Author

Rui Zhou

Shanghai Jiao Tong University

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Biology Disciplines

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Bioinformatics· 2 Genomics· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Assay:ATAC-seq· 1 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:clustering· 1 Research Focus:database / resource· 1 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Akiya JourakuiD· 1 shared Daniel Mark CzajkowskyiD· 1 shared Hao WangiD· 1 shared Hidemasa U. BonoiD· 1 shared Hongpeng ZhouiD· 1 shared Jing LiiD· 1 shared Jinhao LiuiD· 1 shared Kakeru YokoiiD· 1 shared

Activity by Year

2022-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 12 mutual co-author links

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1 shared paperBioinformatics

Akiya JourakuORCID

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3 papers

Recent·Most cited

An invariant network architecture with broadly expressed regulators distinguishes cell-type from cell-state identity in situ

Rui Zhou, Li Ge, Jing Li, Zeqian Xu, Min Chen, Yan Guo, Daniel Mark Czajkowsky, Zhifeng Shao

The paper constructs state-level regulatory networks in mouse liver hepatocytes, revealing an invariant sub-network of broadly expressed TFs that defines cell-type identity, distinct from state-specific variations.

bioRxiv · Oct 30, 2026 · PreprintGenomics

A Unified and Interpretable Framework for Evaluating Fluorescence Trace Quality in Transcription Kinetics

Yiwen Xing, Wei-Tung Lu, Jinhao Liu, Zhiyong Zou, Rui Zhou, Hao Wang, Yusheng Yang, Yabing Yao, Qian Yang, Xiaomin Xu, Hongpeng Zhou

This paper develops a framework to evaluate fluorescence trace quality for transcription kinetics by identifying thresholds for signal-to-noise ratio and trace length using synthetic data.

International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC) · Jan 1, 2026Peer-reviewedBioinformatics

Reference genome sequences of the oriental armyworm, Myth-imna separata (Lepidoptera: Noctuidae)

Kakeru Yokoi, Seiichi Furukawa, Rui Zhou, Akiya Jouraku, Hidemasa U. Bono

The paper constructs a reference genome for the oriental armyworm, Mythimna separata, identifying key immune pathway components and C-type lectins.

Insects · Dec 17, 2022Peer-reviewedBioinformatics