Author

Long Yuan

Johns Hopkins UniversityORCID 0000-0002-9774-3446Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Research Focus:benchmarking· 2 Research Focus:differential expression· 2 Organism:human· 2 Assay:spatial transcriptomics· 2 Research Focus:cell type annotation· 1 Research Focus:cell-cell communication· 1 Research Focus:dimensionality reduction· 1

Frequent Co-Authors

Atul M. DeshpandeiD· 3 shared Aleksander S. PopeliD· 1 shared Alexander S. SzalayiD· 1 shared Alexander T.F. BelliD· 1 shared Alexander V. FavoroviD· 1 shared Andrej Hartnett· 1 shared Ashley L. KiemeniD· 1 shared Cedric R. UytingcoiD· 1 shared

Activity by Year

2023-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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3 shared papersBioinformatics

Atul M. DeshpandeORCID

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3 papers

Recent·Most cited

Interpretable spherical geometry of single-cell state transitions from dominant principal components

Long Yuan, Xuyang Li, My Le, Stephanie C. Hicks, Atul Deshpande, Janis Marie Taube, Alexander S. Szalay

The paper introduces SPHERE-PCA, a method to interpret single-cell state transitions using spherical geometry, revealing structured patterns in developmental and disease datasets.

bioRxiv · Sep 18, 2026 · PreprintSystems Biology

Reconstructing biologically coherent cellular profiles from imaging-based spatial transcriptomics

Long Yuan, Youyun Zheng, Shuming Zhang, Rameen Beroukhim, Atul Deshpande

TRACER improves cellular profile coherence in spatial transcriptomics by resolving mixed profiles and reconstructing undetected cells, enhancing downstream analyses.

bioRxiv · Apr 8, 2026 · PreprintBioinformatics

Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces

Atul M. Deshpande, Melanie Loth, Dimitrios N. Sidiropoulos, Shuming Zhang, Long Yuan, Alexander T.F. Bell, Qingfeng Zhu, Won Jin Ho, Cesar Augusto Santa-Maria, Daniele M. Gilkes, Stephen R. Williams, Cedric R. Uytingco, Jennifer G. Chew, Andrej Hartnett, Zachary Bent, , Elana Judith Fertig

This paper introduces SpaceMarkers, a method to infer molecular changes from cell-cell interactions in spatial transcriptomics data, applied to tumor-immune interactions in metastasis and immunotherapy.

Cell Systems · Apr 1, 2023Peer-reviewedBioinformatics