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Welcome to Nakato lab!

  • Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo
  • Laboratory of Informatics of Biological Functions, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo

Recruiting students

We welcome enthusiastic and motivated students both of biology and of informatics who are interested in computational genomics using large-scale NGS datasets. The current themes are as follows:

  • Feature extraction algorithm from large-scale epigenome data (e.g., ChIP-seq)
  • Algorithm development for chromosome conformation data (Hi-C, ChIA-PET)
  • Data analysis of single-cell data in colaboration with wet labs
  • Functional analysis of cohesin protein and related factors for cohesinopathy
  • Tools for integrated analysis based on multi-NGS assays

Feel free to contact us!


  • 2021.1.13 Dr. Nakato has been selected for a research fund of 2020 iPS Academia Japan Grant. Project title: "Development of a single-cell analysis system toward elucidating the mechanism of cell differentiation defects in rare diseases-derived iPS cells"
  • 2021.1.4 We welcome Dr. Nagai as a project researcher!
  • 2020.12.2-4 Dr. Nakato will hold a workshop titled "Toward understanding cellular diversity by single cell analyses and interdisciplinary approaches" in MBSJ2020. Dr. Nakajima had an oral talk at the workshop. Dr. Saijou, Ph.D students Wang and Oba had a poster presentation.
  • 2020.9.29 Dr. Nakato has been selected for a research fund of AMED-PRIME "Early Life Stage". Project title: "Development of a robust computational platform for data-driven epigenome analysis"
  • 2020.9.4 Dr. Nakato had a talk in 2nd Mathematical Biology Workshop at Kyoto University.
  • 2020.8.21 Paper accepted in Computational and Structural Biotechnology Journal: "Toward understanding the dynamic state of 3D genome"
  • 2020.3.30 Paper accepted in Methods: "Methods for ChIP-seq analysis: A practical workflow and advanced applications"
  • 2020.3.15-19 Ph.D student Wang will have a poster presentation in Keystone Symposia "Higher-Order Chromatin Architecture in Time and Space" -> cancelled due to COVID19.
  • 2019.12.19 Paper accepted in Epigenetics & Chromatin: "Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells"
  • 2019.12.3-6 Dr. Nakato held a workshop titled "Mathematical Sciences of Single Molecule and Cell for Understanding and Controling Cellular Diversity" in MBSJ2019.
  • 2019.9.24-26 Dr. Nakato gave a talk in RNA Frontier Meeting 2019.
  • 2019.9.19 Dr. Nakato gave a talk in The 4th IQB symposium.
  • 2019.6.26 Dr. Nakato gave a talk in The 13th International Workshop on Advanced Genomics.


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