Author

Ying Shi

Arizona State University

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

Same name, identified by ORCID

Biology Disciplines

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Bioinformatics· 2 Immunology· 2 Neuroscience· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Research Focus:cell type annotation· 2 Organism:human· 2 Approach:contrastive learning· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Research Focus:drug response / drug discovery· 1 Assay:electronic health records· 1

Frequent Co-Authors

Shifu LuoiD· 2 shared Songming ZhangiD· 2 shared Chaojiang ChengiD· 1 shared Christopher A. BuneoiD· 1 shared Chun Pan· 1 shared Gregory A. Apker· 1 shared Haiqin Jiang· 1 shared Hao HuangiD· 1 shared

Activity by Year

2021-2026 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 9 mutual co-author links

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2 shared papersImmunology

Shifu LuoORCID

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

Shared and distinct immunometabolic states link to divergent pathology in cutaneous mycobacterial infections

Huangtao Guo, Rui Zeng, Qin Wei, Jingshu Xiong, Haiqin Jiang, Ying Shi, Wenyue Zhang, Chun Pan, Chaojiang Cheng, Hongsheng Wang, Yetao Wang

This study identifies shared and distinct innate immune programs in cutaneous mycobacterial infections and links them to divergent pathological outcomes through metabolic interactions.

bioRxiv · Oct 23, 2026 · PreprintImmunology

Deep mapping of structural perturbations to energetics enables precise TCR design

Shifu Luo, Songming Zhang, Ying Shi, J W Li, Jiaxin Cai, Ning‐Yi Shao, Pan Yanchun

The paper introduces mpTCRai, a deep learning framework that maps structural perturbations to energetic changes in TCRs, enabling precise and safe TCR design for immunotherapy.

Cell Reports Methods · Aug 20, 2026Peer-reviewedImmunology

Mapping disease traits onto spatiotemporal domain landscapes through scalable multi-sample integration of spatial transcriptomics

Songming Zhang, Shifu Luo, Yuxiao Luo, Shuquan Su, Ling Liu, Ying Shi, Wu-Jun Li, Tian Tian, Jinyan Li

STUltra integrates spatial transcriptomics data to map disease traits onto spatiotemporal tissue landscapes, outperforming existing methods in scalability and speed.

bioRxiv · Aug 10, 2026 · PreprintBioinformatics

PlotGDP: an AI Agent for Bioinformatics Plotting

Xiaotong Luo, Ying Shi, Hao Huang, Hongge Wang, Wenyi Cao, Zhixiang Zuo, Qi Zhao, Yueyuan Zheng, Yubin Xie, Shuai Jiang, Jian Ming Ren

PlotGDP provides an AI-powered web server for generating publication-quality bioinformatics plots using natural language commands without requiring coding or environment setup.

bioRxiv · Feb 7, 2026 · PreprintBioinformatics

Sensory feedback-dependent coding of arm position in local field potentials of the posterior parietal cortex

Paul S. VanGilder, Ying Shi, Gregory A. Apker, Christopher A. Buneo

The paper investigates how sensory feedback affects local field potential activity in the posterior parietal cortex during arm position tasks, finding feedback-dependent tuning and suppression of beta band power.

Scientific Reports · Apr 27, 2021Peer-reviewedNeuroscience