Positions held

• 2025/4 - current Visiting Associate Professor, Bioinformatics Center, Institute for Chemical Research, Kyoto University
• 2022/7 - current Associate Professor, Institute for Quantitative Biosciences, The University of Tokyo
• 2019/4 - 2022/6 Lecturer, Institute for Quantitative Biosciences, The University of Tokyo
• 2018/4 - 2019/3 Research Associate, Institute for Quantitative Biosciences, The University of Tokyo
• 2010/4 - 2018/3 Research Associate, Institute of Molecular and Cellular Biosciences, The University of Tokyo

Education

• 2007/4 - 2010/3 Ph.D. Department of Intelligence Science and Technology, Kyoto University
• 2005/4 - 2007/3 M.S. Department of Intelligence Science and Technology, Kyoto University
• 2000/4 - 2005/3 B.S. Faculty of Engineering, Kyoto University

Research theme

• Data-driven analysis using large-scale NGS data
• Exploration of novel functional regulatory genomic regions using multi-omics data
• Functional analysis of 3D genome structures in gene expression regulation
• Development of methods for epigenome analysis using deep learning technologies
• Development of methods for gene network reconstruction and analysisks
• Trajectory analysis using single-cell data to study cell fate determination

Works

• Papers
  • See Publication list
• Invited Talks
  • Large language models to explore the syntax in the epigenome, International Conference on Quantum & AI Technologies in Biomedical Science, the National Taiwan University, Taipei, Taiwan, April 7th, 2025.
  • Computational pipelines for integrative analysis of multi-omics data, Asia Pacific Spatial Omics Technology 2024 (APSOT2024), the National Taiwan University Cancer Center (NTUCC), Taipei, Taiwan, May 24th, 2024.
  • Large-scale multi-omics analysis to explore the function of cohesin complex, NTU-UTokyo Joint Conference 2023, National Taiwan University, Taipei, Taiwan, Dec. 8th, 2023.
  • Large-scale computational genomics: tools for decoding genomic features, Human Genetics Asia 2023, Tokyo, Japan, Oct. 14th, 2023.
  • Data-driven epigenomic analysis with large-scale datasets: the International Human Epigenome Consortium (IHEC), The 16th Annual Meeting of the Japanese Society for Epigenetics, Tokyo, Japan, Jun. 19th, 2023.
  • Large-scale analysis of multi-omics data toward the elucidation of epigenomic diversity, The 2nd ASHBi Mathematical Biology Workshop, Kyoto (online), Japan, Sep. 4th, 2020.
  • Comprehensive epigenome characterization reveals the diverse transcriptional heterogeneity across human vascular endothelial cells, Kyoto University Bioinformatics Center Seminar, Kyoto, Japan, Feb. 1st, 2018.
• Oral Presentations
  • Deep learning-based approaches to elucidate unknown functional regions of the genome, EMBO Workshop "Global insights in life sciences", European Molecular Biology Laboratory (EMBL), Heidelberg, Germany, Feb. 27th, 2025.
  • Context-specific roles of cohesin for higher-order chromatin folding and transcription, The 47th Annual Meetings of the Molecular Biology Society of Japan (MBSJ2024), Hakata, Japan, Nov. 29th, 2024.
  • Large-scale multi-omics analysis to dissect the context-specific role of cohesin in chromatin folding and gene expression, CEEHRC 9th Annual Canadian Conference on Epigenetics, Banff, Alberta, Canada, Nov. 15th, 2023.
  • Context-dependent 3D genome regulation by cohesin and related factors, The 3rd workshop on Hi-C analysis, Kobe, Japan, May 11th, 2023.
  • Context-dependent regulation of gene expression and 3D genome structure by cohesin, The 45th Annual Meetings of the Molecular Biology Society of Japan (MBSJ2022), Makuhari, Japan, Dec. 1st, 2022.
  • Recent advances in computational analyses for single-cell data, The 42th Annual Meetings of the Molecular Biology Society of Japan (MBSJ2019), Hakata, Japan, Dec., 2019.
  • (Short talk) Integrated analysis of gene expression and chromatin folding regulated by cohesin, cohesin loader and CTCF, The 13th International Workshop on Advanced Genomics (13AGW), Tokyo, Japan, Jun., 2019.
  • A bioinformatics approach to data imputation and systems biology for single-cell RNA-seq data, The 41th Annual Meetings of the Molecular Biology Society of Japan (MBSJ2018), Yokohama, Japan, Nov., 2018.
  • (Short talk) Comparison of genome-wide binding sites for cohesin and related proteins for investigation of transcriptional regulation function, The International Institute for Advanced Studies (IIAS) Research Conference 2014 "Chromatin Decoding", Kyoto, Japan, May, 2014.
  • A novel method for reducing computational complexity of whole genome sequence alignment, In Proceedings of The Sixth Asia Pacific Bioinformatics Conference (APBC2008), pp.101-110, Kyoto, Jan, 2008.

Funding (Lead principal investigator)

• Development of a computational platform for novel large-scale genomic analysis.
  • Fusion Oriented REsearch for disruptive Science and Technology (FOREST)
  • Project Period: 2024-04-01 - 2031-3-31
• Comparative single-cell analysis of disease-derived stem cells to identify the cell fate defect on the cell differentiation trajectory.
  • JSPS Grant-in-Aid for Scientific Research (B)
  • Project Period: 2023-04-01 - 2027-3-31
• Time-course genomic analysis for elucidation of the mechanism of an inherited disease.
  • 2022 Astellas Foundation Grant
  • Project Period: 2023-01-01 - 2024-12-31
• Identification of novel marker genes from single cell transcriptome data using signed network analysis.
  • 2022 Sumitomo Foundation Grant
  • Project Period: 2022-11-01 - 2023-10-31
• Development of a robust computational platform for data-driven epigenome analysis.
  • AMED-PRIME "Understanding of the biological phenomena and responses at the early life stages to improve the quality of health and medical care"
  • Project Period: 2020-10-01 - 2024-03-31
  • (also joining International Human Epigenome Consortium (IHEC) as an activity of AMED-PRIME)
• Development of a single-cell analysis system toward elucidating the mechanism of cell differentiation defects in rare diseases-derived iPS cells.
  • 2020 iPS Academia Japan Grant
  • Project Period: 2021-01-01 - 2021-12-31
• Development of an integrated platform for analysis of epigenome and single-cell data.
  • JSPS Grant-in-Aid for Scientific Research on Innovative Areas
  • Project Period: 2017-06-30 - 2022-03-31
• Integration and normalization method for improving the comparative epigenome pipeline.
  • JSPS Grant-in-Aid for Young Scientists (B)
  • Project Period: 2015-04-01 - 2018-03-31
• The method for reconstructing chromosomal conformation through informatics.
  • JSPS Grant-in-Aid for Young Scientists (B)
  • Project Period: 2011-04-01 - 2013-03-31

Professional activities

• Editor, Springer Book "Computational Methods for 3D Genome Analysis", 2024.
• Area Advisor, JST ACT-X "Life and Information", 2024~ (ongoing)
• Organizer, KI-UT Doctoral course "Bioinformatics Analysis and Visualisation of Medical Genomics Data" with Karolinska Institutet (part of the UTokyo-KI link)
  • KI-UT Doctoral course, March 13 - March-27, 2025.
  • KI-UT Doctoral course, March 6 - March 22, 2023.
• Organizer, The workshop on Hi-C analysis, 2017~ (ongoing)
• Conference Symposium Organizer:
  • "Large-scale computational epigenomics for the elucidation of genomic regulatory mechanisms", Workshop in MBSJ2024, Hakata, Nov. 2024.
  • "Genome analysis based on large-scale NGS data", Workshop in IIBMP2022, Toyonaka, Japan, Sep. 2022.
  • "Toward understanding cellular diversity by single cell analyses and interdisciplinary approaches", Workshop in MBSJ2020, Online, Dec. 2020.
  • "Mathematical Sciences of Single Molecule and Cell for Understanding and Controling Cellular Diversity", Workshop in MBSJ2019, Hakata, Japan, Dec. 2019.
  • "Young researchers' challenge to interdisciplinary approaches encourages a new era in cellular diversity analysis", Workshop in MBSJ2018, Yokohama, Japan, Nov. 2018.

Academic Societies

• Japanese Society for Bioinformatics
• The Molecular Biology Society of Japan
• The Biophysical Society of Japan
• The Japanese Society for Epigenetics