Author

Dee Velazquez

Johns Hopkins UniversityORCID 0009-0004-4380-4794Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:spatial transcriptomics· 3 Organism:mouse· 2 Approach:statistical model· 2 Research Focus:cell type annotation· 1 Research Focus:database / resource· 1 Approach:deep learning· 1 Research Focus:dimensionality reduction· 1 Research Focus:software / tool· 1

Frequent Co-Authors

Jean FaniD· 3 shared Caleb HallinaniD· 1 shared Hamid RabbiD· 1 shared Kalen CliftoniD· 1 shared Roujin AniD· 1 shared Ryo MatsuuraiD· 1 shared Sanjeev NoeliD· 1 shared Shishir Kumar PateliD· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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3 shared papersBioinformatics

Jean FanORCID

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Author profile →

3 papers

Recent·Most cited

BioinformaticsPLoS Computational BiologyPeer-reviewedOct 6, 2026

Spatial Transcriptomics As Rasterized Image Tensors (STARIT) characterizes cell states with subcellular molecular heterogeneity

Dee Velazquez, Caleb Hallinan, Roujin An…·Jean Fan

STARIT converts spatial transcriptomics data into image tensors for deep learning analysis, enabling subcellular heterogeneity-based cell state identification.

DOI 10.1371/journal.pcbi.1014845

spatial transcriptomicsdeep learning

𝕏 PostBluesky

BioinformaticsDOAJ (DOAJ: Directory of Open Access Journals)Peer-reviewedJun 1, 2026

Spatiotemporal transcriptomic analysis during cold ischemic injury to the murine kidney reveals compartment-specific changes

Srujan Singh, Shishir Kumar Patel, Ryo Matsuura…·Jean Fan

The paper uses spatial transcriptomics to analyze cold ischemia injury in murine kidneys, identifying compartment-specific metabolic changes and providing an interactive browser for results.

DOI 10.1186/s13059-026-04167-y

mousespatial transcriptomics

𝕏 PostBluesky

BioinformaticsBioinformaticsPeer-reviewedJan 28, 2025

scatterbar: an R package for visualizing proportional data across spatially resolved coordinates

Dee Velazquez, Jean Fan

The paper introduces scatterbar, an R package for visualizing proportional data across spatial coordinates, demonstrating its use on spatial transcriptomics data.

DOI 10.1093/bioinformatics/btaf047

mousespatial transcriptomics

𝕏 PostBluesky