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Informatics analysis on selectivity and diversity of enzymatic reaction

Research Project

Project/Area Number 26430198
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field System genome science
Research InstitutionKobe University

Principal Investigator

araki michihiro  神戸大学, 科学技術イノベーション研究科, 特命准教授 (40396867)

Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2016: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2015: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2014: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
Keywordsバイオインフォマティクス / 合成生物学 / 代謝工学
Outline of Final Research Achievements

In constructing a novel metabolic pathway, selection of enzyme gene candidates required for metabolic pathways, whether unknown or known, is an important task. In this research, in order to more efficiently select such enzyme genes, we reconstructed a new enzyme reaction database that integrated information diffused in each database in a form suitable for this purpose. Based on this, we have developed biological and chemical information analysis and machine learning methods that can support selection of representative gene sequences while considering selectivity and diversity of enzyme genes.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report
  • Research Products

    (30 results)

All 2017 2016 2015 2014 Other

All Journal Article (7 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 7 results,  Open Access: 4 results,  Acknowledgement Compliant: 1 results) Presentation (20 results) (of which Invited: 7 results) Book (2 results) Remarks (1 results)

  • [Journal Article] A Systematic Approach to Time-series Metabolite Profiling and RNA-seq Analysis of Chinese Hamster Ovary Cell Culture2017

    • Author(s)
      Hsu, HH., Araki, M., Mochizuki, M., Hori, Y., Murata, M., Kahar, P., Yoshida, T., Hasunuma, T. and Kondo A.
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 43518-43518

    • DOI

      10.1038/srep43518

    • NAID

      120006346139

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Application of LC-MS/MS analysis for time-lapse amino acid metabolomics analysis in CHO cell culture2017

    • Author(s)
      Hsu, H.H., Hasunuma, T., Araki, M., Yoshida, T., Hori, Y., Murata, M., Kondo, A.
    • Journal Title

      Shimadzu Journal

      Volume: 5 Pages: 17-17

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems2016

    • Author(s)
      Nishida, K., Arazoe, T., Yachie, N., Banno, S., Kakimoto, M., Tabata, M., Mochizuki, M., Miyabe, A., Araki, M., Hara, K.Y., Shimatani, Z. and Kondo, A.
    • Journal Title

      Science

      Volume: 353 Issue: 6305 Pages: 6305-6305

    • DOI

      10.1126/science.aaf8729

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Improvement of oxidized glutathione fermentation by thiol redox metabolism engineering in Saccharomyces cerevisiae2015

    • Author(s)
      Hara, K.Y., Aoki, N., Kobayashi, J., Kiriyama, K., Nishida, K., Araki, M., Kondo, A.
    • Journal Title

      Appl. Microbiol. Biotechnol.

      Volume: 99 Issue: 22 Pages: 9771-9778

    • DOI

      10.1007/s00253-015-6847-z

    • Related Report
      2015 Research-status Report
    • Peer Reviewed
  • [Journal Article] Evaluation of genes involved in oxidative phosphorylation in yeast by developing a simple and rapid method to measure mitochondrial ATP synthetic activity.2015

    • Author(s)
      Ye X, Morikawa K, Ho SH, Araki M, Nishida K, Hasunuma T, Hara KY, Kondo A.
    • Journal Title

      Microbial Cell Factories

      Volume: 14 Issue: 1 Pages: 56-56

    • DOI

      10.1186/s12934-015-0239-z

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] M-path: A Compass for Navigating Potential Metabolic Pathways2015

    • Author(s)
      Araki, M., Cox III, RS., Makiguchi, H., Ogawa, T., Taniguchi, T., Miyaoku, K., Nakatsui M., Hara, K.Y., Kondo, A.
    • Journal Title

      Bioinformatics

      Volume: 31 Issue: 6 Pages: 905-911

    • DOI

      10.1093/bioinformatics/btu750

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Development of bio-based fine chemical production through synthetic bioengineering2014

    • Author(s)
      Hara, K.Y., Araki, M., Okai, N., Wakai, S., Hasunuma, T., Kondo, A.
    • Journal Title

      Microbial Cell Factories

      Volume: 13 Issue: 1 Pages: 173-173

    • DOI

      10.1186/s12934-014-0173-5

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] 代謝経路デザインの限界2017

    • Author(s)
      荒木通啓
    • Organizer
      第11回日本ゲノム微生物学会年会
    • Place of Presentation
      慶応義塾大学(神奈川県、藤沢市)
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Development of Design Platform for Metabolic Pathways2016

    • Author(s)
      Ogawa, T., Makiguchi, H. and Araki, M
    • Organizer
      生命医薬情報学連合大会2016年大会
    • Place of Presentation
      東京国際交流館プラザ平成(東京都)
    • Year and Date
      2016-09-29
    • Related Report
      2016 Annual Research Report
  • [Presentation] In Silico代謝設計ツールの開発とその展開2016

    • Author(s)
      荒木通啓
    • Organizer
      農芸化学会2016年度大会
    • Place of Presentation
      札幌コンベンションセンター(北海道・札幌市)
    • Year and Date
      2016-03-30
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] 大腸菌における1,4-ブタンジオール人工生合成経路の構築2016

    • Author(s)
      江口晃一、工藤基徳、荒木通啓、石井純、山本浩明、近藤昭彦
    • Organizer
      農芸化学会2016年度大会
    • Place of Presentation
      札幌コンベンションセンター(北海道・札幌市)
    • Year and Date
      2016-03-30
    • Related Report
      2015 Research-status Report
  • [Presentation] インシリコ代謝経路設計基盤の展開2016

    • Author(s)
      荒木通啓、牧口大旭、小川哲平、近藤昭彦
    • Organizer
      日本薬学会第136回年会
    • Place of Presentation
      パシフィコ横浜(神奈川県・横浜市)
    • Year and Date
      2016-03-28
    • Related Report
      2015 Research-status Report
  • [Presentation] 代謝デザインの展開2016

    • Author(s)
      荒木通啓
    • Organizer
      第1回デザイン生命工学研究会
    • Place of Presentation
      東京工業大学(神奈川県・横浜市)
    • Year and Date
      2016-03-08
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] Expanding the Scope of Metabolic Pathway In Silico2016

    • Author(s)
      Michihiro Araki
    • Organizer
      The 7th International Symposium of Innovative BioProduction Kobe (iBioK)
    • Place of Presentation
      神戸大学(兵庫県・神戸市)
    • Year and Date
      2016-01-27
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] スマートセル開発に向けたIT/AI技術の展望2016

    • Author(s)
      荒木通啓
    • Organizer
      産業構造審議会 商務流通情報分科会 バイオ小委員会(第4回)
    • Place of Presentation
      経済産業省(東京都)
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] バイオプロセスデザインプラットフォームの構築2016

    • Author(s)
      牧口 大旭、小川 哲平、荒木通啓
    • Organizer
      第39回日本分子生物学会
    • Place of Presentation
      パシフィコ横浜(神奈川県、横浜市)
    • Related Report
      2016 Annual Research Report
  • [Presentation] M-Path&PathPod:バイオプロセスデザインプラットフォームと統合型パスウェイデータベースシステム2015

    • Author(s)
      牧口大旭、小川哲平、近藤昭彦、荒木通啓
    • Organizer
      第38回分子生物学会
    • Place of Presentation
      神戸国際会議場(兵庫県・神戸市)
    • Year and Date
      2015-12-02
    • Related Report
      2015 Research-status Report
  • [Presentation] M-path Database: Navigating Potential Metabolic Pathways2015

    • Author(s)
      小川哲平、牧口大旭、中津井雅彦、Cox III, RS.、近藤昭彦、荒木通啓
    • Organizer
      M-path Database: Navigating Potential Metabolic Pathways
    • Place of Presentation
      京都大学(京都府・宇治市)
    • Year and Date
      2015-10-29
    • Related Report
      2015 Research-status Report
  • [Presentation] Development of M-path platform for Navigating Potential Metabolic Pathways2015

    • Author(s)
      Ogawa, T., Makiguchi, H., Cox III, RS., Nakatsui M., Kondo, A., and Araki, M.
    • Organizer
      ISMB 2015
    • Place of Presentation
      the Convention Centre Dublin【Dublin(Ireland)】
    • Year and Date
      2015-07-10
    • Related Report
      2015 Research-status Report
  • [Presentation] New approach for Metabolomics pathway analysis2015

    • Author(s)
      Oshida, T., Ogawa, T., Yokoi, Y., Fukamachi, Y., Araki, M., Makiguchi, H.
    • Organizer
      ASMS2015
    • Place of Presentation
      America's Center【St. Louis(USA)】
    • Year and Date
      2015-05-31
    • Related Report
      2015 Research-status Report
  • [Presentation] M-path: Construction of a Database for Expanded Metabolic Pathways2014

    • Author(s)
      Ogawa, T., Makiguchi, H., Cox III, RS., Nakatsui M., Kondo, A., Taniguchi, T., Miyaoku, K. and Araki, M.
    • Organizer
      Active Enzyme Molecule 2014
    • Place of Presentation
      Toyama International Conference Center, Toyama
    • Year and Date
      2014-12-17 – 2014-12-19
    • Related Report
      2014 Research-status Report
  • [Presentation] Meta-synthetic metabolism: in silico design of novel amino acids from all-organism data2014

    • Author(s)
      Cox III, RS., Nakatsui M., Makiguchi, H., Ogawa, T., Kondo, A., Araki, M.
    • Organizer
      GIW ISCB-ASIA 2014
    • Place of Presentation
      CBRC, Tokyo
    • Year and Date
      2014-12-15 – 2014-12-17
    • Related Report
      2014 Research-status Report
  • [Presentation] M-path: 拡張代謝パスウェイデータベースの構築2014

    • Author(s)
      牧口大旭、小川哲平、中津井雅彦、Cox III, RS.、近藤昭彦、谷口岳志、宮奥康平、荒木通啓
    • Organizer
      第37回分子生物学会
    • Place of Presentation
      パシフィコ横浜、横浜
    • Year and Date
      2014-11-26
    • Related Report
      2014 Research-status Report
  • [Presentation] 代謝設計基盤(M-path)によるバイオ合成スコープの拡張2014

    • Author(s)
      荒木通啓
    • Organizer
      合成生物工学シンポジウム
    • Place of Presentation
      神戸大学、神戸
    • Year and Date
      2014-11-25
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] バイオプロセス合成経路データベース"M-path"の構築2014

    • Author(s)
      小川哲平、牧口大旭、谷口岳志、宮奥康平、中津井雅彦、Cox III, RS.、近藤昭彦、荒木通啓
    • Organizer
      第3回生命医薬情報学連合大会
    • Place of Presentation
      仙台国際センター、仙台
    • Year and Date
      2014-10-02 – 2014-10-04
    • Related Report
      2014 Research-status Report
  • [Presentation] Computational platform for designing synthetic metabolic pathways2014

    • Author(s)
      Michihiro Araki
    • Organizer
      7th International Congress on Biocatalysis
    • Place of Presentation
      Hamburg University of Technology, Hamburg, Germany
    • Year and Date
      2014-09-03
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Mpath: Computationally-Aided Design of Synthetic Metabolic Pathways2014

    • Author(s)
      Cox III, RS., Nakatsui M., Makiguchi, H., Ogawa, T., Kondo, A., Araki, M.
    • Organizer
      SEED2014
    • Place of Presentation
      Manhattan Beach, LA, USA
    • Year and Date
      2014-07-14 – 2014-07-17
    • Related Report
      2014 Research-status Report
  • [Book] 合成生物工学によるモノづくり微生物のデザインに向けて2015

    • Author(s)
      石井純、荒木通啓、中津井雅彦、崎濱 由梨、柘植 陽太、蓮沼 誠久、近藤 昭彦
    • Total Pages
      5
    • Publisher
      生物工学会誌
    • Related Report
      2015 Research-status Report
  • [Book] データベースからの再発見2014

    • Author(s)
      荒木通啓
    • Total Pages
      1
    • Publisher
      生物工学会誌(バイオミディア)
    • Related Report
      2014 Research-status Report
  • [Remarks] M-path EN

    • URL

      http://bp.scitec.kobe-u.ac.jp/m-path/en

    • Related Report
      2014 Research-status Report

URL: 

Published: 2014-04-04   Modified: 2018-03-22  

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