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2023 Fiscal Year Annual Research 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 – 2024-03-31
Keywordsテンソル分解 / 教師なし学習 / 変数選択
Outline of Annual Research Achievements

single cell multiomicsの解析にテンソル分解の方法が有効であることを確認して、
学術論文や国際会議の研究報告として出版した。特に、遺伝子発現プロファイル、メチル化、ATAC-seqの統合解
析に有効であることを確認できた。これによって今後シングルセル解析にテンソル分解を用いることが容易にな
ると期待される。このような研究はいままでされていなかったので非常に貴重な研究成果であるということがで
きる。

  • Research Products

    (17 results)

All 2024 2023

All Journal Article (14 results) (of which Int'l Joint Research: 8 results,  Peer Reviewed: 14 results,  Open Access: 9 results) Presentation (2 results) (of which Int'l Joint Research: 2 results) Book (1 results)

  • [Journal Article] Integrative Meta-Analysis of Huntington’s Disease Transcriptome Landscape2023

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

      Genes

      Volume: 13 Pages: 2385~2385

    • DOI

      10.3390/genes13122385

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Bioinformatic tools for epitranscriptomics2023

    • Author(s)
      Taguchi Y.-H.
    • Journal Title

      American Journal of Physiology-Cell Physiology

      Volume: 324 Pages: C447~C457

    • DOI

      10.1152/ajpcell.00437.2022

    • Peer Reviewed
  • [Journal Article] Features extracted using tensor decomposition reflect the biological features of the temporal patterns of human blood multimodal metabolome2023

    • Author(s)
      Fujita Suguru、Karasawa Yasuaki、Hironaka Ken-ichi、Taguchi Y.-h.、Kuroda Shinya
    • Journal Title

      PLOS ONE

      Volume: 18 Pages: e0281594

    • DOI

      10.1371/journal.pone.0281594

    • Peer Reviewed / Open Access
  • [Journal Article] A new machine learning based computational framework identifies therapeutic targets and unveils influential genes in pancreatic islet cells2023

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

      Gene

      Volume: 853 Pages: 147038~147038

    • DOI

      10.1016/j.gene.2022.147038

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Principal component analysis- and tensor decomposition-based unsupervised feature extraction to select more suitable differentially methylated cytosines: Optimization of standard deviation versus state-of-the-art methods2023

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

      Genomics

      Volume: 115 Pages: 110577~110577

    • DOI

      10.1016/j.ygeno.2023.110577

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Tensor decomposition discriminates tissues using scATAC-seq2023

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

      Biochimica et Biophysica Acta (BBA) - General Subjects

      Volume: 1867 Pages: 130360~130360

    • DOI

      10.1016/j.bbagen.2023.130360

    • Peer Reviewed / Open Access
  • [Journal Article] Integrated analysis of human DNA methylation, gene expression, and genomic variation in iMETHYL database using kernel tensor decomposition-based unsupervised feature extraction2023

    • Author(s)
      Taguchi Y-h.、Komaki Shohei、Sutoh Yoichi、Ohmomo Hideki、Otsuka-Yamasaki Yayoi、Shimizu Atsushi
    • Journal Title

      PLOS ONE

      Volume: 18 Pages: e0289029

    • DOI

      10.1371/journal.pone.0289029

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Optimized Tensor Decomposition and Principal Component Analysis Outperforming State-of-the-Art Methods When Analyzing Histone Modification Chromatin Immunoprecipitation Profiles2023

    • Author(s)
      Turki Turki、Roy Sanjiban Sekhar、Taguchi Y.-H.
    • Journal Title

      Algorithms

      Volume: 16 Pages: 401~401

    • DOI

      10.3390/a16090401

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Integrated Analysis of Gene Expression and Protein?Protein Interaction with Tensor Decomposition2023

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

      Mathematics

      Volume: 11 Pages: 3655~3655

    • DOI

      10.3390/math11173655

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] GENEvaRX: A novel AI-driven method and web tool can identify critical genes and effective drugs for Lichen Planus2023

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

      Engineering Applications of Artificial Intelligence

      Volume: 124 Pages: 106607~106607

    • DOI

      10.1016/j.engappai.2023.106607

    • Peer Reviewed / Open Access
  • [Journal Article] Application note: TDbasedUFE and TDbasedUFEadv: bioconductor packages to perform tensor decomposition based unsupervised feature extraction2023

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

      Frontiers in Artificial Intelligence

      Volume: 6 Pages: 1

    • DOI

      10.3389/frai.2023.1237542

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Investigating Neuron Degeneration in Huntington’s Disease Using RNA-Seq Based Transcriptome Study2023

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

      Genes

      Volume: 14 Pages: 1801~1801

    • DOI

      10.3390/genes14091801

    • Peer Reviewed / Open Access
  • [Journal Article] Advanced Tensor Decomposition-Based Integrated Analysis of Protein-Protein Interaction with Cancer Gene Expression Can Improve Coincidence with Clinical Labels2023

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

      11th International Conference on Bioinformatics and Computational Biology (ICBCB)

      Volume: 1 Pages: 1-2

    • DOI

      10.1109/ICBCB57893.2023.10246633

    • Peer Reviewed / Open Access
  • [Journal Article] Characterization of circulating <scp>miRNAs</scp> in the treatment of primary liver tumors2023

    • Author(s)
      Umezu Tomohiro、Tanaka Shogo、Kubo Shoji、Enomoto Masaru、Tamori Akihiro、Ochiya Takahiro、Taguchi Y.‐H.、Kuroda Masahiko、Murakami Yoshiki
    • Journal Title

      Cancer Reports

      Volume: 7 Pages: 1-9

    • DOI

      10.1002/cnr2.1964

    • Peer Reviewed / Int'l Joint Research
  • [Presentation] TDbasedUFE and TDbasedUFEadv: bioconductor packages to perform tensor decomposition based unsupervised feature extraction2023

    • Author(s)
      Y-h. Taguchi
    • Organizer
      BiocAsia2023
    • Int'l Joint Research
  • [Presentation] Advanced Tensor Decomposition-Based Integrated Analysis of Protein-Protein Interaction with Cancer Gene Expression Can Improve Coincidence with Clinical labels2023

    • Author(s)
      YH Taguchi , Turki Turki
    • Organizer
      2023 11th International Conference on Bioinformatics and Computational Biology (ICBCB)
    • Int'l Joint Research
  • [Book] はじめての機械学習 中学数学でわかるAIのエッセンス2024

    • Author(s)
      田口 善弘
    • Total Pages
      272
    • Publisher
      講談社
    • ISBN
      978-4065239605

URL: 

Published: 2024-12-25  

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