Positions held

• 2025.12.1 - 2026.1.31 Visiting Researcher (funded by EMBO Scientific Exchange Grants), Data Science in Systems Biology (Prof. Markus List), TUM School of Life Sciences, Technical University of Munich, Germany
• 2025.4 - 2026.3 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 and epigenome regulation
• Epigenome analysis using deep learning technology, specifically large language models
• Multi-modal network analysis using graph theory
• Cell fate analysis using single-cell expression data

Works

• Key Publications (See Publication list for all publications)
  • Lee S, Lin C, Chen CY, *Nakato R. ChromBERT: Uncovering Chromatin State Motifs in the Human Genome Using a BERT-based Approach, bioRxiv (preprint), July 26, 2024.
  • *Nakato R et al. Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors, Nature Communications, vol 14, issue 1, 2023.
  • Wang J, Bando M, Shirahige K, *Nakato R. Large-scale multi-omics analysis suggests specific roles for intragenic cohesin in transcriptional regulation, Nature Communications, vol 13, issue 1, 2022.
  • Nakajima N, Hayashi T, Fujiki K, Shirahige K, Akiyama T, Akutsu T, *Nakato R. Codependency and mutual exclusivity for gene community detection from sparse single-cell transcriptome data, Nucleic Acids Research, vol. 49, issue 18, e104, 2021.
  • *Nakato R, Sakata T. Methods for ChIP-seq analysis: A practical workflow and advanced applications, Methods, vol. 187, 44-53, 2020.
  • Nakato R et al. Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells, Epigenetics & Chromatin, vol. 12, issue 1, 77, 2019.
  • *Nakato R, Shirahige K. Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation, Briefings in Bioinformatics, vol. 18, issue 2, 279-290, 2017.
• Invited Talks
  • Data-driven analysis of multi-omics for a systematic understanding of genome regulatory mechanisms, Bioinformatics Center Seminar, Kyoto University, Kyoto, Japan, Oct. 30th, 2025.
  • Large-scale comparative analysis of the 3D genome structure for data-driven annotation of the human genome, The 63rd Annual Meeting of the Biophysical Society of Japan, Nara, Japan, Sep. 24th, 2025.
  • 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, Bioinformatics Center Seminar, Kyoto University, Kyoto, Japan, Feb. 1st, 2019.
• Oral Presentations
  • Large language models to identify syntax and function of the epigenome, the AMED International Symposium “The Early-Life Nexus”, Keio University, Tokyo, Nov. 10th, 2025.
  • 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.

Books

• (In Japanese) Computational Analysis for Epigenome, Corona-sha, 2025.
• Editor, Springer Book "Computational Methods for 3D Genome Analysis", 2024.

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

• 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:
  • AMED International Symposium "The Early-Life Nexus", Keio University, Tokyo, Nov. 2025.
  • "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