Rchr
J-GLOBAL ID：200901096694313316   Update date: Nov. 19, 2024

Akiyama Yutaka

アキヤマ ユタカ | Akiyama Yutaka
Affiliation and department：
Institute of Science Tokyo School of Computing

About Institute of Science Tokyo School of Computing


Job title： Professor
Homepage URL  (2)： http://www.bi.cs.titech.ac.jp/ ,  http://www.bi.cs.titech.ac.jp/web/top_en.html
Research field  (1)： Biological, health, and medical informatics
Research keywords  (3)： Computatinal Drug Design ,  Parallel Computing Applications ,  Bioinformatics
Research theme for competitive and other funds  (9)：
  • 2022 - 2025 Virtual screening method for large-scale compound databases utilizing the commonality of partial structures
  • 2021 - 2024 Research on the relevance between fungal growth and mite population
  • 2020 - 2023 ミトコンドリア病細胞死阻止機構の解明と創薬
  • 2017 - 2020 Development of computational methods for supporting druggable cyclic peptide design
  • 2015 - 2019 In silico, in vitro, X-ray crystallography, and integrated strategies for discovering spermidine synthase inhibitors for Chagas disease
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Papers (112)：
  • Taisuke Boku, Masatake Sugita, Ryohei Kobayashi, Shinnosuke Furuya, Takuya Fujie, Masahito Ohue, Yutaka Akiyama. Improving Performance on Replica-Exchange Molecular Dynamics Simulations by Optimizing GPU Core Utilization. ACM International Conference Proceeding Series. 2024. 1082-1091
  • Ryunosuke Yoshino, Nobuaki Yasuo, Yohsuke Hagiwara, Takashi Ishida, Daniel Ken Inaoka, Yasushi Amano, Yukihiro Tateishi, Kazuki Ohno, Ichiji Namatame, Tatsuya Niimi, et al. Discovery of a Hidden Trypanosoma cruzi Spermidine Synthase Binding Site and Inhibitors through In Silico, In Vitro, and X-ray Crystallography. ACS Omega. 2023
  • Jianan Li, Keisuke Yanagisawa, Masatake Sugita, Takuya Fujie, Masahito Ohue, Yutaka Akiyama. CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides. Journal of chemical information and modeling. 2023. 63. 7. 2240-2250
  • Masatake Sugita, Takuya Fujie, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama. Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations. Journal of chemical information and modeling. 2022. 62. 18. 4549-4560
  • Keisuke Yanagisawa, Rikuto Kubota, Yasushi Yoshikawa, Masahito Ohue, Yutaka Akiyama. Effective Protein-Ligand Docking Strategy via Fragment Reuse and a Proof-of-Concept Implementation. ACS omega. 2022. 7. 34. 30265-30274
ｍore...
MISC (323)：
  • Masahito Ohue, Hiroki Watanabe, Yutaka Akiyama. MEGADOCK-Web-Mito: human mitochondrial protein-protein interaction prediction database. 2021
  • 井澤和也, 井澤和也, 柳澤渓甫, 柳澤渓甫, 大上雅史, 大上雅史, 秋山泰, 秋山泰. Antisense oligonucleotide activity analysis based on opening and binding energies to targets. 情報処理学会研究報告(Web). 2021. 2021. MPS-134
  • 井澤和也, 柳澤渓甫, 柳澤渓甫, 大上雅史, 大上雅史, 秋山泰, 秋山泰. Inhibitory Activity Model of Antisense Oligonucleotide Based on Estimation of Binding and Opening Energies to Target Sequences. 情報処理学会研究報告(Web). 2021. 2021. BIO-65
  • 高畠和輝, 伊澤和輝, 秋川元宏, 大上雅史, 秋山泰. Improvement of homology search for metagenomic analysis by two-step seed search with reduced amino acid alphabet. 情報処理学会研究報告(Web). 2020. 2020. BIO-61
  • 久保田陸人, 柳澤渓甫, 吉川寧, 大上雅史, 秋山泰. Development of an efficient protein-ligand docking method by reuse of fragments. 情報処理学会研究報告(Web). 2020. 2020. BIO-61
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Patents (16)：
  • 情報処理装置、情報処理方法、情報処理プログラム、及び情報処理システム
  • 予測装置、学習済みモデルの生成装置、予測方法、学習済みモデルの生成方法、予測プログラム、及び学習済みモデルの生成プログラム
  • 予測装置、学習済みモデルの生成装置、予測方法、学習済みモデルの生成方法、予測プログラム、及び学習済みモデルの生成プログラム
  • 情報処理装置、情報処理方法、および、プログラム
  • 情報処理装置、情報処理方法、および、プログラム
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Books (8)：
  • 細胞丸ごとRNA解析に向けたバイオインフォマティクス技術
    CMC出版 2006 ISBN:4882315955
  • ポストゲノム-ライフサイエンス最前線
    丸善 2002
  • 並列タンパク質情報解析(PAPIA)システム
    共立出版 1999
  • WWWによる統合データベース環境
    共立出版 1996
  • トリッキープログラムの謎を解け-RNA2次構造予測への組合せ最適化的アプローチ
    共立出版 1994
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Lectures and oral presentations  (231)：
  • Proposal of an all-to-all protein-protein interaction prediction technique
    (2010)
  • Improvement of accuracy of the protein-protein docking calculation by a re-ranking method and its application to all-to-all protein-protein interaction predictions
    (IPSJ SIG Technical Report 2010)
  • A computational screening system of protein-protein interactions: connecting structural information to pathway estimation.
    (The 2nd Biosupercomputing Symposium 2010)
  • MEGADOCK: An all-to-all protein-protein interaction prediction system -- Improving the accuracy using boosting and binding energy reranking.
    (The 2nd Biosupercomputing Symposium 2010)
  • Improvement of rigid-body prediction for unbound docking based on protein feature
    (IPSJ SIG Technical Report 2010)
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Education (3)：
  • 1986 - 1990 Keio University Graduate School of Science and Technology Electrical Engineering
  • 1984 - 1986 Keio University Graduate School of Engineering Department of Electorical Engineering
  • 1980 - 1984 Keio University Faculty of Engineering Department of Electrical Engineering
Professional career (1)：
  • Doctor of Engineering (Keio University)
Work history (6)：
  • 2007/04 - 現在 Tokyo Institute of Technology School of Computing Professor
  • 2001/04 - 2007/03 National Institute of Advanced Industrial Science and Technology Computational Biology Research Center Director
  • 2000/04 - 2001/03 Agency of Industrial Science and Technology Electrotechnical laboratory Senior researcher
  • 1996/04 - 2000/03 Real World Computing Partnership Tsukuba Research Center Laboratory head
  • 1992/04 - 1996/03 Kyoto University Institute for Chemical Research Associate Professor
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Committee career (6)：
  • 2008 - 2010 Information Processing Society of Japan editorial board of SIGMPS、Secretary of SIGMPS
  • 2008 - 2010 Japanese Society for Bioinformatics Secretary、Board member、Vice President、Secretary
  • 2008 - 2010 情報処理学会 研究会運営委員(MPS)、研究会運営委員(HPS)、研究会論文誌編集委員、研究会幹事(MPS)
  • 2008 - 2010 日本バイオインフォマティクス学会 幹事、評議員、副会長、幹事
  • 2005 - 2007 Japanese Society of Artificial Intelligence Board member
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Awards (3)：
  • 2013/08 - 内閣府 第11回 産学官連携功労者表彰 厚生労働大臣賞 「顧みられない熱帯感染症」創薬研究データベースの開発
  • 1988 - Best Paper Award for Young Researcher
  • 1988 - 学術奨励賞
Association Membership(s) (14)：
The Molecular Biology Society of Japan ,  Japanese Neural Network Society ,  The Biophysical Society of Japan ,  The Japanese Society for the Study of Xenobiotics ,  Japanese Society of Artificial Intelligence ,  Information Processing Society of Japan ,  Japanese Society for Bioinformatics ,  日本分子生物学会 ,  日本神経回路学会 ,  日本生物物理学会 ,  日本薬物動態学会 ,  人工知能学会 ,  情報処理学会 ,  日本バイオインフォマティクス学会
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