Author

Gyehyun Lee

University of California, San FranciscoORCID 0000-0003-3789-3319Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Immunology· 1

Signature Assays, Organisms & Methods

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Approach:benchmark study· 2 Research Focus:cell type annotation· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:cell-cell communication· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Elvira MennilloiD· 2 shared A.D. Choudhury· 1 shared Ahmad SalehiiD· 1 shared Alan Gi-Lun ChengiD· 1 shared Alexis J. CombesiD· 1 shared Ali Reza Rais Sadati· 1 shared Amber Casillas· 1 shared Andres Gottfried‐BlackmoreiD· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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2 shared papersImmunology

Elvira MennilloORCID

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2 papers

Recent·Most cited

ImmunologyJournal of Clinical InvestigationPeer-reviewedJun 9, 2026

Single-cell spatial transcriptomics of fixed, paraffin-embedded biopsies reveals colitis-associated cell networks

Elvira Mennillo, Madison L. Lotstein, Gyehyun Lee…·Alexis J. Combes

This study develops an iSCST framework for FFPE biopsies, identifying colitis-associated cell networks and VDZ response signatures in IBD patients.

6 citationstop 4%

humanspatial transcriptomics

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BioinformaticsNature CommunicationsPeer-reviewedOct 28, 2025

Benchmarking Cell Type and Gene Set Annotation by Large Language Models with AnnDictionary

George Crowley, Robert C. Jones, Mark A. Krasnow…·David Seong

The paper benchmarks large language models for cell-type and gene set annotation using AnnDictionary, finding high accuracy in cell-type annotation and strong functional gene set recovery.

11 citations

bulk RNA-seqmachine learning (classical)

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