Dive into large-scale multi-omics genomics for epoch-making discovery

About Research

A genome of an organism contains all information for its biological activity and heredity, on which various events (e.g., gene activation, DNA replication and chromatin folding) are cooperatively regulated. Genome-wide analyses with Next Generation Sequencer (NGS) is a mainstream method in computational genomics and has led to important discoveries for dynamic regulation on the genome. We are interested in understanding the cooperative regulation of genomic events and its dysregulation in diseases by using computational genomics strategy. In collaboration with multiple wet labs, we have been investigating various cell-lines such as rare-disease patients and knockout mice by NGS assays including:
– ChIP-seq: protein-DNA binding,
– ATAC-seq: open chromatin,
– RNA-seq: gene expression,
– Exome-seq: gene mutation,
– Hi-C: 3D genome folding,
– ChIA-PET: chromatin looping, and
– Single-cell analysis: cellular heterogeneity and differential analysis.
Our research focus is “data-driven NGS analysis” that extracts important biological information from large NGS datasets (~hundreds of samples) without help from existing biological knowledge. We aim to develop a pipeline for multi-NGS omics that integratively analyzes large datasets from multiple NGS assays and achieve an epoch-making discovery, e.g., higher-order coordination of multiple DNA-binding factors.
We also put effort into cultivating next-generation computational genomicists. We welcome enthusiastic and motivated students both of biology and of informatics who are interested in computational genomics.


  1. *Nakato R, Shirahige K. Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile. Bioinformatics, vol. 34, issue 14, 2356-2363, 2018.
  2. Nakato R, Shirahige K. Statistical Analysis and Quality Assessment of ChIP-seq Data with DROMPA. Methods in Molecular Biology, 1672, 631-643, 2018.
  3. *Nakato R, Shirahige K. Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation. Brief. Bioinform., 18: 279-290, 2017.
  4. Sutani T, Sakata T, Nakato R, Masuda K, Ishibashi M, Yamashita D, Suzuki Y, Hirano T, Bando M, Shirahige K. Condensin targets and reduces unwound DNA structures associated with transcription in mitotic chromosome condensation. Nature Commun., 6: 7815, 2015.
  5. Izumi K, Nakato R, Zhang Z, Edmondson AC, Noon S, Dulik MC, Rajagopalan R, Venditti CP, Gripp K, Samanich J, Zackai EH, Deardorff MA, Clark D, Allen JL, Dorsett D, Misulovin Z, Komata M, Bando M, Kaur M, Katou Y, *Shirahige K, *Krantz ID. (2015) Germline gain-of-function mutations in AFF4 cause a developmental syndrome functionally linking the super elongation complex and cohesin. Nat Genet. 47:338-44.
  6. *Nakato R, Itoh T., *Shirahige K. DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data.
    Genes Cells,18(7): 589-601, 2013.
  7. *‡Deardorff MA, ‡Bando M, ‡Nakato R, ‡Watrin E, Itoh T, Minamino M, Saitoh K, Komata M, Katou Y, Clark D, Cole KE, De Baere E, Decroos C, Di Donato N, Ernst S, Francey LJ, Gyftodimou Y, Hirashima K, Hullings M, Ishikawa Y, Jaulin C, Kaur M, Kiyono T, Lombardi PM, Magnaghi-Jaulin L, Mortier GR, Nozaki N, Petersen MB, Seimiya H, Siu VM, Suzuki Y, Takagaki K, Wilde JJ, Willems PJ, Prigent C, Gillessen-Kaesbach G, Christianson DW, Kaiser FJ, Jackson LG, Hirota T, Krantz ID, Shirahige K. (2012) HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle. Nature. 489:313-7.
  8. Tanaka S, Nakato R, Katou Y, Shirahige K, *Araki H. Origin association of Sld3, Sld7, and Cdc45 proteins is a key step for determination of origin-firing timing.
    Current Biol., 21(24), 2055-2063, 2011.
  9. Nakato R., Gotoh O., Cgaln: fast and space-efficient whole-genome alignment, BMC Bioinformatics, Vol. 11, 224, 2010.
Ryuichiro Nakato
Graduate School of Medicine, Graduate School of Frontier Sciences
Eiko Saijou
Technical Specialist
Naoko Yokota
Technical Specialist