Development of protein function prediction methods with global substructures and interaction stochastic models

• Project/Area Number: 16K00392
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Life / Health / Medical informatics
• Research Institution: Matsue National College of Technology (2017-2019); Kyoto University (2016)
• Principal Investigator: HAYASHIDA Morihiro 松江工業高等専門学校, 電気情報工学科, 准教授 (40402929)
• Co-Investigator(Kenkyū-buntansha): 小谷野 仁 国立研究開発法人農業・食品産業技術総合研究機構, 農業情報研究センター, 研究員 (10570989)
• Project Period (FY): 2016-04-01 – 2020-03-31
• Project Status: Completed (Fiscal Year 2019)
• Budget Amount: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000); Fiscal Year 2018: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2017: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
• Keywords: タンパク質相互作用予測 / タンパク質二量体予測 / 中央文字列 / 文法圧縮 / 一般化Series-Parallelグラフ / ラプラス様混合確率分布 / EMアルゴリズム / 畳み込みニューラルネットワーク / タンパク質ドメイン / ニューラルネットワーク / タンパク質RNA相互作用 / 条件付き確率場 / イジングモデル / 一般化series-parallelグラフ / 整数線形計画問題 / 宿主病原体相互作用 / 局所トポロジー / Dicer切断部位 / 三角不等式 / タンパク質 / アルゴリズム / 画像認識 / 生体生命情報学 / 機械学習

Outline of Final Research Achievements

It is useful for understanding protein functions to identify biomolecules interacting with proteins and proteins consisted in a complex. We improved prediction methods for protein-RNA residue-base contacts and heterodimeric protein complexes. We developed an estimation method of a Laplace-like mixture on a set of strings, and enhanced the speed of finding median strings. Furthermore, we developed grammar-based compression methods for domain sequences of proteins and generalized series-parallel graphs.

Academic Significance and Societal Importance of the Research Achievements

タンパク質相互作用およびタンパク質複合体の予測精度を向上させることによってタンパク質の機能を推定する手がかりとし，病原菌の感染経路の解明など生物学，医学へ貢献する．また文字列の集合上の確率分布や中央文字列の厳密解法，一般化Series-Parallelグラフの最小文法を与えることはタンパク質やRNAの配列解析や生物学的ネットワーク構造の解析に有用であるだけでなく数理学的にも意義がある．

Research Products

• [Journal Article] Optimal string clustering based on a Laplace-like mixture and EM algorithm on a set of strings (2019)
  • Author(s): Koyano Hitoshi、Hayashida Morihiro、Akutsu Tatsuya
  • Journal Title: Journal of Computer and System Sciences Volume: 106 Pages: 94-128
  • DOI: 10.1016/j.jcss.2019.07.003
  • Peer Reviewed / Open Access
• [Journal Article] Convolutional neural network approach to lung cancer classification integrating protein interaction network and gene expression profiles (2019)
  • Author(s): Teppei Matsubara, Tomoshiro Ochiai, Morihiro Hayashida, Tatsuya Akutsu and Jose C. Nacher
  • Journal Title: Journal of Bioinformatics and Computational Biology Volume: 17 Issue: 03 Pages: 1940007-1940007
  • DOI: 10.1142/s0219720019400079
  • Peer Reviewed
• [Journal Article] ncRNA-disease association prediction based on sequence information and tripartite network (2018)
  • Author(s): T. Mori, H. Ngouv, M. Hayashida, T. Akutsu and J. C. Nacher
  • Journal Title: BMC Systems Biology Volume: 12 Issue: S1 Pages: 1-1
  • DOI: 10.1186/s12918-018-0527-4
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Determining the minimum number of protein-protein interactions required to support known protein complexes (2018)
  • Author(s): Natsu Nakajima, Morihiro Hayashida, Jesper Jansson, Osamu Maruyama, Tatsuya Akutsu
  • Journal Title: PLOS ONE Volume: 13 Issue: 4 Pages: e0195545-e0195545
  • DOI: 10.1371/journal.pone.0195545
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Improving conditional random field model for prediction of protein-RNA residue-base contacts (2018)
  • Author(s): Morihiro Hayashida, Noriyuki Okada, Mayumi Kamada, Hitoshi Koyano
  • Journal Title: Quantitative Biology Volume: 6 Issue: 2 Pages: 155-162
  • DOI: 10.1007/s40484-018-0136-7
  • Peer Reviewed / Open Access
• [Journal Article] Analysis of critical and redundant vertices in controlling directed complex networks using feedback vertex sets (2018)
  • Author(s): Yu Bao, Morihiro Hayashida, Pengyu Liu, Masayuki Ishitsuka, Jose Nacher, Tatsuya Akutsu
  • Journal Title: Journal of Computational Biology Volume: 25 Issue: 10 Pages: 1071-1090
  • DOI: 10.1089/cmb.2018.0019
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Improving prediction of heterodimeric protein complexes using combination with pairwise kernel (2018)
  • Author(s): Ruan Peiying、Hayashida Morihiro、Akutsu Tatsuya、Vert Jean-Philippe
  • Journal Title: BMC Bioinformatics Volume: 19 Issue: S1 Pages: 39-39
  • DOI: 10.1186/s12859-018-2017-5
  • NAID: 120006537092
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Finding median and center strings for a probability distribution on a set of strings under Levenshtein distance based on integer linear programming (2017)
  • Author(s): Hayashida, M. and Koyano, H.
  • Journal Title: Communications in Computer and Information Science Volume: 690 Pages: 108-121
  • DOI: 10.1007/978-3-319-54717-6_7
  • ISBN: 9783319547169, 9783319547176
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length (2016)
  • Author(s): Y. Bao, M. Hayashida, T. Akutsu
  • Journal Title: BMC Bioinformatics Volume: 17 Issue: 1 Pages: 487-487
  • DOI: 10.1186/s12859-016-1353-6
  • NAID: 120005973378
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Presentation] Artificial neural network approach to prediction of protein-RNA residue-base contacts (2019)
  • Author(s): Morihiro Hayashida, Jose Nacher, Hitoshi Koyano
  • Organizer: The 12th International Conference on Bioinformatics Models, Methods and Algorithms
  • Int'l Joint Research
• [Presentation] Convolutional neural network approach to lung cancer classification integrating protein interaction network and gene expression profiles (2018)
  • Author(s): Teppei Matsubara, Tomoshiro Ochiai, Morihiro Hayashida, Tatsuya Akutsu, Jose Nacher
  • Organizer: The 18th IEEE International Conference on Bioinformatics and BioEngineering
  • Int'l Joint Research
• [Presentation] Analyzing order of domains in grammar-based compression of proteomes (2018)
  • Author(s): Morihiro Hayashida, Kousei Ishibashi, Hitoshi Koyano
  • Organizer: The 24th International Conference on Parallel and Distributed Processing Techniques and Applications
  • Int'l Joint Research
• [Presentation] ncRNA-disease association prediction based on sequence information and tripartite network (2018)
  • Author(s): Takuya Mori, Hayliang Ngouv, Morihiro Hayashida, Tatsuya Akutsu, Jose Nacher
  • Organizer: The 16th Asia Pacific Bioinformatics Conference
  • Int'l Joint Research
• [Presentation] Grammar-based compression for directed and undirected generalized series-parallel graphs using integer linear programming (2018)
  • Author(s): Morihiro Hayashida, Hitoshi Koyano, Tatsuya Akutsu
  • Organizer: The 9th International Conference on Bioinformatics Models, Methods and Algorithms
  • Int'l Joint Research
• [Presentation] Improving conditional random field model for prediction of protein-RNA residue-base contacts (2017)
  • Author(s): Morihiro Hayashida, Noriyuki Okada, Mayumi Kamada, Hitoshi Koyano
  • Organizer: The 11th International Conference on Computational Systems Biology
  • Int'l Joint Research
• [Presentation] Host-pathogen protein interaction prediction based on local topology structures of a protein interaction network (2016)
  • Author(s): Jira Jindalertudomdee, Morihiro Hayashida, Jianning Song, Tatsuya Akutsu
  • Organizer: IEEE 16th International Conference on Bioinformatics and BioEngineering
  • Place of Presentation: 台中
  • Year and Date: 2016-10-31
  • Int'l Joint Research