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RIKEN Center for Brain Science Laboratory for Molecular Mechanisms of Brain Development

Laboratory Head: Tomomi Shimogori (Ph.D.)

Research Summary

Tomomi  Shimogori(Ph.D.)

It is known that adolescent brain development and subsequent brain function are largely affected by the environment and experience. For example, growing up abroad allows children to become bilingual, which is a positive influence on brain function. However, children who have a history of neglect or physical abuse are at risk of developing psychiatric problems. Often these psychiatric problems appear later in their life which makes it difficult to solve and treat the disorder. How are these bad memories 'stored’ and then appear in their later life? One possibility is, under a stressful environment, the maturing child’s brain generates fragile circuits which are not strong enough to survive during adulthood. Therefore, it is important to understand the mechanism of neuronal circuit development which is controlled by environment and experience. In my lab, we are focusing on mouse thalamus-cortex connections to dissect how neuronal circuits are refined by neuronal activity and reveal the molecular mechanisms which underlie it. Moreover, we are trying to understand how the young brain can rewire its circuits to develop cross-modality, and thus compensate for lost connections.


  • Cerebral cortex
  • thalamus

Selected Publications

  • 1. Onishi K, Kikuchi SS, Abe T, Tokuhara T, Shimogori T.:
    "Molecular cell identities in the mediodorsal thalamus of infant mice and marmoset."
    J Comp Neurol. (2022) doi: 10.1002/cne.25203.
  • 2. Kita Y, Nishibe H, Wang Y, Hashikawa T, Kikuchi SS, U M, Yoshida AC, Yoshida C, Kawase T, Ishii S, Skibbe H, Shimogori T.:
    "Cellular-resolution gene expression profiling in the neonatal marmoset brain reveals dynamic species- and region-specific differences"
    Proc Natl Acad Sci U S A. (2021) 18:e2020125118. doi:10.1073/pnas.2020125118.
  • 3. Kinoshita N, Huang AJY, McHugh TJ, Miyawaki A, Shimogori T.:
    "Diffusible GRAPHIC to visualize morphology of cells after specific cell-cell contact."
    Sci Rep.10:14437. (2020) doi: 10.1038/s41598-020-71474-0.
  • 4. Kinoshita N, Huang AJY, McHugh TJ, Suzuki SC, Masai I, Kim IH, Soderling SH, Miyawaki A, Shimogori T.:
    "Genetically Encoded Fluorescent Indicator GRAPHIC Delineates Intercellular Connections.
    iScience. 15:28-38. (2019) doi: 10.1016/j.isci.2019.04.013.
  • 5. Shimogori T, Abe A, Go Y, Hashikawa T, Kishi N, Kikuchi SS, Kita Y, Niimi K, Nishibe H, Okuno M, Saga K, Sakurai M, Sato M, Serizawa T, Suzuki S, Takahashi E, Tanaka M, Tatsumoto S, Toki M, U M, Wang Y, Windak KJ, Yamagishi H, Yamashita K, Yoda T, Yoshida AC, Yoshida C, Yoshimoto T, Okano H.:
    "Digital gene atlas of neonate common marmoset brain."
    Neurosci Res. 128:1-13.(2018) doi: 10.1016/j.neures.2017.10.009
  • 6. Matsui A, Tran M, Yoshida AC, Kikuchi SS, U M, Ogawa M, Shimogori T.:
    "BTBD3 controls dendrite orientation toward active axons in mammalian neocortex."
    Science 342:1114-8.(2013) doi: 10.1126/science.1244505
  • 7. Mashiko H, Yoshida AC, Kikuchi SS, Niimi K, Takahashi E, Aruga J, Okano H, Shimogori T.:
    "Comparative anatomy of marmoset and mouse cortex from genomic expression."
    J Neurosci. 32:5039-53.(2012) doi: 10.1523/JNEUROSCI.4788-11.2012
  • 8. Suzuki-Hirano A, Ogawa M, Kataoka A, Yoshida AC, Itoh D, Ueno M, Blackshaw S, Shimogori T.:
    "Dynamic spatiotemporal gene expression in embryonic mouse thalamus."
    J Comp Neurol. 519: 528-43.(2011) doi: 10.1002/cne.22531
  • 9. Yuge K, Kataoka A, Yoshida AC, Itoh D, Aggarwal M, Mori S, Blackshaw S, Shimogori T.:
    "Region-specific expression in early postnatal mouse thalamus."
    J Comp Neurol. 519:544-61.(2011) doi: 10.1002/cne.22532
  • 10. Shimogori T, Lee DA, Miranda-Angulo A, Yang Y, Jiang L, Yoshida AC, Kataoka A, Mashiko H, Avetisyan M, Qi L, Qian J, and Blackshaw S.:
    "A genomic atlas of mouse hypothalamic development."
    Nat Neurosci. 13:767-75. *corresponding authors.(2010) doi: 10.1038/nn.2545

Related Links

Lab Members

Principal investigator

Tomomi Shimogori
Laboratory Head

Core members

Kohei Onishi
Research Scientist
Moe Nakanishi
Research Scientist
Jay Patrick Nakamura
Special Postdoctoral Researcher
Mami U
Technical Staff I
Masae Sato
Technical Staff II
Hirozumi Nishibe
Technical Staff II
Satomi Kikuchi
Technical Staff II
Yayoi Nozaki
Technical Staff I
Natsuki Arai
Technical Staff II
Miyano Sakurai
Research Part-time Worker II
Sachie Suzuki
Research Part-time Worker II
Mami Tanaka
Research Part-time Worker II
Mao Yamaguchi
Research Part-time Worker II
Makiko Someya
Research Part-time Worker II
Mari Shishikura
Temporary Staffing
Atsuko Nakamura
Temporary Staffing
Miki Asada
Temporary Staffing
Erina Kubo
Temporary Staffing
Atsuko Sunose
Temporary Staffing
Takafumi Hoshino
Temporary Staffing
Nobuyo Watari
Temporary Staffing
Hiromi Endo
Temporary Staffing
Tomoko Horikoshi
Temporary Staffing

Contact Information

2-1 Hirosawa, Wako, Saitama 351-0198, Japan
Email: tomomi.shimogori [at] riken.jp