Author

John Thompson

Duke UniversityORCID 0000-0003-0248-8743Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:differential expression· 2 Approach:experimental assay· 2 Assay:scRNA-seq· 2 Approach:statistical model· 2 Organism:zebrafish· 2 Research Focus:cell type annotation· 1 Research Focus:clustering· 1 Research Focus:database / resource· 1

Frequent Co-Authors

Aidan F. WintersiD· 1 shared Airol A. Ubas· 1 shared Ajay Sapre· 1 shared Alexander Rosenberg· 1 shared Bryan HariadiiD· 1 shared C. Ben LovelyiD· 1 shared Charles Roco· 1 shared Crina Curca Alec Salvino· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

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1 shared paperGenomics

Aidan F. WintersORCID

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3 papers

Recent·Most cited

Developmental BiologybioRxivPreprintJun 29, 2026

Transcriptional divergence of the zebrafish sox17 lineage begins during gastrulation

Po Shu Tu, John Thompson, Oscar A. Davalos…·Stefan C. Materna

The paper uses single-cell transcriptomics to study the zebrafish sox17 lineage during gastrulation, revealing transcriptional changes in endoderm and dorsal forerunner cells.

DOI 10.64898/2026.06.27.734843

zebrafishscRNA-seq

𝕏 PostBluesky

Developmental BiologybioRxivPreprintOct 25, 2025

Buffering of genetic defects in animal development by regeneration programs

Kazunori Ando, Sushant Bangru, John Welsby…·Kenneth D. Poss

The paper identifies genetic mutations that affect regeneration programs in zebrafish, showing that these programs can buffer developmental defects.

1 citation

zebrafishwhole-genome sequencing

𝕏 PostBluesky

GenomicsbioRxivPreprintFeb 20, 2025

✦ In-depth digest

Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling

Jesse M. Zhang, Airol A. Ubas, Richard de Borja…·Johnny X. Yu

A 100-million-cell atlas: 50 cancer lines pooled as spheroid villages, treated with 379 drugs at several doses, profiled by combinatorial-barcoding scRNA-seq and embedded with a 10-dimensional scVI model.

108 citations

humanscRNA-seq

𝕏 PostBluesky