Positions held

• 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
  • 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.
  • 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
  • Nakato R., 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.
  • Nakato R., 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.
  • Nakato R., Context-dependent 3D genome regulation by cohesin and related factors, The 3rd workshop on Hi-C analysis, Kobe, Japan, May 11th, 2023.
  • Nakato R., 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.
  • Nakato R., 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) Nakato R., Sakata T. Bando M. and Shirahige K., 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.
  • Nakato R., 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) Nakato R. and Shirahige K., 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.
  • Nakato R. and Gotoh O., 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

• Area Advisor, JST ACT-X "Life and Information", 2024~
• Organizer, "Multi-NGS omics semiar" supported by AMED-PRIME, monthly (online), 2021-01 - 2022-03.
• Organizer, The 3rd Workshop for Young Scientists in KAKENHI project "Cellular diversity", Atami, Japan, Mar. 2020.
• Chair, "Genome analysis based on large-scale NGS data", Workshop in IIBMP2022, Toyonaka, Japan, Sep. 2022.
• Chair, "Toward understanding cellular diversity by single cell analyses and interdisciplinary approaches", Workshop in MBSJ2020, Online, Dec. 2020.
• Chair, "Mathematical Sciences of Single Molecule and Cell for Understanding and Controling Cellular Diversity", Workshop in MBSJ2019, Hakata, Japan, Dec. 2019.
• Chair, "Young researchers' challenge to interdisciplinary approaches encourages a new era in cellular diversity analysis", Workshop in MBSJ2018, Yokohama, Japan, Nov. 2018.
• Host, Tutorial of Single-cell transcriptome analysis, the University of Tokyo, Japan, Oct. 2019.

Academic Societies

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