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A big data approach to function prediction of metabolites by clustering of structural similarity networks

Research Project

Project/Area Number 17K00406
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Life / Health / Medical informatics
Research InstitutionNara Institute of Science and Technology

Principal Investigator

AMIN MD. ALTAFUL  奈良先端科学技術大学院大学, 先端科学技術研究科, 准教授 (30379531)

Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Fiscal Year 2019: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2018: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2017: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
KeywordsMetabolomics / Metabolic Network / Network Clustering / Metabolite Activity / Big Data Biology / Algorithm / Systems Biology / Algorithms / Big data biology / Network clustering / Secondary metabolites
Outline of Final Research Achievements

We have developed a method to predict the activity of metabolites and have been able to predict the function of 1340 unknown metabolites using this method. As part of the project, we have also developed a tool called DPClusSBO for clustering simple graphs and bipartite graphs. We have published many papers centered around this project and the tool we developed is being used by our collaborators in Malaysia, Brazil and Indonesia. We hope that this tool will be used more widely in the future, and we would like to expand the application of the tool ourselves such as for searching for antibiotics based on traditional medicines.

Academic Significance and Societal Importance of the Research Achievements

By utilizing our method we predicted the functions of 1340 unknown metabolites. As part of this project we developed a tool for clustering of simple and bipartite graphs which we have utilized in several other research works. This tool is a significant academic and social achievement.

Report

(4 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • Research Products

    (31 results)

All 2020 2019 2018 2017 Other

All Journal Article (14 results) (of which Peer Reviewed: 3 results,  Open Access: 2 results) Presentation (12 results) (of which Int'l Joint Research: 5 results,  Invited: 5 results) Book (4 results) Remarks (1 results)

  • [Journal Article] Discovery of inflammatory bowel disease-associated miRNAs using a novel bipartite clustering approach2020

    • Author(s)
      Altaf-Ul-Amin, M., Karim, M. B., Hu, P., Naoaki, O. N. O., & Kanaya, S.
    • Journal Title

      BMC Medical Genomics

      Volume: 13(3) Issue: S3 Pages: 1-10

    • DOI

      10.1186/s12920-020-0660-y

    • Related Report
      2019 Annual Research Report
  • [Journal Article] Graph cluster approach in identifying novel proteins and significant pathways involved in polycystic ovary syndrome2020

    • Author(s)
      Afiqah-Aleng, N., Altaf-Ul-Amin, M., Kanaya, S., & Mohamed-Hussein, Z. A.
    • Journal Title

      Reproductive biomedicine online

      Volume: 40(2) Issue: 2 Pages: 319-330

    • DOI

      10.1016/j.rbmo.2019.11.012

    • Related Report
      2019 Annual Research Report
  • [Journal Article] BiClusO: A novel biclustering approach and its application to species-VOC relationship data2019

    • Author(s)
      Mohammad Bozlul Karim, Ming Huang, Naoaki ONO, Shigehiko Kanaya, Md. Altaf-Ul Amin
    • Journal Title

      IEEE/ACM transactions on computational biology and bioinformatics

      Volume: 2019 Issue: 6 Pages: 1-12

    • DOI

      10.1109/tcbb.2019.2914901

    • Related Report
      2019 Annual Research Report
  • [Journal Article] Implementation of BiClusO and its comparison with other biclustering algorithms2019

    • Author(s)
      Mohammad Bozlul Karim, Shigehiko Kanaya, Md. Altaf-Ul-Amin
    • Journal Title

      Applied Network Science

      Volume: 4(1) Pages: 1-15

    • Related Report
      2019 Annual Research Report
  • [Journal Article] [Special Issue for Honor Award dedicating to Prof Kimito Funatsu]Prediction of Metabolite Activities by Repetitive Clustering of the Structural Similarity Based Networks2019

    • Author(s)
      Wakamatsu, N., Huang, M., Ono, N., Altaf-Ul-Amin, M., & Kanaya, S.
    • Journal Title

      Journal of Computer Aided Chemistry

      Volume: 20 Issue: 0 Pages: 76-83

    • DOI

      10.2751/jcac.20.76

    • NAID

      130007775607

    • ISSN
      1345-8647
    • Related Report
      2019 Annual Research Report
  • [Journal Article] On the determination of important plants for ayurvedic formulas in Bangladesh using unsupervised machine learning approach2019

    • Author(s)
      Hossain M. Mofazzal, M. S. A. Gazi, M. Mahbub, A. A. P. Sayed, S. Kanaya and M. Altaf-Ul-Amin
    • Journal Title

      Academia Journal of Medicinal Plants

      Volume: 7(2) Pages: 036-041

    • Related Report
      2018 Research-status Report
  • [Journal Article] An integrative network-based approach to identify novel disease genes and pathways: a case study in the context of inflammatory bowel disease2018

    • Author(s)
      Eguchi, R., Karim, M. B., Hu, P., Sato, T., Ono, N., Kanaya, S., & Altaf-Ul-Amin, M.
    • Journal Title

      BMC bioinformatics

      Volume: 19(1) Issue: 1 Pages: 264-264

    • DOI

      10.1186/s12859-018-2251-x

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Metabolite-Content-Guided Prediction of Medicinal/Edible Prop-erties in Plants for Bioprospecting2018

    • Author(s)
      Liu, K., Morita, A. H., Kanaya, S., & Atlaf-Ul-Amin, M
    • Journal Title

      Current Research in Complementary & Alternative Medicine

      Volume: CRCAM-130 Issue: 2 Pages: 2577-2201

    • DOI

      10.29011/2577-2201/100030

    • Related Report
      2018 Research-status Report
  • [Journal Article] Data Intensive Study of Accessibility of Edible Species and Healthcare Across the Globe2018

    • Author(s)
      Watanabe, Satoshi, K. Y. O. Hoko, K. A. N. G. Liu, Ryohei Eguchi, Md Altaf-Ul-Amin, Aki MORITA, Minako OHASHI et al.
    • Journal Title

      Japanese Journal of Complementary and Alternative Medicine

      Volume: 15 Issue: 1 Pages: 37-60

    • DOI

      10.1625/jcam.15.37

    • NAID

      130006708552

    • ISSN
      1348-7922, 1348-7930
    • Related Report
      2018 Research-status Report
  • [Journal Article] Classification of lung adenocarcinoma transcriptome subtypes from pathological images using deep convolutional networks2018

    • Author(s)
      3.Antonio, V. A. A., Ono, N., Saito, A., Sato, T., Altaf-Ul-Amin, M., & Kanaya, S.
    • Journal Title

      International journal of computer assisted radiology and surgery

      Volume: 13(12) Issue: 12 Pages: 1905-1913

    • DOI

      10.1007/s11548-018-1835-2

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Metabolite-Content-Guided Prediction of Medicinal/Edible Prop-erties in Plants for Bioprospecting2018

    • Author(s)
      Liu, K., Morita, A. H., Kanaya, S., & Atlaf-Ul-Amin, M.
    • Journal Title

      Curr Res Complement Altern Med

      Volume: 130 Pages: 1-15

    • Related Report
      2017 Research-status Report
  • [Journal Article] Metabolomic Studies of Indonesian Jamu Medicines: Prediction of Jamu Efficacy and Identification of Important Metabolites2017

    • Author(s)
      Sony Hartono Wijaya, Irmanida Batubara, Takaaki Nishioka, Md. Altaf-Ul-Amin, and Shigehiko Kanaya
    • Journal Title

      Molecular Informatics

      Volume: 36 Issue: 12 Pages: 1-16

    • DOI

      10.1002/minf.201700050

    • Related Report
      2017 Research-status Report
  • [Journal Article] [Dedicated to Prof. T. Okada and Prof. T. Nishioka: data science in chemistry]Classification of Alkaloid Compounds Based on Subring Skeleton (SRS) Profiling: On Finding Relationship of Compounds with Metabolic Pathways2017

    • Author(s)
      Eguchi, R., Ono, N., Horai, H., Amin, M. A. U., Hirai, A. M., Kawahara, J., ... & Kanaya, S.
    • Journal Title

      Journal of Computer Aided Chemistry

      Volume: 18 Issue: 0 Pages: 58-75

    • DOI

      10.2751/jcac.18.58

    • NAID

      130005877929

    • ISSN
      1345-8647
    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] [Dedicated to Prof. T. Okada and Prof. T. Nishioka: data science in chemistry]DPClusOST: A Software Tool for General Purpose Graph Clustering2017

    • Author(s)
      Mohammad Bozlul Karim, Nobutaka Wakamatsu and Md. Altaf-Ul-Amin
    • Journal Title

      Journal of Computer Aided Chemistry

      Volume: 18 Issue: 0 Pages: 76-93

    • DOI

      10.2751/jcac.18.76

    • NAID

      130005877930

    • ISSN
      1345-8647
    • Related Report
      2017 Research-status Report
  • [Presentation] Applications of KNApSAcK Database and DPClus Algorithm: Plants to Metabolites to Target Proteins in the Context of Jamu Medicines and IBD Gene Prediction2020

    • Author(s)
      Md. Altaf-Ul-Amin
    • Organizer
      Asian Regional Conference on Systems Biology
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Novel Method and Tool for Clustering of Simple and Bipartite Graphs: Applications in Ecology and Identification of Inflammatory Bowel Disease(IBD) Related Genes and miRNAs2020

    • Author(s)
      Md. Altaf-Ul-Amin
    • Organizer
      University of south Australia, Adelaide
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Inter Disease Relations Based on Human Biomarkers by Network Analysis2019

    • Author(s)
      Md. Altaf-Ul-Amin
    • Organizer
      IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Discovery of inflammatory bowel disease-associated miRNAs using a novel bipartite clustering approach2019

    • Author(s)
      Md. Altaf-Ul-Amin
    • Organizer
      International Conference on Genome Informatics (GIW 2019)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Development of an Integrated System for Clustering of Simple and Bipartite Graphs and its Application to Different Types of Biological Data2019

    • Author(s)
      Md. Altaf-Ul-Amin
    • Organizer
      University of Manitoba, Canada
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Applications of KNApSAcK Database and DPClus Algorithm: Plants to Metabolites to Target Proteins in the Context of Jamu Medicines and IBD Gene Prediction2019

    • Author(s)
      Md. Altaf-Ul-Amin
    • Organizer
      ICBET 2019, Meiji University, Tokyo
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Introduction to Big Data Science Focusing Health Care and Ecology: A Case Study based on Indonesian Traditional Medicines2019

    • Author(s)
      Md. Altaf-Ul-Amin
    • Organizer
      Big data: Linking Ecosystem, health and wellbeing, BUET, Dhaka, Bangladesh
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Data-Intensive Science of Jamu Medicines2018

    • Author(s)
      Md. Altaf-Ul-Amin
    • Organizer
      Universidade Federal de São Paulo, Brazil
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Comparison of BiClusO with five different biclustering algorithms using biological and Synthetic data2018

    • Author(s)
      Mohammand Bozlul Karim
    • Organizer
      7th International Conference on Complex Networks and Their Applications, Cambridge, UK
    • Related Report
      2018 Research-status Report
  • [Presentation] Prediction of Plant-Disease Relations Based on Unani Formulas by Network Analysis2018

    • Author(s)
      Shaikh Farhad Hossain
    • Organizer
      18th IEEE International Conference on BioInformatics and BioEngineering, Taichung, Taiwan
    • Related Report
      2018 Research-status Report
  • [Presentation] A Network based Approach to Predict Functions of Metabolites2018

    • Author(s)
      Md. Altaf-Ul-Amin
    • Organizer
      International Conference on Metabolomics,
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Multifaceted analysis of sequence similarity based network of allergens2018

    • Author(s)
      Yasue Aoyama
    • Organizer
      International Conference on Computational Mathematics , Physics and It's Applications
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Book] Applications of Network Clustering in Natural Product Research, In book: Reference Module in Chemistry, Molecular Sciences and Chemical Engineering2020

    • Author(s)
      Altaf-Ul-Amin, M., & Kanaya, S.
    • Total Pages
      33
    • Publisher
      Elsevier
    • Related Report
      2019 Annual Research Report
  • [Book] Databases for Natural Product Research, In book: Reference Module in Chemistry, Molecular Sciences and Chemical Engineering2020

    • Author(s)
      Kanaya, S., Altaf-Ul-Amin, M., Aki, M. H., Huang, M., & Ono, N.
    • Total Pages
      16
    • Publisher
      Elsevier
    • Related Report
      2019 Annual Research Report
  • [Book] Volatile Organic Compound Analysis in Biomedical Diagnosis Applications(Chapter 9)2018

    • Author(s)
      Azian Azamimi Abdullah, Md. Altaf-Ul-Amin, and Shigehiko Kanaya
    • Total Pages
      20
    • Publisher
      Apple Academic Press
    • ISBN
      9781771887441
    • Related Report
      2018 Research-status Report
  • [Book] Investigating Metabolic Pathways and Networks, In the book: Reference Module in Life Sciences2018

    • Author(s)
      Altaf-Ul-Amin, M., Mohamed-Hussein, Z.-A., & Kanaya, S
    • Total Pages
      16
    • Publisher
      Elsevier
    • Related Report
      2018 Research-status Report
  • [Remarks] DPClusO & BiClusO (DPClusSBO1.1)

    • URL

      http://www.knapsackfamily.com/GRAPH_CLUSTERING/

    • Related Report
      2019 Annual Research Report

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Published: 2017-04-28   Modified: 2021-02-19  

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