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RIKEN Center for Biosystems Dynamics Research Laboratory for Developmental Genome System

Team Leader: Takefumi Kondo (Ph.D.)

Research Summary

Takefumi Kondo

Our bodies are composed of multiple organs with appropriate "forms" and "functions." It has recently become clear that a system based on bidirectional feedback across the genome-cell-tissue hierarchy is crucial to establish functional organs in which "form" and "function" are in harmony. Our laboratory aims to reveal the diversity and universality of this feedback regulation by analyzing the dynamics at each level of the hierarchy using single-cell genomics, imaging techniques, and Drosophila genetics, leading to the control of complex multicellular systems.

Main Research Fields

  • Biology

Related Research Fields

  • Biological Sciences
  • Developmental biology
  • System genome science


  • Organogenesis
  • Cell fate control
  • Morphogenesis
  • Genomics
  • Imaging

Selected Publications

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

  • 1. Alice Tsuboi, Koichi Fujimoto and Takefumi Kondo
    "Spatio-temporal remodeling of extracellular matrix orients epithelial sheet folding."
    Science Advances 9, eadh2154 (2023) doi: 10.1126/sciadv.adh2154
  • 2. Shunta Sakaguchi, Sonoko Mizuno, Yasushi Okochi, Chiharu Tanegashima, Osamu Nishimura, Tadashi Uemura, Mitsutaka Kadota, Honda Naoki and Takefumi Kondo
    "Single-cell transcriptome atlas of Drosophila gastrula 2.0."
    Cell Reports 42, 112707 (2023) doi: 10.1016/j.celrep.2023.112707
  • 3. *Yasushi Okochi, Shunta Sakaguchi, Ken Nakae, Takefumi Kondo and Honda Naoki
    "Model-based prediction of spatial gene expression via generative linear mapping"
    Nature Communications 12, 3731 (2021) doi: 10.1038/s41467-021-24014-x
  • 4. Takefumi Kondo and Shigeo Hayashi
    "Two-step regulation of trachealess ensures tight coupling of cell fate with morphogenesis in the Drosophila trachea"
    elife 8, e45145 (2019) doi: 10.7554/eLife.45145
  • 5. Takefumi Kondo and Shigeo Hayashi
    "Mechanism of cell height changes that mediate epithelial invagination"
    Development Growth and Differentiation 57(4), 313-23 (2015) doi: 10.1111/dgd.12224
  • 6. Takefumi Kondo, Tetsushi Sakuma, Housei Wada, Ai Akimoto-Kato, Takashi Yamamoto and Shigeo Hayashi
    "TALEN-induced gene knock out in Drosophila"
    Development Growth and Differentiation 56, 86?91 (2014) doi: 10.1111/dgd.12097
  • 7. Takefumi Kondo and Shigeo Hayashi
    "Mitotic cell rounding accelerates epithelial invagination"
    Nature 494, 125-129 (2013) doi: 10.1038/nature11792
  • 8. *T. Kondo, S. Plaza, J. Zanet, E. Benrabah, P. Valenti, Y. Hashimoto, S. Kobayashi, F. Payre and Y. Kageyama
    "Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis"
    Science 329, 336-339 (2010) doi: 10.1126/science.1188158
  • 9. Takefumi Kondo, Yoshiko Hashimoto, Kagayaki Kato, Sachi Inagaki, Shigeo Hayashi and Yuji Kageyama
    "Small peptide regulators of actin-based cell morphogenesis encoded by a polycistronic mRNA"
    Nature Cell Biology 9, 660?665 (2007) doi: 10.1038/ncb1595

Related Links

Lab Members

Principal investigator

Takefumi Kondo
Team Leader

Core members

Arisu Tsuboi
Research Scientist
Mitsutaka Kadota
Technical Scientist
Osamu Nishimura
Technical Scientist
Chiharu Tanegashima
Expert Technician
Kaori Tatsumi
Technical Staff II
Dooseon Cho
Technical Staff I
Sayo Saito
Sonoko Mizuno
Student Trainee
Shutaro Endo
Student Trainee

Contact Information

Developmental Biology Buildings C S204
2-2-3 Minatojima-minamimachi, Chuo-ku,
Kobe, Hyogo 650-0047
Email: takefumi.kondo [at] riken.jp