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2020 Fiscal Year Research-status Report

scRNA-seq analysis using PCA and TD based unsupervised feature extraction

Research Project

Project/Area Number 20K12067
Research InstitutionChuo University

Principal Investigator

田口 善弘  中央大学, 理工学部, 教授 (30206932)

Project Period (FY) 2020-04-01 – 2023-03-31
Keywordsテンソル分解
Outline of Annual Research Achievements

昨年度は当該研究について10本以上の原著論文を出版することができた。また、テンソル分解を拡張してカーネルテンソル分解を実装することに成功した。5月にはICBC2020でkey note講演を行い、また、ISET2020ではBest Paper Awardをとり、情報処理学会バイオ情報学研究会からはベストプレゼンテーション賞をもらうなど、国内外から広範な評価を受けた。
具体的な研究内容としてはCOVID-19治療薬のリポジショニングを行い、現在、注目されているイベルメクチンを見出し、コンソーシアムから根拠論文としてリンクを張られている。

Current Status of Research Progress
Current Status of Research Progress

1: Research has progressed more than it was originally planned.

Reason

従来からの懸案であった非線形性を取り入れられるカーネルテンソル分解を提案で来た。

Strategy for Future Research Activity

現在、カーネルテンソル分解を拡張してマルチオミックスデータ解析に特化したアルゴリズムを構想中である

Causes of Carryover

コロナ禍で研究活動が十分にできなかったため

  • Research Products

    (29 results)

All 2020 Other

All Int'l Joint Research (3 results) Journal Article (9 results) (of which Int'l Joint Research: 7 results,  Peer Reviewed: 9 results,  Open Access: 9 results) Presentation (16 results) (of which Int'l Joint Research: 5 results,  Invited: 3 results) Book (1 results)

  • [Int'l Joint Research] Asia University(その他の国・地域)

    • Country Name
      その他の国・地域
    • Counterpart Institution
      Asia University
  • [Int'l Joint Research] King Abdulaziz University(サウジアラビア)

    • Country Name
      SAUDI ARABIA
    • Counterpart Institution
      King Abdulaziz University
  • [Int'l Joint Research] IIT Madras/Vellore Institute of Technology(インド)

    • Country Name
      INDIA
    • Counterpart Institution
      IIT Madras/Vellore Institute of Technology
  • [Journal Article] Identifying suitable tools for variant detection and differential gene expression using RNA-seq data2020

    • Author(s)
      Dharshini S. Akila Parvathy、Taguchi Y.-H.、Gromiha M. Michael
    • Journal Title

      Genomics

      Volume: 112 Pages: 2166~2172

    • DOI

      10.1016/j.ygeno.2019.12.011

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Incremental Dilations Using CNN for Brain Tumor Classification2020

    • Author(s)
      Roy Sanjiban Sekhar、Rodrigues Nishant、Taguchi Y-h.
    • Journal Title

      Applied Sciences

      Volume: 10 Pages: 4915~4915

    • DOI

      10.3390/app10144915

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Universal Nature of Drug Treatment Responses in Drug-Tissue-Wide Model-Animal Experiments Using Tensor Decomposition-Based Unsupervised Feature Extraction2020

    • Author(s)
      Taguchi Yh.、Turki Turki
    • Journal Title

      Frontiers in Genetics

      Volume: 11 Pages: 695

    • DOI

      10.3389/fgene.2020.00695

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A new advanced in silico drug discovery method for novel coronavirus (SARS-CoV-2) with tensor decomposition-based unsupervised feature extraction2020

    • Author(s)
      Taguchi Y-h.、Turki Turki
    • Journal Title

      PLOS ONE

      Volume: 15 Pages: 0238907~0238907

    • DOI

      10.1371/journal.pone.0238907

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Identification of miRNA signatures for kidney renal clear cell carcinoma using the tensor-decomposition method2020

    • Author(s)
      Ng Ka-Lok、Taguchi Y.-H.
    • Journal Title

      Scientific Reports

      Volume: 10 Pages: 15149

    • DOI

      10.1038/s41598-020-71997-6

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Tensor-Decomposition-Based Unsupervised Feature Extraction Applied to Prostate Cancer Multiomics Data2020

    • Author(s)
      Taguchi Y-h.、Turki Turki
    • Journal Title

      Genes

      Volume: 11 Pages: 1493~1493

    • DOI

      10.3390/genes11121493

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Developing a diagnostic method for latent tuberculosis infection using circulating miRNA2020

    • Author(s)
      Hashimoto Shoji、Zhao Hong、Hayakawa Michiyo、Nakajima Koichi、Taguchi Y-h、Murakami Yoshiki
    • Journal Title

      Translational Medicine Communications

      Volume: 5 Pages: 25

    • DOI

      10.1186/s41231-020-00078-7

    • Peer Reviewed / Open Access
  • [Journal Article] Comprehensive analysis of liver and blood miRNA in precancerous conditions2020

    • Author(s)
      Umezu Tomohiro、Tsuneyama Koichi、Kanekura Kohsuke、Hayakawa Michiyo、Tanahashi Toshihito、Kawano Mitsuoki、Taguchi Y-h、Toyoda Hidenori、Tamori Akihiro、Kuroda Masahiko、Murakami Yoshiki
    • Journal Title

      Scientific Reports

      Volume: 10 Pages: 21766

    • DOI

      10.1038/s41598-020-78500-1

    • Peer Reviewed / Open Access
  • [Journal Article] Identification of Transcription Factors, Biological Pathways, and Diseases as Mediated by N6-methyladenosine Using Tensor Decomposition-Based Unsupervised Feature Extraction2020

    • Author(s)
      Taguchi Y-h.、Dharshini S. Akila Parvathy、Gromiha M. Michael
    • Journal Title

      Applied Sciences

      Volume: 11 Pages: 213~213

    • DOI

      10.3390/app11010213

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] テンソル分解に基づく教師なし学習による変数選択のRNAi 処理を行ったプラナリアのRNA-seq解析への適用2020

    • Author(s)
      田口善弘 , 鹿島誠
    • Organizer
      情報処理学会バイオ情報学研究会
  • [Presentation] Conjecturing human genes that are easy to be double strand breaks by tensor decomposition2020

    • Author(s)
      Nobuo Hosaka , Y-h. Taguchi
    • Organizer
      情報処理学会バイオ情報学研究会
  • [Presentation] テンソル分解を用いた教師無し学習による変数選択法によるmiRNA/mRNA/プロテオームの統合解析2020

    • Author(s)
      田口善弘
    • Organizer
      情報処理学会バイオ情報学研究会
  • [Presentation] カーネルテンソル分解を用いた教師なし学習による変数選択法 ~ バイオインフォマティクスへの応用 ~2020

    • Author(s)
      田口善弘
    • Organizer
      情報論的学習理論と機械学習 (IBISML) 研究会
  • [Presentation] カーネルテンソル分解を用いた教師なし学習による変数選択法 ~ バイオインフォマティクスへの応用 ~2020

    • Author(s)
      田口善弘
    • Organizer
      情報処理学会バイオ情報学研究会
  • [Presentation] Application of Tensor Decomposition based Unsupervised Feature Extraction to Single Cell RNA-seq Data Analysis2020

    • Author(s)
      Y-h. Taguchi
    • Organizer
      ICBCB2020
    • Int'l Joint Research / Invited
  • [Presentation] Tensor decomposition based unsupervised Feature Extraction applied to in silico COVID-19 drug siscovery based upon analysis of gene expression profiles altered by SARS-CoV-2 infection2020

    • Author(s)
      Y-h. Taguchi
    • Organizer
      第九回生命医薬情報学連合大会(IIBMP2020)
  • [Presentation] テンソル分解により二本鎖切断になりやすいヒト遺伝子の推定2020

    • Author(s)
      保坂伸生 , 田口善弘
    • Organizer
      第九回生命医薬情報学連合大会(IIBMP2020)
  • [Presentation] In silico drug discovery for COVID-19 using gene expression profiles of mouse infected by MHV and those of human cell lines infected by SARS-CoV-22020

    • Author(s)
      Y-h. Taguchi
    • Organizer
      7th Annual Congress of the European Society for Translational Medicine on Covid-19
    • Int'l Joint Research / Invited
  • [Presentation] Selecting the genes related to COVID-19 with PCA-based unsupervised feature extraction2020

    • Author(s)
      Kota Fujisawa , Mamoru Shimo , Yoshihiro Taguchi , Shinya Ikematu , Ryota Miyata
    • Organizer
      CBI学会2020年会
  • [Presentation] Identification of Transcription Factors, Biological Pathways, and Diseases as Mediated by N6-methyladenosine using Tensor Decomposition-Based Unsupervised Feature Extraction.2020

    • Author(s)
      Y-h. Taguchi , S Akila Parvathy Dharshini , M. Michael , Gromiha
    • Organizer
      The 2nd International Symposium on Engineering and Technology (ISET 2020)
    • Int'l Joint Research
  • [Presentation] テンソル分解を用いた教師無し学習による変数選択法を用いたCOVID-19治療薬の探索2020

    • Author(s)
      田口善弘
    • Organizer
      IBIS2020
  • [Presentation] Unsupervised tensor decomposition-based method to extract candidate transcription factors as histone modification bookmarks in post-mitotic transcriptional reactivation2020

    • Author(s)
      Y-h. Taguchi
    • Organizer
      The 19th International Conference on Bioinformatics (InCoB 2020)
    • Int'l Joint Research
  • [Presentation] テンソル分解を用いた教師無し学習による変数選択法を用いたCOVID-19治療薬のリポジショニング2020

    • Author(s)
      田口善弘
    • Organizer
      第43回日本分子生物学会年会
  • [Presentation] テンソル分解を用いた教師なし学習による変数選択法を用いたゲノムデータ解析2020

    • Author(s)
      田口善弘
    • Organizer
      イノベーションジャパン
  • [Presentation] Principal Component Analysis, Tensor Decomposition, and Kernel Tensor Decomposition Based Unsupervised Feature Extraction Applied to Bioinformatics2020

    • Author(s)
      Y-h. Taguchi
    • Organizer
      2020 International Symposium on Automation, Information and Computing
    • Int'l Joint Research / Invited
  • [Book] 生命はデジタルでできている 情報から見た新しい生命像2020

    • Author(s)
      田口 善弘
    • Total Pages
      224
    • Publisher
      講談社
    • ISBN
      978-4065195970

URL: 

Published: 2021-12-27  

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