Author

Tuo Shi

Scripps Research InstituteORCID 0000-0002-5268-0146Unclaimed 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:drug response / drug discovery· 2 Approach:experimental assay· 2 Organism:mouse· 2 Assay:scRNA-seq· 2 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:database / resource· 1 Research Focus:differential expression· 1

Frequent Co-Authors

Alexander SuniD· 2 shared David DeTomaso· 2 shared Patrick C. ThompsoniD· 2 shared Seoyeon KimiD· 2 shared Xin JiniD· 2 shared Amelia Liu· 1 shared Cindy T. J. van VelthoveniD· 1 shared Cole TrapnelliD· 1 shared

Activity by Year

2023-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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2 shared papersGenomics

Alexander SunORCID

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Author profile →

3 papers

Recent·Most cited

Distributed AI agents enable comprehensive discovery of biological insights at scale

Alexander Sun, Joshua J Park, David DeTomaso, Seoyeon Kim, Amelia Liu, Suyash Shringarpure, Kenny Kim, Patrick C. Thompson, Tuo Shi, Yunyun Wang, Eran A. Mukamel, Grace XY Zheng, Y Joy Jiao, Xin Jin

The paper introduces distributed AI agents to analyze large-scale biological datasets, demonstrating their ability to rapidly extract insights and predict outcomes across a Perturb-seq atlas.

bioRxiv · Oct 16, 2026 · PreprintGenomics

Genome-scale functional mapping of the mammalian whole brain with in vivo Perturb-seq

Tuo Shi, Maria V. Korshunova, Seoyeon Kim, David DeTomaso, Xinhe Zheng, Lavanya Vishvanath, Thokozile Nyasulu, Nhan Huynh, Alexander Sun, Patrick C. Thompson, Yifan Zhang, Emilie M. Wigdor, Narjes Rohani, Salma Ali, Huixian Qiu, , Xin Jin

The paper maps gene expression responses to loss of 1,947 disease-associated genes across the mouse brain using Perturb-seq, revealing cell-type-specific essentiality and transcriptional programs.

bioRxiv · Mar 18, 2026 · PreprintGenomics

Single-Cell Transcriptomic Profiling of the Zebrafish Inner Ear Reveals Molecularly Distinct Hair Cell and Supporting Cell Subtypes

Tuo Shi, Marielle O Beaulieu, Lauren M. Saunders, Péter Fábián, Cole Trapnell, Neil Segil, Justin Gage Crump, David W. Raible

The paper uses single-cell RNA sequencing to analyze zebrafish inner ear cells, identifying distinct hair cell and supporting cell subtypes and their spatial organization.

eLife · Jan 4, 2023Peer-reviewedNeuroscience