Author

Xiaoke Duan

Fudan University

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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Bioinformatics· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Organism:human· 2 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1 Approach:machine learning (classical)· 1 Assay:scATAC-seq· 1 Assay:scRNA-seq· 1 Approach:statistical model· 1 Research Focus:variant calling· 1

Frequent Co-Authors

Amir ValizadehiD· 1 shared Andreas SchereriD· 1 shared Bradley E. AouizeratiD· 1 shared Claudia MartineziD· 1 shared Dana B. HancockiD· 1 shared Depeng WangiD· 1 shared Eric Otto JohnsoniD· 1 shared Fan LiangiD· 1 shared

Activity by Year

2023-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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1 shared paperGenomics

Amir ValizadehORCID

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2 papers

Recent·Most cited

A single-nucleus multiome analysis of transcriptome and chromatin accessibility reveals cell-type-specific immune modulation for chronic cannabis use among people with HIV infection

Mingrui Li, Kesava R. Asam, Xiaoke Duan, Grier P. Page, Yue Hu, Claudia Martinez, Mardge H. Cohen, Nancie M. Archin, Amir Valizadeh, Dana B. Hancock, Eric Otto Johnson, Bradley E. Aouizerat, Ke Xu

This study uses single-nucleus multi-omic analysis to show cannabis use in HIV patients alters gene expression and chromatin accessibility in immune cell types, with cell-type-specific effects on inflammation and transcription factor regulation.

bioRxiv · Feb 27, 2026 · PreprintGenomics

Quartet DNA reference materials and datasets for comprehensively evaluating germline variants calling performance

Luyao Ren, Xiaoke Duan, Lianhua Dong, Rui Zhang, Jingcheng Yang, Yuechen Gao, Rongxue Peng, Wanwan Hou, Yaqing Liu, Jingjing Li, Ying Yu, Naixin Zhang, Jun Shang, Fan Liang, Depeng Wang, , Yuanting Zheng

This paper introduces Quartet DNA reference materials to comprehensively evaluate germline variant calling accuracy across the genome, including difficult regions and batch effects.

Genome biology · Nov 27, 2023Peer-reviewedBioinformatics