Centers & Labs

RIKEN Brain Science Institute

Laboratory for Molecular Mechanisms of Thalamus Development

Laboratory Head: Tomomi Shimogori (Ph.D.)
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. 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 (6162):1114-8. doi: 10.1126/science.1244505. (2013)
  2. Huilgol D, Udin S, Shimogori T, Saha B, Roy A, Aizawa S, Hevner RF, Meyer G, Ohshima T, Pleasure SJ, Zhao Y, Tole S.:
    "Dual origins of the mammalian accessory olfactory bulb revealed by an evolutionarily conserved migratory stream."
    Nat Neurosci. doi: 10.1038/nn.3297. (2013)
  3. Kumagai A, Ando R, Miyatake H, Greimel P, Kobayashi T, Hirabayashi Y, Shimogori T, Miyawaki A.
    "A bilirubin-inducible fluorescent protein from eel muscle."
    Cell. 153:1602-11.(2013)
  4. 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)
  5. Hama H, Kurokawa H, Kawano H, Ando R, Shimogori T, Noda H, Fukami K, Sakaue-Sawano A, Miyawaki A.:
    "Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain."
    Nature Neurosci. 14:1481-8. (2011)
  6. Matsui A, Yoshida AC, Kubota M, Ogawa M and Shimogori T.:
    "Mouse in utero electroporation: Controlled spatio-temporal gene transefection."
    J Vis Exp. 54 pii: 3024. (2011)
  7. 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)
  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)
  9. 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)

Lab Members

Principal Investigator

Tomomi Shimogori
Laboratory Head

Core Members

Nagatoki Kinoshita
Research Scientist
Yoshiaki Kita
Research Scientist
Timothy Raymond Young
Special Postdoctoral Researcher
Tsutomu Hashikawa
Research Consultant
Ihssane Zouikr
Visiting Researcher
Mami U
Technical Staff I
Masae Sato
Technical Staff II
Hirozumi Nishibe
Technical Staff Ⅱ
Aya Yoshida
Technical Staff II
Chihiro Yoshida
Technical Staff Ⅱ
Satomi Kikuchi
Technical Staff II
Ayumi Abe
Technical Staff II
Karl Windak
Technical Staff II

Contact information

2-1 Hirosawa, Wako, Saitama 351-0198, Japan

Email: tshimogori [at]

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