• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Bayesian modeling for analyzing, integrating and understanding of intracellular metabolic shifts

Research Project

Project/Area Number 15H05325
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypeSingle-year Grants
Research Field Life / Health / Medical informatics
Research InstitutionNagoya University

Principal Investigator

Shimamura Teppei  名古屋大学, 医学系研究科, 特任准教授 (00623943)

Research Collaborator OSAWA Tsuyoshi  
Project Period (FY) 2015-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥15,730,000 (Direct Cost: ¥12,100,000、Indirect Cost: ¥3,630,000)
Fiscal Year 2018: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Fiscal Year 2017: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2016: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2015: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Keywords代謝ネットワーク / システム生物学 / ネットワーク解析 / 代謝シフト / マルチオミクス / 生体生命情報学 / バイオインフォマティクス
Outline of Final Research Achievements

In this research, we developed a integrated Bayesian approach for multi omics data in order to analyze, integrate, and understand intracellular metabolic shifts by estimating hierarchical cross-sectional metabolic flow networks with high prediction accuracy. We tried to apply to drug elucidation of energy metabolism in metabolic disorders and cancer, disease diagnosis, and search for various disease markers. As a result, we obtained the following results. (1) We clarified the metabolic shift for cancer growth in harsh environments, and (2) we discovered that the metabolic regulatory protein corresponding to the malignant transformation of the tumor in the acidic environment contributes.

Academic Significance and Societal Importance of the Research Achievements

本研究課題は、本来多階層である情報を一部の分子のみ、あるいは1つの階層のみに着目して解析することで生じる情報損失を回避し、従来型アプローチの限界を克服することを目的としている。このための数理モデルの構築、推測、評価に関する一連の研究を確固たる理論基盤の上で実施することが本研究課題の学術的特色である。
本研究が完遂されることで、分子生物学的アプローチだけでこれまで得ることの出来なかった新しい知見が得られる可能性は極めて高く、多因子疾患の分子病態解明や新規薬剤標的候補の合理的スクリーニングなど社会的ニーズの高い課題の解決に寄与することが期待されるため、本研究課題を推進する意義は大きい。

Report

(5 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • Research Products

    (40 results)

All 2019 2018 2017 2016 2015

All Journal Article (27 results) (of which Int'l Joint Research: 14 results,  Peer Reviewed: 27 results,  Open Access: 21 results,  Acknowledgement Compliant: 3 results) Presentation (13 results) (of which Int'l Joint Research: 3 results,  Invited: 10 results)

  • [Journal Article] ENIGMA: An Enterotype-Like Unigram Mixture Model for Microbial Association Analysis.2019

    • Author(s)
      Abe K, Hirayama H, Ohno K, Shimamura T.
    • Journal Title

      BMC Genomics

      Volume: 20(Suppl 2) Issue: S2 Pages: 191-191

    • DOI

      10.1186/s12864-019-5476-9

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Regnase-1-mediated post-transcriptional regulation is essential for hematopoietic stem and progenitor cell homeostasis2019

    • Author(s)
      Kidoya H, Muramatsu F, Shimamura T, Jia W, Satoh T, Hayashi Y, Naito H, Kunisaki Y, Arai F, Seki M, Suzuki Y, Osawa T, Akira S., Takakura N.
    • Journal Title

      Nature Commun,

      Volume: 10 Issue: 1 Pages: 1072-1072

    • DOI

      10.1038/s41467-019-09028-w

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A Network of Networks Approach for Modeling Interconnected Brain Tissue-Specific Networks.2019

    • Author(s)
      Kawakubo H, Matsui Y, Kushima I, Ozaki N, Shimamura T.
    • Journal Title

      Bioinformatics

      Volume: - Issue: 17 Pages: 1-10

    • DOI

      10.1093/bioinformatics/btz032

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] GIMLET: Identifying biological modulators in context-specific gene regulation using local energy statistics.2018

    • Author(s)
      Shimamura T, Matsui Y, Kajino T, Ito S, Takahashi T, Miyano S.
    • Journal Title

      Lecture Notes in Bioinformatics

      Volume: 10834 Pages: 115-123

    • DOI

      10.1101/349928

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Tumor subclonal progression model for cancer hallmark acquisition.2018

    • Author(s)
      Matsui Y, Miyano S, Shimamura T.
    • Journal Title

      Lecture Notes in Bioinformatics

      Volume: 10834 Pages: 124-137

    • DOI

      10.1101/149252

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Comparative Analyses of Copy-Number Variation in Autism Spectrum Disorder and Schizophrenia Reveal Etiological Overlap and Biological Insights.2018

    • Author(s)
      Kushima I, (27名中略), Hashimoto R,(80名中29番目) , et al.
    • Journal Title

      Cell Rep

      Volume: 24(11) Issue: 11 Pages: 2838-2856

    • DOI

      10.1016/j.celrep.2018.08.022

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A latent allocation model for the analysis of microbial composition and disease2018

    • Author(s)
      Abe K, Hirayama H, Ohno K, Shimamura T.
    • Journal Title

      BMC Bioinformatics

      Volume: 19(Suppl 19) Issue: S19 Pages: 519-519

    • DOI

      10.1186/s12859-018-2530-6

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A temporal shift of the evolutionary principle shaping intratumor heterogeneity in colorectal cancer2018

    • Author(s)
      Saito T, Niida A, Uchi R, Hirata H, Kodama M, Okimoto T, Murakami K, Suzuki Y, Ogawa S, Miyano S, Mimori K, et al.
    • Journal Title

      Nature Communications

      Volume: 9 Issue: 1 Pages: 2884-2884

    • DOI

      10.1038/s41467-018-05226-0

    • NAID

      120006551763

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] hibition controls aggressive prostate tumors deficient in Y-linked histone demethylase KDM5D.2018

    • Author(s)
      Komura K、Yoshikawa Y, Shimamura T, Chakraborty G, Gerke TA, Hinohara K, Chadalavada K, Jeong SH, Armenia J, Du SY, Mazzu YZ, Taniguchi K, Ibuki N, Meyer CA, Nanjangud GJ, Inamoto T, Lee GM, Mucci LA, Azuma H, Sweeney CJ, Kantoff PW.
    • Journal Title

      Journal of Clinical Investigation

      Volume: 128(7) Issue: 7 Pages: 2979-95

    • DOI

      10.1172/jci96769

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Identification of Cardiomyocyte-Fated Progenitors from Human-Induced Pluripotent Stem Cells Marked with CD822018

    • Author(s)
      Takeda Masafumi、Kanki Yasuharu、Masumoto Hidetoshi、Funakoshi Shunsuke、Hatani Takeshi、Fukushima Hiroyuki、Izumi-Taguchi Akashi、Matsui Yusuke、Shimamura Teppei、Yoshida Yoshinori、Yamashita Jun K.
    • Journal Title

      Cell Reports

      Volume: 22 Issue: 2 Pages: 546-556

    • DOI

      10.1016/j.celrep.2017.12.057

    • NAID

      120006460050

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Integrated Molecular Characterization of the Lethal Pediatric Cancer Pancreatoblastoma2018

    • Author(s)
      Isobe T, Seki M, Yoshida K, Sekiguchi M, Shiozawa Y, Shiraishi Y,..., Kataoka K, Sato Y, Kawai T, Chiba K, Tanaka H, Shimamura T, Kato M, Iguchi A, Hama A, Taguchi T, Akiyama M, Fujimura J, Inoue A, Ito T, Deguchi T, Kiyotani C, Iehara T, Hosoi H, Oka A, Sanada M, Tanaka Y, Hata K, Miyano S, Ogawa S, Takita J
    • Journal Title

      Cancer Res

      Volume: 78(4) Issue: 4 Pages: 865-876

    • DOI

      10.1158/0008-5472.can-17-2581

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Adaptive NetworkProfiler for Identifying Cancer Characteristic-Specific Gene Regulatory Networks2018

    • Author(s)
      Park H, Shimamura T, Imoto S, Miyano S
    • Journal Title

      J Comput Biol

      Volume: 25(2) Issue: 2 Pages: 130-145

    • DOI

      10.1089/cmb.2017.0120

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] ER Stress Signaling Promotes the Survival of Cancer “Persister Cells” Tolerant to EGFR Tyrosine Kinase Inhibitors2017

    • Author(s)
      Terai Hideki、Kitajima Shunsuke、Potter Danielle S.、Matsui Yusuke、et al.
    • Journal Title

      Cancer Research

      Volume: 78 Issue: 4 Pages: 1044-1057

    • DOI

      10.1158/0008-5472.can-17-1904

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Comprehensive genetic analysis of donor cell derived leukemia with KMT2A rearrangement.2017

    • Author(s)
      Taniguchi R, Muramatsu H, Okuno Y, Suzuki K, Obu S, Nakatochi M, Shimamura T, Takahashi Y, Horikoshi Y, Watanabe K, Kojima S.
    • Journal Title

      Pediatr Blood Cancer

      Volume: 65(2) Issue: 2

    • DOI

      10.1002/pbc.26823

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Japanese genome-wide association study identifies a significant colorectal cancer susceptibility locus at chromosome 10p14.2017

    • Author(s)
      Takahashi Y, Sugimachi K, Yamamoto K, Niida A, Shimamura T, Sato T, Watanabe M, Tanaka J, Kudo S, Sugihara K, Hase K, Kusunoki M, Yamada K, Shimada Y, Moriya Y, Suzuki Y, Miyano S, Mori M, Mimori K
    • Journal Title

      Cancer Sci.

      Volume: 108(11) Issue: 11 Pages: 2239-2247

    • DOI

      10.1111/cas.13391

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] PRC2-mediated transcriptomic alterations at the embryonic stage govern tumorigenesis and clinical outcome in MYCN-driven neuroblastoma.2017

    • Author(s)
      Tsubota S, Kishida S, Shimamura T, Ohira M, Yamashita S, Cao D, Kiyonari S, Ushijima T, Kadomatsu K.
    • Journal Title

      Cancer Res

      Volume: 77(19) Pages: 5259-5271

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Prognostic relevance of genetic alterations in diffuse lower-grade gliomas2017

    • Author(s)
      Aoki Kosuke、Nakamura Hideo、Suzuki Hiromichi et al.
    • Journal Title

      Neuro-Oncology

      Volume: 20 Issue: 1 Pages: 66-77

    • DOI

      10.1093/neuonc/nox132

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Recurrent SPI1 (PU.1) fusions in high-risk pediatric T cell acute lymphoblastic leukemia.2017

    • Author(s)
      Seki M, Kimura S, Isobe T, Yoshida K, (13 authors), Masuda K, Kawamoto H, Ohki K, Kato M, Arakawa Y, Koh K, Hanada R, Moritake H, Akiyama M, Kobayashi R, Deguchi T, Hashii Y, Imamura T, Sato A, Kiyokawa N, Oka A, Hayashi Y, Takagi M, Manabe A, Ohara A, Horibe K, Sanada M, Iwama A, Mano H, Miyano S, Ogawa S, Takita J
    • Journal Title

      Nature Genetics

      Volume: 49 Issue: 8 Pages: 1274-1281

    • DOI

      10.1038/ng.3900

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Long Noncoding RNA JHDM1D-AS1 Promotes Tumor Growth by Regulating Angiogenesis in Response to Nutrient Starvation2017

    • Author(s)
      Kondo A, Nonaka A, Shimamura T, Yamamoto S, Yoshida T, Kodama T, Aburatani H, Osawa T
    • Journal Title

      Molecular and Cellular Biology

      Volume: 37 Issue: 18

    • DOI

      10.1128/mcb.00125-17

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] phyC: Clustering cancer evolutionary trees.2017

    • Author(s)
      Matsui Y, Niida A, Uchi R, Mimori K, Miyano S, Shimamura T:
    • Journal Title

      PLoS Comput Biol.

      Volume: 13(5) Issue: 5 Pages: 1005509-1005509

    • DOI

      10.1371/journal.pcbi.1005509

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Dynamically and epigenetically coordinated GATA/ETS/SOX transcription is indispensable for endothelial cell differentiation2017

    • Author(s)
      Kanki Y, Nakaki R, Shimamura T, Matsunaga T, Yamamizu K, Katayama S, Suehiro JI, Osawa T, Aburatani H, Kodama T, Wada Y, Yamashita JK, Minami T.
    • Journal Title

      Nucleic Acids Research

      Volume: 印刷中 Issue: 8 Pages: 4344-4358

    • DOI

      10.1093/nar/gkx159

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Addiction to the IGF2-ID1-IGF2 circuit for maintenance of the breast cancer stem-like cells2017

    • Author(s)
      Tominaga K, Shimamura T, Kimura N, Murayama T, Matsubara D, Kanauchi H, Niida A, Shimizu S, Nishioka K, Tsuji EI, Yano M, Sugano S, Shimono Y, Ishii H, Saya H, Mori M, Akashi K, Tada KI, Ogawa T, Tojo A, Miyano S, Gotoh N
    • Journal Title

      Oncogene

      Volume: 36(9) Issue: 9 Pages: 1276-1286

    • DOI

      10.1038/onc.2016.293

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Extracellular Acidic pH Activates the Sterol Regulatory Element-binding Protein 2 to Promote Tumor Progression2017

    • Author(s)
      Kondo A, Yamamoto S, Nakaki R, Shimamura T, Hamakubo T, Sakai J, Kodama T, Yoshida T, Aburatani H and Osawa T
    • Journal Title

      Cell Reports

      Volume: 18 Issue: 9 Pages: 2228-2242

    • DOI

      10.1016/j.celrep.2017.02.006

    • Related Report
      2017 Annual Research Report 2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Detection of differential distributions of methylation patterns2016

    • Author(s)
      Matsui Y, Mizuta M, Miyano S, Shimamura T
    • Journal Title

      Bioinformatics

      Volume: 印刷中 Issue: 15 Pages: 1-8

    • DOI

      10.1093/bioinformatics/btw138

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] NECAB3 Promotes Activation of Hypoxia-inducible factor-1 during Normoxia and Enhances Tumourigenicity of Cancer Cells2016

    • Author(s)
      1.Nakaoka HJ, Hara T, Yoshino S, Kanamori A, Matsui Y, Shimamura T, Sato H, Murakami Y, Seiki M, Sakamoto T
    • Journal Title

      Sci Rep

      Volume: 6 Issue: 1 Pages: 22784-22784

    • DOI

      10.1038/srep22784

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Integrated Multiregional Analysis Proposing a New Model of Colorectal Cancer Evolution.2016

    • Author(s)
      R. Uchi (他40名, 山本36番目)
    • Journal Title

      PLoS Genetics

      Volume: 12 Issue: 2 Pages: 1-24

    • DOI

      10.1371/journal.pgen.1005778

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Aberrant Methylation of FOXE1 Contributes to a Poor Prognosis for Patients with Colorectal Cancer.2016

    • Author(s)
      Sugimachi K, Matsumura T, Shimamura T, Hirata H, Uchi R, Ueda M, Sakimura S, Iguchi T, Eguchi H, Masuda T, Morita K, Takenaka K, Maehara Y, Mori M, Mimori K.
    • Journal Title

      Ann Surg Oncol.

      Volume: 23(12) Issue: 12 Pages: 3948-3955

    • DOI

      10.1245/s10434-016-5289-x

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Sparse Regression Modeling of Drug Response with A Localized Estimation Framework2018

    • Author(s)
      島村徹平
    • Organizer
      The Pacific Symposium on Biocomputing (PSB) 2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] データサイエンスとの連携・融合による生命科学研究の新時代2018

    • Author(s)
      島村徹平
    • Organizer
      第61回日本神経化学会大会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] バイオインフォマティクスにおけるスパースモデリング2018

    • Author(s)
      島村徹平
    • Organizer
      日本行動計量学会 第46回大会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] がん微小環境における細胞間相互作用のモデリング2018

    • Author(s)
      島村徹平
    • Organizer
      2018年度統計関連学会連合大会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 疾患メタゲノム解析のためのベイズモデリング2018

    • Author(s)
      島村徹平
    • Organizer
      第7回生命医薬情報学連合大会(IIBMP2018)
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 腫瘍内不均一性の一細胞トランスクリプトーム解析のためのバイオインフォマティクス2018

    • Author(s)
      島村徹平
    • Organizer
      第77回日本癌学会学術総会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] がん免疫システムの時間・空間・個体間多様性を読み解くデータサイエンス2018

    • Author(s)
      島村徹平
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] GIMLET: Identifying Biological Modulators in Context-Specific Gene Regulation Using Local Energy Statistics2017

    • Author(s)
      島村徹平
    • Organizer
      CIBB2017(Computational Intelligence methods for Bioinformatics and Biostatistics)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 生命科学におけるビッグデータ駆動型科学の実践と将来2017

    • Author(s)
      島村徹平
    • Organizer
      2017年度生命科学系学会合同年次大会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Sparse Regression Modeling of Drug Response with A Localized Estimation Framework2017

    • Author(s)
      島村徹平
    • Organizer
      ISMB/ECCB2017(Intelligent Systems for Molecular Biology and the 16TH European Conference on Computational Biology)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] マルチオミックス情報に基づくがんのモジュレーター因子の網羅的探索2016

    • Author(s)
      島村徹平
    • Organizer
      第5回生命医薬情報学連合大会
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] システム生物学的アプローチに基づくオミックス統合解析2016

    • Author(s)
      島村徹平
    • Organizer
      第39回日本分子生物学会年会
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] がんの俯瞰的理解のための統合的統計モデリング2015

    • Author(s)
      島村徹平
    • Organizer
      第38回日本分子生物学会年会
    • Place of Presentation
      神戸ポートアイランド(兵庫県神戸市)
    • Related Report
      2015 Annual Research Report
    • Invited

URL: 

Published: 2015-04-16   Modified: 2020-03-30  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi