Author

Shanshan Duan

Chinese Academy of Sciences

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· 1 Genetics· 1 Genomics· 1 Immunology· 1

Signature Assays, Organisms & Methods

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Research Focus:gene regulatory network inference· 4 Research Focus:database / resource· 3 Assay:scATAC-seq· 3 Assay:scRNA-seq· 3 Approach:statistical model· 3 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Approach:experimental assay· 2

Frequent Co-Authors

Chuanyu LiuiD· 4 shared Yue YuaniD· 4 shared Longqi LiuiD· 3 shared Peng GaoiD· 3 shared Jianhua YiniD· 2 shared Jun XieiD· 2 shared Pengfei CaiiD· 2 shared Qiuting DengiD· 2 shared

Activity by Year

2024-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 41 mutual co-author links

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4 shared papersGenetics

Chuanyu LiuORCID

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4 papers

Recent·Most cited

Decoding Immune Reconstitution Failure in People Living with HIV through Single-cell Genomics

Yuxing Wang, Shichen Yang, Yue Yuan, Mingli Zhu, Jun Chen, Yong Bai, Shanshan Duan, Xuyang Shi, Tianyu Lu, Zongxing Yang, Zhuoli Huang, Dingyan Yan, Yuhui Zheng, Xuanchi Zhou, Jun Yan, , Chuanyu Liu

This study uses single-cell multi-omics to analyze immune reconstitution failure in HIV patients, identifying genetic and epigenetic factors and developing a predictive model.

bioRxiv · May 23, 2026 · PreprintGenetics

Single-Cell Genomics Elucidates Molecular Variations and Regulatory Mechanisms in Circulating Immune Cells

Jianhua Yin, Yuhui Zheng, Zhuoli Huang, Wenwen Zhou, Yue Yuan, Pengfei Cai, Yong Bai, Shichen Yang, Yue Gao, Shanshan Duan, Yang Wang, Zekai Xu, W H Zhang, Xinyu Zhang, Yilin Wei, , Chuanyu Liu

The paper introduces CIMA, a multi-omics atlas of human immune cells, identifying regulatory mechanisms and genetic associations across sex, age, and genetic factors.

Science · Jan 8, 2026Peer-reviewedImmunology

Deciphering gene regulatory programs in mouse embryonic skin through single-cell multiomics analysis

Qiuting Deng, Pengfei Cai, Yingjie Luo, Zhongjin Zhang, Wen Ma, Zijie Huang, Xiaoya Chen, Shijie Hao, Weiguang Ma, Jiangshan Xu, Chunqing Wang, Mengnan Cheng, Xiumei Lin, Ru Zhou, Shanshan Duan, , Chuanyu Liu

The paper uses single-cell multiomics to study gene regulatory programs in mouse embryonic skin, identifying cis-regulatory elements and transcription factors involved in development.

Genome biology · Jul 1, 2025Peer-reviewedDevelopmental Biology

Single-nucleus multiple-organ chromatin accessibility mapping in the rat

Ronghai Li, Yue Yuan, Shanshan Duan, Qiuting Deng, Wen Ma, Chang Liu, Peng Gao, Lu Li, Chuanyu Liu

The paper generates a single-cell chromatin accessibility atlas in nine rat organs, identifies 77 cell types, and analyzes transcription factor dynamics and gene expression conservation across species.

bioRxiv · Nov 11, 2024 · PreprintGenomics