Author

Alev Baysoy

Yale UniversityORCID 0000-0001-5526-5848Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Systems Biology· 2 Genomics· 1 Pathology· 1

Signature Assays, Organisms & Methods

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Organism:human· 4 Approach:experimental assay· 3 Assay:spatial transcriptomics· 3 Research Focus:cell type annotation· 2 Research Focus:cell-cell communication· 2 Approach:deep learning· 2 Research Focus:differential expression· 2 Assay:imaging· 2

Frequent Co-Authors

Rong FaniD· 4 shared Archibald EnninfuliD· 2 shared Bo Tao· 2 shared Mei ZhongiD· 2 shared Shuozhen BaoiD· 2 shared Sidi CheniD· 2 shared Xiaolong TianiD· 2 shared Yao LuiD· 2 shared

Activity by Year

2024-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 42 mutual co-author links

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4 shared papersSystems Biology

Rong FanORCID

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4 papers

Recent·Most cited

PathologybioRxivPreprintJul 12, 2026

Spatial Glyco-Codes Define Human Liver Pathology and Progression

Xiaolong Tian, Anthony A. Fung, Xingbo Shang…·Rong Fan

This study introduces spatial-GPT, a platform for spatial glycan, protein, and transcriptome profiling in human liver tissues, revealing glyco-codes that define disease states and progression.

DOI 10.64898/2026.07.08.737217

humanspatial transcriptomics

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Systems BiologyNature MethodsPeer-reviewedJan 15, 2026

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Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus

Archibald Enninful, Zhaojun Zhang, Dmytro Klymyshyn…·Rong Fan

Thermostable RNaseH release of barcoded cDNA keeps sections intact for CODEX imaging, yielding same-section whole-transcriptome and protein maps plus CODEX-guided spot deconvolution in FFPE tissues.

34 citationstop 1%

humanmouse

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GenomicsbioRxivPreprintNov 18, 2024

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Spatially Resolved in vivo CRISPR Screen Sequencing via Perturb-DBiT

Alev Baysoy, Xiaolong Tian, Feifei Zhang…·Rong Fan

Perturb-DBiT co-sequences spatial transcriptomes and gRNAs on one tissue section, supporting genome-wide in vivo CRISPR screens in FFPE and fresh-frozen tumors across three cancer models.

45 citations

mousehuman

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Systems BiologybioRxivPreprintOct 28, 2024

Mapping intratumoral myeloid-T cell interactomes at single-cell resolution reveals targets for overcoming checkpoint inhibitor resistance

Kate Bridges, Gabriela A. Pizzurro, Alev Baysoy…·Kathryn Miller‐Jensen

The paper develops a computational method to analyze single-cell RNA-seq data to study cell-cell interactions in tumors, showing that CD40 agonist enhances immune checkpoint blockade by modulating myeloid-T cell interactions.

1 citation

humanscRNA-seq

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