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Untangling species-environment interactions using metabolic networks: theory and its applications

Research Project

Project/Area Number 25700030
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypePartial Multi-year Fund
Research Field Life / Health / Medical informatics
Research InstitutionKyushu Institute of Technology

Principal Investigator

Takemoto Kazuhiro  九州工業大学, 大学院情報工学研究院, 准教授 (40512356)

Project Period (FY) 2013-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥21,060,000 (Direct Cost: ¥16,200,000、Indirect Cost: ¥4,860,000)
Fiscal Year 2016: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2015: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2014: ¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000)
Fiscal Year 2013: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
Keywordsネットワーク科学 / 代謝ネットワーク / 数値モデル / 生態学 / 進化 / ネットワーク理論 / 数理モデル / 微生物生態
Outline of Final Research Achievements

Species-environment interactions are important in environmental and medical sciences; however, previous methods for estimating the interactions have several limitations. Thus, I focused on the importance of metabolite interactions in microbial ecosystems, and proposed a novel method based on metabolic networks. The proposed method is useful for understating ecosystems at the molecular level. A number of interesting findings were obtained from the applications of the proposed method. These results promise to advance medical diagnosis and environment assessment based on genome information.

Report

(5 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • Research Products

    (41 results)

All 2017 2016 2015 2014 2013 Other

All Journal Article (20 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 18 results,  Open Access: 9 results,  Acknowledgement Compliant: 11 results) Presentation (15 results) (of which Int'l Joint Research: 5 results,  Invited: 4 results) Remarks (6 results)

  • [Journal Article] Data integration aids understanding of butterfly-host plant networks2017

    • Author(s)
      Muto-Fujita A, Takemoto K, Kanaya S, Nakazato T, Tokimatsu T, Matsumoto N, Kono M, Chubach, Y, Ozaki K, Kotera M
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 43368-43368

    • DOI

      10.1038/srep43368

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Exosomes in mammals with greater habitat variability contain more proteins and RNAs2017

    • Author(s)
      Takemoto K, Imoto M
    • Journal Title

      Royal Society Open Science

      Volume: 4 Issue: 4 Pages: 170162-170162

    • DOI

      10.1098/rsos.170162

    • NAID

      120006649513

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] 代謝ネットワークを用いた微生物生態系の可視化2017

    • Author(s)
      竹本和広
    • Journal Title

      実験医学増刊

      Volume: 35 Pages: 211-214

    • Related Report
      2016 Annual Research Report
  • [Journal Article] Human impacts and climate change influence nestedness and modularity in food-web and mutualistic networks2016

    • Author(s)
      Takemoto K, Kajihara K
    • Journal Title

      PLoS ONE

      Volume: 11 Issue: 6 Pages: e0157929-e0157929

    • DOI

      10.1371/journal.pone.0157929

    • NAID

      120006649514

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Analysis of the effect of degree correlation on the size of minimum dominating sets in complex networks2016

    • Author(s)
      Takemoto K, Akutsu T
    • Journal Title

      PLoS ONE

      Volume: 11 Issue: 6 Pages: e0157868-e0157868

    • DOI

      10.1371/journal.pone.0157868

    • NAID

      120005819482

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Importance of metabolic rate to the relationship between the number of genes in a functional category and body size in Peto's paradox for cancer2016

    • Author(s)
      Takemoto K, Ii M, Nishizuka SS
    • Journal Title

      Royal Society Open Science

      Volume: 3 Issue: 9 Pages: 160267-160267

    • DOI

      10.1098/rsos.160267

    • NAID

      120006649512

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] An automated system for evaluation of the potential functionome: MAPLE version 2.1.02016

    • Author(s)
      Takami H, Tanigichi T, Arai W, Takemoto K, Moriya Y, Goto S
    • Journal Title

      DNA Research

      Volume: 23 Issue: 5 Pages: 467-475

    • DOI

      10.1093/dnares/dsw030

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Habitat variability does not generally promote metabolic network modularity in flies and mammals2016

    • Author(s)
      Takemoto K
    • Journal Title

      Biosystems

      Volume: 139 Pages: 46-54

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Systematic Protein Level Regulation via Degradation Machinery Induced by Genotoxic Drugs2016

    • Author(s)
      Kume K, Ishida K, Ikeda M, Takemoto K, Shimura T, Young L, Nishizuka SS.
    • Journal Title

      J Proteome Res

      Volume: 15 Issue: 1 Pages: 205-15

    • DOI

      10.1021/acs.jproteome.5b00759

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] The proportion of genes in a functional category is linked to mass-specific metabolic rate and lifespan2015

    • Author(s)
      Takemoto K, Kawakami Y
    • Journal Title

      Scientific Reports

      Volume: 5 Issue: 1 Pages: 10008-10008

    • DOI

      10.1038/srep10008

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Functional classification of uncultured “Candidatus Caldiarchaeum subterraneum” using the MAPLE system2015

    • Author(s)
      Hideto Takami, Wataru Arai, Kazuhiro Takemoto, Ikuo Uchiyama, Takeaki Taniguchi
    • Journal Title

      PLoS ONE

      Volume: 10 Issue: 7 Pages: e0132994-e0132994

    • DOI

      10.1371/journal.pone.0132994

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Heterogeneity of cells may explain allometric scaling of metabolic rate2015

    • Author(s)
      Takemoto K
    • Journal Title

      Biosystems

      Volume: 130 Pages: 11-16

    • DOI

      10.1016/j.biosystems.2015.02.003

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Climatic seasonality may affect ecological network structure: Food webs and mutualistic networks2014

    • Author(s)
      Takemoto K, Kanamaru S, Feng W
    • Journal Title

      Biosystems

      Volume: 121 Pages: 29-37

    • DOI

      10.1016/j.biosystems.2014.06.002

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Heterogeneity in ecological mutualistic networks dominantly determines community stability2014

    • Author(s)
      Feng W, Takemoto K
    • Journal Title

      Scientific Reports (Nature Publishing Group)

      Volume: 4 Issue: 1 Pages: 5912-5912

    • DOI

      10.1038/srep05912

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Metabolic networks are almost nonfractal: A comprehensive evaluation2014

    • Author(s)
      Takemoto K
    • Journal Title

      Physical Review E

      Volume: 90 Issue: 2 Pages: 022802-022802

    • DOI

      10.1103/physreve.90.022802

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] 代謝ネットワークのロバストネス2014

    • Author(s)
      竹本和広
    • Journal Title

      細胞工学

      Volume: 33 Pages: 31-36

    • Related Report
      2013 Annual Research Report
  • [Journal Article] 代謝ネットワークの数理モデルとその応用2014

    • Author(s)
      竹本和広
    • Journal Title

      応用数理

      Volume: 24 Pages: 10-18

    • NAID

      110009807320

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Limited influence of oxygen on the evolution of chemical diversity in metabolic networks2013

    • Author(s)
      Takemoto K, Yoshitake I
    • Journal Title

      Metabolites

      Volume: 3 Issue: 4 Pages: 979-992

    • DOI

      10.3390/metabo3040979

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Theoretical estimation of metabolic network robustness against multiple reaction knockouts using branching process approximation2013

    • Author(s)
      Takemoto K, Tamura T, Akutsu T
    • Journal Title

      Physica A

      Volume: 392 Issue: 21 Pages: 5525-5535

    • DOI

      10.1016/j.physa.2013.07.003

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Modular organization of cancer signaling networks is associated with patient survivability2013

    • Author(s)
      Takemoto K. Kihara K
    • Journal Title

      Biosystems

      Volume: 113 Issue: 3 Pages: 149-154

    • DOI

      10.1016/j.biosystems.2013.06.003

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Presentation] Network complexity, disease and health2017

    • Author(s)
      Takemoto K
    • Organizer
      The 2nd International Symposium on BioComplexity (ISBC2)
    • Place of Presentation
      Beppu
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 何が代謝ネットワークの進化を促進したのか2017

    • Author(s)
      竹本和広
    • Organizer
      生命の起源および進化学会第42回講演会
    • Place of Presentation
      九州工業大学飯塚キャンパス
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Impacts of Climate Change and Human Activity on Nestedness and Modularity of Food Webs and Mutualistic Networks2016

    • Author(s)
      Takemoto K, Kajihara K
    • Organizer
      NetSci 2016: International School and Conference on Networks Science
    • Place of Presentation
      The K-Hotel Seoul, Korea
    • Year and Date
      2016-05-30
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 遺伝子数-体サイズ関係における代謝速度の重要性:がん発症率のパラドクスと関連して2016

    • Author(s)
      竹本和広, 伊井将人, 西塚哲
    • Organizer
      第4回がんと代謝研究会
    • Place of Presentation
      かごしま県民交流センター
    • Related Report
      2016 Annual Research Report
  • [Presentation] Environmental change influences ecological network structure on a global scale2016

    • Author(s)
      Takemoto K
    • Organizer
      Conference on Complex Systems (CCS) 2016
    • Place of Presentation
      Beurs Van Berlage, Amsterdam
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 生体分子ネットワークと環境相互作用:がんロバスト性と生息域変動性を例にして2015

    • Author(s)
      竹本和広
    • Organizer
      平成27年度JSBi生命システム理論研究会 (AMED再生医療実現ネットワーク併催) ~細胞システムの機能獲得と進化のメカニズム~
    • Place of Presentation
      東京医科歯科大学
    • Year and Date
      2015-11-27
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Relative abundance of oxic reaction genes may determine metabolic rate and lifespan2015

    • Author(s)
      Takemoto K, Kawakami Y
    • Organizer
      Conference on Complex Systems (CCS) '15
    • Place of Presentation
      Tempe, Arizona, USA
    • Year and Date
      2015-09-26
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 代謝速度や最大寿命はゲノムデータから推定可能か.2015

    • Author(s)
      竹本和広, 川上祐子
    • Organizer
      NGS現場の会 第四回研究会
    • Place of Presentation
      つくば国際会議場
    • Year and Date
      2015-07-01
    • Related Report
      2015 Annual Research Report
  • [Presentation] Heterogeneity is the main factor in determining the stability of ecological mutualistic networks.2015

    • Author(s)
      Feng W, Takemoto K
    • Organizer
      NetSci 2015: The International School and Conference on Network Science
    • Place of Presentation
      Zaragoza, Spain
    • Year and Date
      2015-06-01
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] がんシグナルネットワークのモジュール性と患者生存率の関連.2014

    • Author(s)
      竹本和広
    • Organizer
      生命医薬情報学連合大会2014年大会
    • Place of Presentation
      仙台国際センター
    • Year and Date
      2014-10-02 – 2014-10-04
    • Related Report
      2014 Annual Research Report
  • [Presentation] ネットワーク理論から捉える代謝・生態システムのロバストネス2014

    • Author(s)
      竹本和広
    • Organizer
      豊田理化学研究所・特定課題研究「制御・情報理論による生物システムのロバストネス解析と設計」第1回講演会
    • Place of Presentation
      東京大学本郷キャンパス
    • Year and Date
      2014-09-18
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] On the interaction between environments and metabolic network structure: in the light of modularity2013

    • Author(s)
      Takemoto K
    • Organizer
      Metabolic Pathway Analysis 2013
    • Place of Presentation
      Corpus Christi College, Oxford, UK
    • Related Report
      2013 Annual Research Report
  • [Presentation] Association between modular organization of cancer signaling networks and patient survivability2013

    • Author(s)
      Takemoto K, Kihara K
    • Organizer
      The 24th International Conference on Genome Informatics (GIW2013)
    • Place of Presentation
      Matrix, 30 Biopolis Street, Singapore
    • Related Report
      2013 Annual Research Report
  • [Presentation] Estimating Metabolic Network Robustness Against Multiple Reaction Knockouts Using Branching Process Approximation2013

    • Author(s)
      Takemoto K, Tamura T, Akutsu T
    • Organizer
      International Workshop on Phase Transition, Critical Phenomena and Related Topics in Complex Networks
    • Place of Presentation
      Hokkaido University
    • Related Report
      2013 Annual Research Report
  • [Presentation] Oxygen exerts limited influence on the chemical diversity of metabolic pathways2013

    • Author(s)
      Takemoto K, Yoshitake I
    • Organizer
      The 14th International Conference on Systems Biology (ICSB2013)
    • Place of Presentation
      Tivoli Congress Center, Copenhagen, DK
    • Related Report
      2013 Annual Research Report
  • [Remarks] 研究代表者の業績リスト

    • URL

      https://sites.google.com/site/kztakemoto/presentation

    • Related Report
      2016 Annual Research Report
  • [Remarks] ECOSMOS software

    • URL

      http://takemoto08.bio.kyutech.ac.jp/ecosmos-lite/

    • Related Report
      2016 Annual Research Report
  • [Remarks] MIPMET database

    • URL

      http://takemoto08.bio.kyutech.ac.jp/mipmet/

    • Related Report
      2016 Annual Research Report
  • [Remarks] 研究代表者の業績リスト

    • URL

      https://sites.google.com/site/kztakemoto/publication

    • Related Report
      2015 Annual Research Report
  • [Remarks] 竹本和広の業績リスト

    • URL

      https://sites.google.com/site/kztakemoto/publication

    • Related Report
      2014 Annual Research Report
  • [Remarks] 竹本和広の研究業績リスト

    • URL

      https://sites.google.com/site/kztakemoto/publication

    • Related Report
      2013 Annual Research Report

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Published: 2013-05-21   Modified: 2019-07-29  

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