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Lab photo 2022

Nakato laboratory

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 of both biology and computer science who are interested in computational genomics using large datasets obtained from multiple NGS assays (e.g., ChIP-seq, RNA-seq, Hi-C, and single-cell analysis). The current topics are:

  • Development of integrated analysis methods using multiple NGS assays (e.g. epigenome, gene expression and 3D structure)
  • Whole genome annotation based on diverse epigenomic data (e.g., histone modifications) to identify novel functional regulatory regions
  • Development of methods for detailed analysis of 3D structural data (e.g., Hi-C and Micro-C)
  • Prediction of chromatin interactions using large-scale epigenomic data
  • Functional analysis of cohesin and CTCF, proteins essential for regulation of chromosome structure and gene transcription
  • Trajectory analysis using single-cell data to investigate cell fate regulation
  • Gene network reconstruction and comparative network analysis using single cell data

NEWS

    2023
  • 2023.1.27
    Dr. Nakato has been selected for a research fund from Fusion Oriented REsearch for disruptive Science and Technology (FOREST). Project title: "Development of a computational platform for novel large-scale genomic analysis".

    2022
  • 2022.11.30-12.2
    In MBSJ2022 (at Makuhari, Chiba), Dr. Nakato held a workshop titled "Toward understanding the role of 3D genome structure by integrative analysis" and had an oral talk in it.
    Also in MBSJ2022, Dr. Saijou had an oral talk. Dr. Nagai and Ph.D. students Wang and Oba had poster presentations.
  • 2022.9.27
    Paper by a Ph.D. student Wang accepted in Nucleic Acids Research. Title: "CohesinDB: a comprehensive database for decoding cohesin-related epigenomes, 3D genomes and transcriptomes in human cells" (Press release)
  • 2022.9.13-15
    Dr. Nakato held a workshop titled "Genome analysis based on large-scale NGS data" in IIBMP2022 (at Osaka). Dr. Lee and Ph.D. student Wang had an oral talk. Dr. Nagai had a poster presentation.
  • 2022.7.1
    Dr. Nakato was promoted to associate professor.
  • 2022.6.9
    Paper by a Ph.D. student Wang accepted in Nature Communications. Title: "Large-scale multi-omics analysis suggests specific roles for intragenic cohesin in transcriptional regulation" (Press release)
  • 2022.4.1
    We welcome Dr. Nagaoka as a project researcher and Zhou-san as a Master's student.
    Dr. Nagai was promoted to research associate.

    2021
  • 2021.12.1
    Paper by Ph.D. student Wang accepted in Briefing in Bioinformatics. Title: "HiC1Dmetrics: framework to extract various one-dimensional features from chromosome structure data" (Press release)
  • 2021.12.1-3
    In MBSJ2021 (at Yokohama, Kanagawa), Dr. Saijou had an oral talk and Dr. Nagai, Ph.D. students Wang and Oba and an intern student Yamada had poster presentations.
  • 2021.10.1
    We welcome Dr. Lee as a project research associate and Ren-san as a reserach student.
  • 2021.9.27-29
    Dr. Nakajima had an oral talk and Oba-san had a poster presentation in IIBMP2021 (online).
  • 2021.7.22
    Paper by Dr. Nakajima accepted in Nucleic Acids Research. Title: "Codependency and mutual exclusivity for gene community detection from sparse single-cell transcriptome data" (Press release)
  • 2021.4.1
    We welcome a new secretary Koga-san.
  • 2021.1.13
    Dr. Nakato had 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
  • 2020.12.2-4
    Dr. Nakato held a workshop titled "Toward understanding cellular diversity by single cell analyses and interdisciplinary approaches" in MBSJ2020 (online). 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 had 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
  • 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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