Author

Joshua Shi

University of California, San Francisco

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 1 Neuroscience· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 2 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Research Focus:cell-cell communication· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Approach:experimental assay· 1 Organism:mouse· 1

Frequent Co-Authors

Adam R. FergusoniD· 1 shared Alka Yadav· 1 shared Andy Xu· 1 shared Anthony Chen· 1 shared Calvin Wang· 1 shared Eason Zhao· 1 shared Gregory A. ChinniD· 1 shared Hua SuiD· 1 shared

Activity by Year

2026-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

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1 shared paperNeuroscience

Adam R. FergusonORCID

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2 papers

Recent·Most cited

Increased Synapse Elimination by Inflammatory Cells Contributes to Long-lasting Post-Stroke Memory Dysfunction in Old Mice

Zahra Shabani, Peipei Pan, Qifeng Li, Zhanqiang Wang, Kun Leng, Shalika Sangras, Kang Huo, Alka Yadav, Calvin Wang, Joshua Shi, Rich Liang, Gregory A. Chinn, Nikos Kyritsis, Adam R. Ferguson, Judith Hellman, Hua Su

This study shows that old mice experience long-term memory issues after stroke due to increased synapse removal by inflammatory cells, which can be mitigated by activating 7-nAchRs.

Cell & Bioscience · Aug 28, 2026Peer-reviewedNeuroscience

EditorForge: An Active-Site-Aware Framework for Inverse-Folding-Based Protein Redesign

Anthony Chen, Jibraan Siddiqui, William Taucar, Leo Tiralongo, Maxim Tkachenko, Andy Xu, Sehaj Bawa, Sihan Guo, Owen Pinska, Jonathan Rim, Joshua Shi, Michael Wang, Eason Zhao

EditorForge refines inverse-folded protein sequences for enzyme and genome-editor domains by applying constraints and audits to ensure structural integrity and active-site protection.

bioRxiv · Jun 11, 2026 · PreprintBioinformatics