL, Ueda HR. "Postsynaptic competition between calcineurin and PKA regulates mammalian sleep-wake cycles" Nature. 2024 Dec;636(8042):412-421. doi: 10.1038/s41586-024-08132-2.
• Matsumoto K, Harada SY, Yoshida SY, Narumi R, Mitani TT, Yada S, Sato A, Morii E, Shimizu Y, Ueda HR. "DECODE enables high-throughput mapping of antibody epitopes at single amino acid resolution", PLoS Biol. 2025 Jan 23;23(1):e3002707. doi: 10.1371/journal.pbio.3002707
• Sato TR, Ode KL, Kinoshita FL, Ueda HR. "A design principle for neuronal firing with up-down oscillation through Na+ dynamics" iScience, 2025 Jan 27;28(2):111904. doi: 10.1016/j.isci.2025.111904.
• Kinoshita FL, Yamada RG, Ode KL, Ueda HR. "A unified framework to model synaptic dynamics during the sleep-wake cycle." PLoS Biol. 2025 Jun 12;23(6):e3003198. doi: 10.1371/journal.pbio.3003198.
• Kanaya HJ, Kuwajima K, Ito Y, Shinohara Y, Okubo Y, Shiono S, Tatsuki F, Ohno RI, Ukai H, Ukai-Tadenuma M, Sumiyama K, Fujishima H, Yamada RG, Tone D, Kiyonari H, Kikuchi M, Umehara T, Murayama T, Kanemaru K, Iino M, Ode KL, Hirokawa T, Ueda HR. "Isoflurane activates the type 1 ryanodine receptor to induce anesthesia in mice." PLoS Biol. 2025 Jun 3;23(6):e3003172. doi: 10.1371/journal.pbio.3003172.

International Journals (review)

• Ode KL, Ueda HR. "Phosphorylation Hypothesis of Sleep" Front Psychol. 2020; 11: 575328. doi: 10.3389/fpsyg.2020.575328 (review)
• Minami Y, Yuan Y, Ueda HR. "Towards organism-level systems biology by next-generation genetics and whole-organ cell profiling" Biophys Rev. 2021 Nov 18;13(6):1113-1126. doi: 10.1007/s12551-021-00859-w. (review)
• Richardson DS, Guan W, Matsumoto K, Pan C, Chung K, Ertürk A, Ueda HR, Lichtman JW "Tissue clearing" Nat Rev Methods Primers. 2021;1(1):84. doi: 10.1038/s43586-021-00080-9. (review)
• Minami Y, Yuan Y, Ueda HR. "High-throughput Genetically Modified Animal Experiments Achieved by Next-generation Mammalian Genetics" J Biol Rhythms. 2022 Apr;37(2):135-151. doi: 10.1177/07487304221075002. (review)
• Wang Y, Minami Y, Ode KL, Ueda HR. "The role of calcium and CaMKII in sleep." Front Syst Neurosci. 2022 Dec 22:16:1059421. doi: 10.3389/fnsys.2022.1059421. (review)
• Chen YY, Evavold CL, Mann M, Davenport ER, McFall-Ngai M, Bienko M, Ueda HR, Tian L, Tjahjono N, Anikeeva P, Liu JG, Deans TL, Shen X. "What tool or method do you wish existed?" Cell. 2024 Aug 22;187(17):4433-4438. doi: 10.1016/j.cell.2024.07.043.
• Akiyama F, Matsumoto K, Yamashita K, Oishi A, Kitaoka T, Ueda HR. "A multiwell plate approach to increase the sample throughput during tissue clearing" Nat Protoc. 2025 Apr;20(4):967-988. doi: 10.1038/s41596-024-01080-1. (review)
• Ode KL, Ueda HR. "A bittersweet relationship between the cell cycle, circadian clock, and diurnal fluctuations in taste" Proc Natl Acad Sci U S A. 2025 Jun 24;122(25):e2510268122. doi: 10.1073/pnas.2510268122. (Commentary)

Symposium and Lectures (Eng)

Media

Note: Japanese titles are translated tentatively