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

Shinji Nakaoka, Mathematical description for invasibility threshold and persistence of pathogenic bacterial species, Proc. of International Symposium on Nonlinear Theory and Its Applications, NOLTA2018.

Mohamed Mahgoub, Jun-ichirou Yasunaga, Shingo Iwami, Shinji Nakaoka, Yoshiki Koizumi, Kazuya Shimura, and Masao Matsuoka, Sporadic on/off switching of HTLV-1 Tax expression is crucial to maintain the whole population of virus-induced leukemic cells, PNAS, 2018 E1269-E1278.

Eri Yamada, Shinji Nakaoka, Lukas Klein, Elisabeth Reith, Simon Langer, Kristina Hopfensperger, Shingo Iwami, Gideon Schreiber, Frank Kirchhoff, Yoshio Koyanagi, Daniel Sauter and Kei Sato, Human-specific adaptations in Vpu conferring anti-tetherin activity are critical for efficient early HIV-1 replication in vivo, Cell Host and Microbe, (2018) Volume 23, Issue 1, 110-120.e7.

Hirokazu Toju, Kabir G. Peay, Masato Yamamichi, Kazuhiko Narisawa, Kei Hiruma, Ken Naito, Shinji Fukuda, Masayuki Ushio, Shinji Nakaoka, Yusuke Onoda, Kentaro Yoshida, Klaus Schlaeppi, Yang Bai, Ryo Sugiura, Yasunori Ichihashi, Kiwamu Minamisawa, E. Toby Kiers, Core microbiomes for sustainable agroecosystems, Nature plant, Volume 4, 247–257 (2018).

Yuki Goshima, Shinji Nakaoka, Kazuteru Ohashi, Hisashi Sakamaki, Kazuko Shibuya, Akira Shibuya, A mathematical model for dynamics of soluble form of DNAM-1 as a biomarker for graft-versus-host disease, PLoS ONE, 15(2):e0228508 (2020).