Staff

NAKAOKA ShinjiAssociate Professor

Laboratory
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.

Charge

Message

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

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.

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).

Shoya Iwanami, Kosaku Kitagawa, Hirofumi Ohashi, Yusuke Asai, Kaho Shionoya, Wakana Saso, Kazane Nishioka, Hisashi Inaba, Shinji Nakaoka, Takaji Wakita, Odo Diekmann, Shingo Iwami, Koichi Watashi, Should a viral genome stay in the host cell or leave? A quantitative dynamics study of how hepatitis C virus deals with this dilemma, PLoS biology 18(7), e300056 2020

Hirofumi Aso, Shumpei Nagaoka, Eiryo Kawakami, Jumpei Ito, Saiful Islam, Benjy Jek Yang Tan, Shinji Nakaoka, Koichi Ashizaki, Katsuyuki Shiroguchi, Yutaka Suzuki, Yorifumi Satou, Yoshio Koyanagi, Kei Sato, Multiomics investigation revealing the characteristics of HIV-1-infected cells in vivo Cell Reports 32(2), 107887 2020

Pedro Costa del Amo, Bisrat Debebe, Milad Razavi-Mohseni, Shinji Nakaoka, Andrew Worth, Diana Wallace, Peter Beverley, Derek Macallan, Becca Asquith, The rules of human T cell fate in vivo, Frontiers in immunology 11, 573 2020

Refer to HOKKAIDO UNIVERSITY RESEARCHERS DIRECTORY
（https://researchers.general.hokudai.ac.jp/profile/en.bPdQtN0vP5FD9WzOb2syHw==.html）

Note

<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]sci.hokudai.ac.jp

Affiliation