Author

Juan Vargas

University of Colorado AnschutzORCID 0009-0002-8715-3757Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2 Immunology· 1

Signature Assays, Organisms & Methods

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Organism:human· 3 Assay:spatial transcriptomics· 2 Research Focus:trajectory inference· 2 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:cell-cell communication· 1 Research Focus:clustering· 1 Approach:deep learning· 1

Frequent Co-Authors

Fan ZhangiD· 3 shared Aaron Wise· 1 shared Accelerating Medicines Partnership: RA/SLE Network· 1 shared Adam T. Chicoine· 1 shared Alexander Yu RudenskyiD· 1 shared Ami Ben-Artzi· 1 shared Amit LakhanpaliD· 1 shared Andrew Cordle· 1 shared

Activity by Year

2023-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersBioinformatics

Fan ZhangORCID

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3 papers

Recent·Most cited

ImmunologyScience Translational MedicinePeer-reviewedJun 24, 2026

SPP1hi macrophages in fibrin niches promote hyperplastic tissue remodeling in rheumatoid arthritis synovium

Ian Mantel, Haoxuan Zhang, Juan Vargas…·Thomas Eisenhaure

SPP1hi macrophages in RA synovial fibrin deposits promote tissue hyperplasia.

4 citationstop 1%

humanspatial transcriptomics

𝕏 PostBluesky

BioinformaticsbioRxivPreprintMay 10, 2026

scLASER: a robust framework for simulating and detecting time-dependent single-cell dynamics in longitudinal studies

Lauren A. Vanderlinden, Juan Vargas, Jun Inamo…·Fan Zhang

scLASER simulates and detects time-dependent cellular dynamics in longitudinal studies, showing higher sensitivity than traditional methods in rare cell types and non-linear patterns.

1 citation

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BioinformaticsbioRxivPreprintOct 10, 2023

Uncover spatially informed shared variations for single-cell spatial transcriptomics with STew

Nanxi Guo, Juan Vargas, Douglas Fritz…·Fan Zhang

STew identifies spatially informed clusters and disease-relevant niches in spatial transcriptomics data by jointly analyzing spatial information and gene expression.

2 citations

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