NAKAOKA ShinjiAssociate Professor

Laboratory of Mathematical Biology
Research Theme
mathematical modeling and data analysis in life science
Research Keywords

mathematical biology, systems biology, bioinformatics, microbial ecology, precision medicine, multi-omics, mathematical modeling, machine learning, big data analysis

Overview of Research

In our laboratory, mathematical and statistical models are employed to work with experimental or field biologists in order to understand biological phenomena of interest, or quantitatively characterize data. Primary research target of our laboratory is to develop ecomics and ecomimetics. The former represents a type of research to investigate a given microbial community by integrating omics data on the basis of community ecology theories and methodologies. While the latter is motivated by biomimetics to represent a type of study to extract the essence of community assembly rules from existing microbial ecosystem to construct a new artificial microbial community. Other related topics in our laboratory include omics data analysis in precision medicine or the development of novel mathematical tools for data analysis in life sciences.



Related traditional research fields of mathematical biology include mathematics, physics, and chemistry. Recent advance and popularization of measurement enable us to integrate quantitative data and associated analysis techniques to develop a data-driven approach in mathematical biology. We welcome anyone who is interested in mathematical modeling, numerical simulation or data analysis. There is essentially no restriction for past study experiences and skills, though elementary knowledge about mathematics, informatics, and molecular biology will be required to learn after joining our lab.

Representative Publications

Kazuhito Miura, Yutaka Watanabe, Haruhisa Baba, Kimiya Ozaki, Takae Matsushita, Miyako Kondoh, Kazutaka Okada, Shinji Nakaoka, Katsuhiko Ogasawara, Teppei Suzuki, Hiroshi Saito, Takashi Kimura, Akiko Tamakoshi, Yutaka Yamazaki,COVID-19-related stress, exercise, and oral health-related quality of life among community-dwelling older adults who participated in the CHEER Iwamizawa project, Japan, Scientific reports 12(1) 20347-20347 2022/11/27.

Ryuichi Kumata, Shoya Iwanami, Katrina B Mar, Yusuke Kakizoe, Naoko Misawa, Shinji Nakaoka, Yoshio Koyanagi, Alan S Perelson, John W Schoggins, Shingo Iwami, Kei Sato,Antithetic effect of interferon-α on cell-free and cell-to-cell HIV-1 infection, PLoS computational biology 18(4) e1010053 2022/04.

Haruhisa Baba, Yutaka Watanabe, Kazuhito Miura, Kimiya Ozaki, Takae Matsushita, Miyako Kondoh, Kazutaka Okada, Akira Hasebe, Tokiyoshi Ayabe, Kiminori Nakamura, Shinji Nakaoka, Katsuhiko Ogasawara, Teppei Suzuki, Hiroshi Saito, Takashi Kimura, Akiko Tamakoshi, Yutaka Yamazaki,Oral frailty and carriage of oral Candida in community-dwelling older adults (Check-up to discover Health with Energy for senior Residents in Iwamizawa; CHEER Iwamizawa), Gerodontology 39(1) 49-58 2022/3.

Kenta Suzuki, Shinji Nakaoka, Shinji Fukuda, Hiroshi Masuya, Energy landscape analysis elucidates the multistability of ecological communities across environmental gradients, ECOLOGICAL MONOGRAPHS 91(3) 2021/8

Shoya Iwanami, Keisuke Ejima, Kwang Su Kim, Koji Noshita, Yasuhisa Fujita, Taiga Miyazaki, Shigeru Kohno, Yoshitsugu Miyazaki, Shimpei Morimoto, Shinji Nakaoka, Yoshiki Koizumi, Yusuke Asai, Kazuyuki Aihara, Koichi Watashi, Robin N Thompson, Kenji Shibuya, Katsuhito Fujiu, Alan S Perelson, Shingo Iwami, Takaji Wakita, Detection of significant antiviral drug effects on COVID-19 with reasonable sample sizes in randomized controlled trials: A modeling study, PLoS medicine 18(7) e1003660 2021/7.



<Office Hour>
– Time: Anytime during the lecture period
– Place: Science Bldg. No.2, 7F, #2-706
Please contact in advance by E-mail.
E-mail: snakaoka[at]