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

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

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

Ian Mantel, Haoxuan Zhang, Juan Vargas, Ce Gao, Hope A. Townsend, Richard D. Bell, Amit Lakhanpal, Miriam R. Fein, Accelerating Medicines Partnership: RA/SLE Network, Thomas M. Norman, Dana E. Orange, Daniel C. Ramirez, Edward F. DiCarlo, Susan M. Goodman, Melanie H. Smith, , Thomas Eisenhaure

SPP1hi macrophages in RA synovial fibrin deposits promote tissue hyperplasia.

Science Translational Medicine · Jun 24, 2026Peer-reviewedImmunology

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

Lauren A. Vanderlinden, Juan Vargas, Jun Inamo, Jade Young, Chuangqi Wang, 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.

bioRxiv · May 10, 2026 · PreprintBioinformatics

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

Nanxi Guo, Juan Vargas, Douglas Fritz, Revanth Krishna, Fan Zhang

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

bioRxiv · Oct 10, 2023 · PreprintBioinformatics