Author

Shaokun An

Brigham and Women's HospitalORCID 0000-0001-5564-3239Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:differential expression· 2 Organism:human· 2 Assay:scRNA-seq· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Approach:deep learning· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Lin WaniD· 2 shared Martin HembergiD· 2 shared Fuzhou Gong· 1 shared Jae-Won Cho· 1 shared Jiankang Xiong· 1 shared Kai CaoiD· 1 shared Liang MaiD· 1 shared Mark S. KelleriD· 1 shared

Activity by Year

2018-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

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2 shared papersBioinformatics

Lin WanORCID

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3 papers

Recent·Most cited

SpatialQuery: scalable discovery and molecular characterization of multicellular motifs from spatial omics data

Shaokun An, Mark S. Keller, Nils Gehlenborg, Martin Hemberg

SpatialQuery identifies multicellular spatial patterns and characterizes their molecular programs in spatial omics data, revealing cross-germ-layer signaling and disease-specific niches.

bioRxiv · Apr 30, 2026 · PreprintBioinformatics

scCausalVI disentangles single-cell perturbation responses with causality-aware generative model

Shaokun An, Jae-Won Cho, Kai Cao, Jiankang Xiong, Martin Hemberg, Lin Wan

scCausalVI disentangles intrinsic cellular states from treatment effects using a causality-aware generative model, outperforming existing methods in causal inference and multi-source data integration.

Cell Systems · Nov 1, 2025Peer-reviewedBioinformatics

DensityPath: a level-set algorithm to visualize and reconstruct cell developmental trajectories for large-scale single-cell RNAseq data

Ziwei Chen, Shaokun An, Xiangqi Bai, Fuzhou Gong, Liang Ma, Lin Wan

DensityPath visualizes and reconstructs cell developmental trajectories from large-scale scRNA-seq data using a level-set algorithm, identifying complex branching patterns in human preimplantation embryos.

Bioinformatics · Dec 6, 2018Peer-reviewedSystems Biology