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.
- School of Science:
Biological Science course (Macromolecular Functions), Core Laboratories
- Graduate School of Life Science:
Division of Life Science, Transdisciplinary Life Science Course, Bioinformation and Molecular Sciences
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
– Time: Anytime during the lecture period
– Place: Science Bldg. No.2, 7F, #2-706
Please contact in advance by E-mail.
- Faculty of Advanced Life Science, Department of Advanced Transdisciplinary Sciences, Tissue and Polymer Sciences
- Frontier Research Center for Advanced Material and Life Science, Advanced Facility Unit