The development of modern life sciences would not be complete without mice. As the most widely used mammalian animal model, mouse research contributes to the understanding of biological phenomena through the use of multiple tools such as gene editing, optogenetics, and various imaging techniques. Our laboratory aims to identify the smallest molecular and neuroscientific unit responsible for the sleep-wake cycle in mice and elucidate its conserved minimal unit by comparing it with other species. Keywords: synaptic plasticity, gene editing, electrophysiology, optogenetics, epigenetics


Modern life science, which has developed around mouse research, has reached a turning point. As of 2023, useful tools that were previously limited to mice research can now be applied to other organisms. As Dr. August Krogh stated in Krogh's Law: "For such a large number of problems, there will be some animal of choice, or a few such animals, on which it can be most conveniently studied.", it is now possible to choose the right species for the questions we have fostered. In our laboratory, we focus on ants, which are social insects, and study how genetically homogeneous ants can acquire phenotypic diversity. Keywords: sociality, gene editing, electrophysiology, mass spectrometry, epigenetics

Data science

Data science and mathematical modeling play an important role in the complex system of life, which consists of trillions of cells with billions of base pairs and their interactions. In our laboratory, we aim to unravel the underlying laws of complex biological phenomena by analyzing multimodal data and constructing mathematical models. Keywords: machine learning, differential equations, time series analysis, bioinformatics

Shoi Shi, Ph.D.
Lab member
Ph.D. in Medicine (The University of Tokyo)
Assistant Professor, School of Medicine, The University of Tokyo
Principal Investigator, International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba
Ph.D. student
Undergrad. student


Selected publications. For more details, go to here. *Equally contributed. **Corresponding.
Yamada T and **Shi S, Estimating infection-related human mobility networks based on time series data of COVID-19 infection in Japan. Applied Sciences, 12(18), 9236 (2022)
*Katori M, *Shi S, Ode KL, Tomita Y, Ueda HR. The 103,200-arm acceleration dataset in the UK Biobank revealed a landscape of human sleep phenotypes. Proc. Natl. Acad. Sci. U.S.A.119(12) e2116729119 (2022)
*Yamada T, *Shi S, Ueda HR. A Design principle of Spindle Oscillations in Mammalian Sleep. iScience 25(3), 103873 (2022)
*Ode KL, *Shi S, *Katori M, Mitsui K, Takahashi S, Oguchi R, Aoki D, Ueda HR. ACCEL: a jerk-based algorithm for the accurate classification of sleep–wake states from arm acceleration. iScience 25(2), 103727 (2022)
*Eguchi A, *Yoneoka D, *Shi S, *Tanoue Y, *Kawashima T, *Nomura S, *Matsuura K, *Makiyama K, *Uryu S, Sawada M, Kawamura Y, Takayanagi S, Gilmour S, Miyata H. Effect of emergency declaration on mental health during the COVID-19 pandemic in Japan: A social network service-based difference-in differences approach. Science Progress 104(3), 1-9 (2021)
*Yoneoka D, *Shi S, *Nomura S, *Tanoue Y, *Kawashima T, *Eguchi A, Matsuura K, Makiyama K, Uryu S, Ejima K, Sakamoto H, Taniguchi T, Kunishima H, Gilmour S, Nishiura H, Miyata H. Assessing the regional impact of the Japan’s COVID-19 state of emergency declaration: a population-level observational study using social networking services. BMJ Open. 15;11(2) (2021)
*Kawashima T, *Nomura S, *Tanoue Y, *Yoneoka D, *Eguchi A, *Shi S, Miyata H. The relationship between fever rate and telework implementation as a social distancing measure against the COVID-19 pandemic in Japan. Public Health. 192, 12-14 (2021)
*Eguchi A, *Yoneoka D, *Shi S, *Tanoue Y, *Kawashima T, *Nomura S, Matsuura K, Makiyama K, Ejima K, Gilmour S, Nishiura H, Miyata H. Trend change of transmission route of COVID-19 related symptom in Japan. Public Health. 187, 157-160 (2020)
*Yoneoka D, *Tanoue Y, *Kawashima T, *Nomura S, *Shi S, Eguchi A, Ejima K, Taniguchi T, Sakamoto H, Kunishima H, Gilmour S, Nishiura H, Miyata H. A large-scale epidemiological monitoring of the COVID-19 in Tokyo. Lancet Reg. Health West. Pac. 3, 100016 (2020)
*Nomura S, *Yoneoka D, *Shi S, *Tanoue Y, *Kawashim T, *Eguchi A, Ejima K, Taniguchi T, Sakamoto H, Kunishima H, Gilmour S, Nishiura H, Miyata H. How Japan's state of emergency declaration for COVID-19 worked against the risk of infection: an assessment of the non-specific symptoms of 227,898 users of a social networking service. Lancet Reg. Health West. Pac. 1, 100011 (2020)
Shi S, Tanaka S, Ueno R, Gilmour S, Tanoue Y, Kawashima T, Nomura S, Miyata H, Yoneoka D. Impact of travel restrictions on importation of novel coronavirus infection: An effective distance approach. Bull World Health Organ. 98, 518-529 (2020)
Shi S, Millius A, Ueda HR. Genes and Ion Channels in the Circadian and Homeostatic Regulation of Sleep. Handbook of Behavioral Neuroscience. 30, 181-194 (2019)
*Yoshida K, *Shi S, Ukai-Tadenuma M, Fujishima H, Ohno RI, and Ueda HR. Leak potassium channels regulate sleep duration. Proc. Natl. Acad. Sci. U.S.A. 115 (40), E9459-E9468 (2018)
Shi S and Ueda HR. Ca2+‐Dependent Hyperpolarization Pathways in Sleep Homeostasis and Mental Disorders.BioEssays News Rev Mol Cell Dev Biol. 40 (2018)
*Tatsuki F, *Sunagawa GA, *Shi S, *Susaki EA, *Yukinaga H, *Perrin D, Sumiyama K, Ukai-Tadenuma M, Fujishima H, Ohno RI, Tone D, Ode KL, Matsumoto K, Ueda HR. Involvement of Ca2+ - Dependent Hyperpolarization in Sleep Duration in Mammals. Neuron. 90, 70-85 (2016)
Shi S, Seki S, Matano T, Yamamoto H. IL-21-producer CD4+ T cell kinetics during primary simian immunodeficiency virus infection. Microbes and Infection. 15(10-11), 697-707 (2013)


Shi Laboratory
IIIS, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
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