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RIKEN Center for Integrative Medical Sciences Laboratory for Integrative Genomics

Team Leader: Jun Seita (M.D., Ph.D.)

Research Summary

Jun  Seita(M.D., Ph.D.)

The goal of our laboratory is to accelerate various researches in the biomedical sciences by combining genomics and other multi-omics with deep learning and machine learning. To achieve this, we are concurrently pursuing research activities that can be broadly classified into three categories: 1) central support activities, 2) strategic collaborative researches, and 3) exploratory research. In particular, by integrating rapidly advancing single cell omics technologies with data-driven science, we aim to elucidate disease mechanisms at high resolution and to pioneer new research areas that will lead to personalized medicine in the future.

Main Research Fields

  • Biology

Related Research Fields

  • Biological Sciences


  • Technology Development in Multiomics
  • Data-driven science
  • Deep Learning

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.

  • 1. *Travaglini KJ, Nabhan AN, Penland L, Sinha R, Gillich A, Sit RV, Chang S, Conley SD, Mori Y, Seita J, Berry GJ, Shrager JB, Metzger RJ, Kuo CS, Neff N, Weissman IL, Quake SQ, Krasnow MA.:
    "A molecular cell atlas of the human lung from single cell RNA sequencing"
    Nature 587(7835):619 (2020)
  • 2. Yazaki J, Kawashima Y, Ogawa T, Kobayashi A, Okoshi M, Watanabe T, Yoshida S, Kii I, Egami S, Amagai M, Hosoya T, Shiroguchi K, Ohara O.:
    "HaloTag-based conjugation of proteins to barcoding-oligonucleotides"
    Nucleic Acids Res. 48(2):e8 (2020)
  • 3. Shimizu K, Sato Y, Kawamura M, Nakazato H, Watanabe T, Ohara O, Fujii SI.:
    "Eomes transcription factor is required for the development and differentiation of invariant NKT cells"
    Commun Biol. 2(1):150 (2019)
  • 4. Kawashima Y, Watanabe E, Umeyama T, Nakajima D, Hattori M, Honda K, Ohara O.:
    "Optimization of Data-Independent Acquisition Mass Spectrometry for Deep and Highly Sensitive Proteomic Analysis"
    Int J Mol Sci. 20(23) 5932 (2019)
  • 5. Kawashima Y, Miyata J, Watanabe T, Shioya J, Arita M, Ohara O.:
    "Proteogenomic Analyses of Cellular Lysates Using a Phenol-Guanidinium Thiocyanate Reagent"
    J Proteome Res. 18(1), 301-308 (2019)
  • 6. Rosental B, Kowarsky M, Seita J, Corey DM, Ishizuka KJ, Palmeri KJ, Chen SY, Sinha R, Okamoto J, Mantalas G, Manni L, Raveh T, Clarke DN, Tsai JM, Newman AM, Neff NF, Nolan GP, Quake SR, Weissman IL, Voskoboynik A.:
    "Complex mammalian-like haematopoietic system found in a colonial chordate”
    Nature. 564(7736) 425 (2018)
  • 7. Kawashima Y, Ohara O.:
    "Development of a NanoLC-MS/MS System Using a Nonporous Reverse Phase Column for Ultrasensitive Proteome Analysis"
    Anal Chem. 90(21), 12334-12338 (2018)
  • 8. Saito Y, Mochizuki Y, Ogahara I, Watanabe T, Hogdal L, Takagi S, Sato K, Kaneko A, Kajita H, Uchida N, Fukami T, Shultz LD, Taniguchi S, Ohara O, Letai AG, Ishikawa F.:
    "Overcoming mutational complexity in acute myeloid leukemia by inhibition of critical pathways"
    Sci Transl Med. 9(413):eaao1214 (2017)
  • 9. Fujiki R, Hijikata A, Shirai T, Okada S, Kobayashi M, Ohara O.:
    "Molecular mechanism and structural basis of gain-of-function of STAT1 caused by pathogenic R274Q mutation"
    J Biol Chem. 292(15):6240-6254 (2017)
  • 10. Yakushiji-Kaminatsui N, Kondo T, Endo TA, Koseki Y, Kondo K, Ohara O, Vidal M, Koseki H.:
    "RING1 proteins contribute to early proximal-distal specification of the forelimb bud by restricting Meis2 expression."
    Development. 143(2), 276-85 (2016)

Recent Research Results

Related Links

Lab Members

Principal investigator

Jun Seita
Team Leader

Core members

Junshi Yazaki
Senior Research Scientist
Yongwoon Han
Research Scientist
Takaho Endo
Technical Scientist
Takashi Watanabe
Technical Scientist
Yoshiki Mochizuki
Expert Technician
Tomoko Hasegawa
Senior Technical Staff
Clive Steven Barker
Technical Staff I
Atsuo Kobayashi
Technical Staff I
Fumie Yokoyama
Technical Staff I
Juri Shioya
Technical Staff I
Reiko Kuwahara
Technical Staff I
Takashi Yamanashi
Student Trainee

Contact Information

1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama City, Kanagawa,
230-0045, Japan