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Construction of state transition model based on energy landscape

Research Project

Project/Area Number 21K19813
Research Category

Grant-in-Aid for Challenging Research (Exploratory)

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 62:Applied informatics and related fields
Research InstitutionHokkaido University

Principal Investigator

Shinji Nakaoka  北海道大学, 先端生命科学研究院, 准教授 (30512040)

Project Period (FY) 2021-07-09 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2023: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
Fiscal Year 2022: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Fiscal Year 2021: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Keywordsエネルギーランドスケープ解析 / データ駆動型数理モデル / 発症ロードマップ / オミクスデータ / 擬似時間再構成法
Outline of Research at the Start

エネルギー地形は、複数のとり得る状態をエネルギーの高低差に基づいて地形図として表現する方法であり、エネルギー地形の概念は、生命医科学分野において、細胞分化や疾患発症に関わるデータ分析に幅広く利用されている。しかしながら、現在しられているエネルギー地形を活用したデータ分析手法は、細胞や個体の状態を静的に把握することが目的であり、細胞分化・発症過程のように動的な遷移の軌跡を推定するには至っていない。そこで本研究では、エネルギー地形に基づくデータ駆動型状態遷移モデルを構築することで、細胞分化や発症のような状態遷移を伴う過程において、数学理論に基づいた新しいデータ分析方法を提供する。

Outline of Final Research Achievements

The concept of energy landscapes has been recently utilized in life sciences for data analysis related to cell differentiation and disease onset. However, it has not been applied to estimate the trajectories of dynamic transitions such as cell differentiation and disease onset progression. To address this issue, we aimed to develop a new data analysis method and its applications to understand state transitions like cell differentiation and disease onset. The research outcomes consisted mainly of seven publications, which reported on the development and application of this novel data analysis method for analyzing dynamic state transitions in different biological processes.

Academic Significance and Societal Importance of the Research Achievements

本研究では、エネルギー地形に基づくデータ駆動型状態遷移モデルや数理モデルを構築することで、細胞分化や発症のような状態遷移を伴う過程において、データ分析方法の開発と応用を行った。腸内細菌叢の関わる乳児の健康、発がんや HIV-1 といった感染症の課題に対して、データから発症に関与が疑われる因子の推定やその性質を定量的に理解することにつながった。数理科学を生命科学に応用するという意味での学術的意義に加えて、研究を主に疾患を理解するという社会課題に応用した点に本研究の意義がある。

Report

(4 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Research-status Report
  • 2021 Research-status Report
  • Research Products

    (16 results)

All 2024 2023 2022 2021

All Journal Article (9 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 9 results,  Open Access: 7 results) Presentation (5 results) (of which Int'l Joint Research: 1 results,  Invited: 5 results) Book (2 results)

  • [Journal Article] Multiscale modeling of HBV infection integrating intra- and intercellular viral propagation to analyze extracellular viral markers2024

    • Author(s)
      Kitagawa Kosaku、Kim Kwang Su、Iwamoto Masashi、Hayashi Sanae、Park Hyeongki、Nishiyama Takara、Nakamura Naotoshi、Fujita Yasuhisa、Nakaoka Shinji、Aihara Kazuyuki、Perelson Alan S.、Allweiss Lena、Dandri Maura、Watashi Koichi、Tanaka Yasuhito、Iwami Shingo
    • Journal Title

      PLOS Computational Biology

      Volume: 20 Issue: 3 Pages: 1011238-1011238

    • DOI

      10.1371/journal.pcbi.1011238

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Disentangling the growth curve of microbial culture2023

    • Author(s)
      Kumakura Daiki、Yamaguchi Ryo、Hara Akane、Nakaoka Shinji
    • Journal Title

      Journal of Theoretical Biology

      Volume: 573 Pages: 111597-111597

    • DOI

      10.1016/j.jtbi.2023.111597

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Anti‐HTLV‐1 immunity combined with proviral load as predictive biomarkers for adult T‐cell leukemia‐lymphoma2023

    • Author(s)
      Yamada Asami、Yasunaga Jun‐ichirou、Liang Lihan、Zhang Wenyi、Sunagawa Junya、Nakaoka Shinji、Iwami Shingo、Kogure Yasunori、Ito Yuta、Kataoka Keisuke、Nakagawa Masanori、Iwanaga Masako、Utsunomiya Atae、Koh Ki‐Ryang、Watanabe Toshiki、Nosaka Kisato、Matsuoka Masao
    • Journal Title

      Cancer Science

      Volume: 115 Issue: 1 Pages: 310-320

    • DOI

      10.1111/cas.15997

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Antithetic effect of interferon-α on cell-free and cell-to-cell HIV-1 infection.2022

    • Author(s)
      Kumata R, Iwanami S, Mar KB, Kakizoe Y, Misawa N, Nakaoka S, Koyanagi Y, Perelson A, Schoggins J, Iwami S, Sato K
    • Journal Title

      PLoS Computational Biology

      Volume: 18 Issue: 4 Pages: 1010053-1010053

    • DOI

      10.1371/journal.pcbi.1010053

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Evolving neural networks through bio-inspired parent selection in dynamic environments2022

    • Author(s)
      Sunagawa Junya、Yamaguchi Ryo、Nakaoka Shinji
    • Journal Title

      Biosystems

      Volume: 218 Pages: 104686-104686

    • DOI

      10.1016/j.biosystems.2022.104686

    • Related Report
      2022 Research-status Report
    • Peer Reviewed
  • [Journal Article] Analysis of the Pancreatic Cancer Microbiome Using Endoscopic Ultrasound-Guided Fine-Needle Aspiration-Derived Samples2022

    • Author(s)
      Nakano S, Kawamoto Y, Komatsu Y, Saito R, Ito K, Yamamura T, Harada K, Yuki S, Kawakubo K, Sugiura R, Kato S, Hirata K, Hirata H, Nakajima M, Furukawa R, Takishin Y, Nagai K, Yokota I, Ota KH, Nakaoka S, Kuwatani M, Sakamoto N.
    • Journal Title

      Pancreas

      Volume: 51 Issue: 4 Pages: 351-357

    • DOI

      10.1097/mpa.0000000000002028

    • Related Report
      2022 Research-status Report
    • Peer Reviewed
  • [Journal Article] Early dynamics of chronic myeloid leukemia on nilotinib predicts deep molecular response2022

    • Author(s)
      Okamoto Yuji、Hirano Mitsuhito、Morino Kai、Kajita Masashi K.、Nakaoka Shinji et al
    • Journal Title

      npj Systems Biology and Applications

      Volume: 8 Issue: 1

    • DOI

      10.1038/s41540-022-00248-3

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Dynamic Associations of Milk Components With the Infant Gut Microbiome and Fecal Metabolites in a Mother-Infant Model by Microbiome, NMR Metabolomic, and Time-Series Clustering Analyses2022

    • Author(s)
      Komatsu Yosuke、Kumakura Daiki、Seto Namiko、Izumi Hirohisa、Takeda Yasuhiro、Ohnishi Yuki、Nakaoka Shinji、Aizawa Tomoyasu
    • Journal Title

      Frontiers in Nutrition

      Volume: 8

    • DOI

      10.3389/fnut.2021.813690

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Chemical-Mediated Microbial Interactions Can Reduce the Effectiveness of Time-Series-Based Inference of Ecological Interaction Networks2022

    • Author(s)
      Suzuki Kenta、Abe Masato S.、Kumakura Daiki、Nakaoka Shinji、Fujiwara Fuki、Miyamoto Hirokuni、Nakaguma Teruno、Okada Mashiro、Sakurai Kengo、Shimizu Shohei、Iwata Hiroyoshi、Masuya Hiroshi、Nihei Naoto、Ichihashi Yasunori
    • Journal Title

      International Journal of Environmental Research and Public Health

      Volume: 19 Issue: 3 Pages: 1228-1228

    • DOI

      10.3390/ijerph19031228

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] 生成AIを用いた論文要約システム2023

    • Author(s)
      中岡慎治
    • Organizer
      IIBMP2023
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] Application of energy landscape analysis method to microbiome data2023

    • Author(s)
      Shinji Nakaoka
    • Organizer
      The 8th CIJK International Conference on Mathematical and Theoretical Biology
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 数理・情報科学手法を用いた 食習慣と腸内細菌叢調節因子の探索2023

    • Author(s)
      中岡慎治
    • Organizer
      日本栄養・食糧学会シンポジウム
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 疑似時間再構成法の腸内細菌叢データへの適用2022

    • Author(s)
      中岡 慎治
    • Organizer
      日本微生物生態学会 第35回大会
    • Related Report
      2022 Research-status Report
    • Invited
  • [Presentation] 数理科学を用いた腸内環境のデザインと保全にむけて2022

    • Author(s)
      中岡 慎治
    • Organizer
      腸内デザイン学会
    • Related Report
      2022 Research-status Report
    • Invited
  • [Book] ウイルス感染の数理モデルとシミュレーション2024

    • Author(s)
      岩見 真吾 著・ 中岡 慎治 著・ 岩波 翔也 著
    • Total Pages
      304
    • Publisher
      共立出版
    • ISBN
      9784320115538
    • Related Report
      2023 Annual Research Report
  • [Book] Exploring similarity between embedding dimension of time-series data and flows of an ecological population model2021

    • Author(s)
      Daiki Kumakura and Shinji Nakaoka
    • Total Pages
      10
    • Publisher
      Springer
    • Related Report
      2021 Research-status Report

URL: 

Published: 2021-07-13   Modified: 2025-01-30  

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