Author

Yupu Xu

University of Science and Technology of ChinaORCID 0000-0002-6060-1268Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2 Systems Biology· 2

Signature Assays, Organisms & Methods

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Approach:statistical model· 4 Research Focus:gene regulatory network inference· 3 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Organism:human· 2 Organism:mouse· 2 Assay:scRNA-seq· 2 Organism:Arabidopsis· 1

Frequent Co-Authors

Shisong MaiD· 4 shared Haiying GengiD· 1 shared Jiazhen GongiD· 1 shared Lirui Chen· 1 shared Meng WangiD· 1 shared Yifan WangiD· 1 shared Yue QiniD· 1 shared Yuzhou WangiD· 1 shared

Activity by Year

2021-2025 · peak 2/yr

Co-Author Collaboration Network

9 top collaborators · 14 mutual co-author links

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4 shared papersBioinformatics

Shisong MaORCID

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4 papers

Recent·Most cited

BioinformaticsbioRxivPreprintOct 29, 2025

A gene program dictionary of human cells

Yupu Xu, Yifan Wang, Zhenxing Geng…·Shisong Ma

The paper introduces GPD, a framework using gene co-expression programs to create an organism-wide cell atlas, revealing disease-related gene programs across tissues.

DOI 10.1101/2025.10.29.685322

humanscRNA-seq

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BioinformaticsbioRxivPreprintOct 1, 2025

SpacGPA: annotating spatial transcriptomes through de novo interpretable gene programs

Yupu Xu, Lirui Chen, Shisong Ma

SpacGPA annotates spatial transcriptomes by identifying interpretable gene programs without single-cell data or segmentation.

1 citation

mousehuman

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Systems BiologyCell Reports MethodsPeer-reviewedJul 1, 2024

SingleCellGGM enables gene expression program identification from single-cell transcriptomes and facilitates universal cell label transfer

Yupu Xu, Yuzhou Wang, Shisong Ma

SingleCellGGM identifies gene expression programs from single-cell transcriptomes and enables cross-study cell-type label transfer.

6 citations

mousescRNA-seq

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Systems BiologyThe Plant JournalPeer-reviewedMay 11, 2021

An Arabidopsis gene expression predictor enables inference of transcriptional regulators

Haiying Geng, Meng Wang, Jiazhen Gong…·Shisong Ma

The paper develops a gene expression predictor for Arabidopsis that uses TF activities to accurately predict transcriptomes and infer TF regulators for specific biological processes.

18 citations

Arabidopsisbulk RNA-seq

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