Author

Atsuko Shimada

The University of Tokyo

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Developmental Biology· 3 Genomics· 1

Signature Assays, Organisms & Methods

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Organism:zebrafish· 4 Research Focus:gene regulatory network inference· 3 Approach:statistical model· 3 Research Focus:cell type annotation· 2 Assay:ChIP-seq· 2 Approach:experimental assay· 2 Assay:bulk RNA-seq· 1 Research Focus:differential expression· 1

Frequent Co-Authors

Hiroyuki TakedaiD· 4 shared Ryohei NakamuraiD· 2 shared Toru KawanishiiD· 2 shared Ann Kathrin Heilig· 1 shared Bo-Tsung WuiD· 1 shared Bradley Robert CairnsiD· 1 shared Candice L. Wike· 1 shared Chia-Hsien WuiD· 1 shared

Activity by Year

2021-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

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4 shared papersDevelopmental Biology

Hiroyuki TakedaORCID

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4 papers

Recent·Most cited

Wntless interacts with Notch signaling to balance the generation of neurons and gliocytes in vertebrate dorsal diencephalon

S. C. Lin, He‐Yen Pan, Bo-Tsung Wu, Joe Sakamoto, Chia-Hsien Wu, Atsuko Shimada, Yasuhiro Kamei, Hiroyuki Takeda, Yung‐Shu Kuan

The paper shows that Wntless restricts Notch signaling to balance neuron and gliocyte generation in zebrafish dorsal diencephalon.

bioRxiv · Aug 6, 2025 · PreprintDevelopmental Biology

Mechanically Sensitive HSF1 is a Key Regulator of Left-Right Symmetry Breaking in Zebrafish Embryos

Jing Du, Shu-Kai Li, Liu‐Yuan Guan, Zheng Guo, Jiang-Fan Yin, Li Gao, Toru Kawanishi, Atsuko Shimada, Qiuping Zhang, Lisha Zheng, Yiyao Liu, Xi‐Qiao Feng, Lin Zhao, Dongyan Chen, Hiroyuki Takeda, Yubo Fan

This study identifies HSF1 as a mechanically sensitive regulator of left-right symmetry breaking in zebrafish embryos through nodal flow-induced gene expression asymmetry.

iScience · Sep 9, 2023Peer-reviewedDevelopmental Biology

Zic1 advances epaxial myotome morphogenesis to cover the neural tube via Wnt11r

Ann Kathrin Heilig, Ryohei Nakamura, Atsuko Shimada, Yuka Hashimoto, Yuta Nakamura, Joachim Wittbrodt, Hiroyuki Takeda, Toru Kawanishi

The paper identifies Zic1's role in epaxial myotome morphogenesis by regulating Wnt11r to guide dorsal movement and neural tube coverage.

eLife · Apr 20, 2022Peer-reviewedDevelopmental Biology

CTCF looping is established during gastrulation in medaka embryos

Ryohei Nakamura, Yuichi Motai, Masahiko Kumagai, Candice L. Wike, Haruyo Nishiyama, Yoichiro Nakatani, Neva C. Durand, Kaori Kondo, Takashi Kondo, Tatsuya Tsukahara, Atsuko Shimada, Bradley Robert Cairns, Erez Lieberman Aiden, Shinichi Morishita, Hiroyuki Takeda

The paper examines genome architecture changes during medaka gastrulation, finding that CTCF loops form while CTCF binding sites remain fixed, and transcription precedes mature domain formation.

Genome Research · Jun 1, 2021Peer-reviewedGenomics