Author

Ziqi Yang

Children's Hospital of PhiladelphiaPrimary ORCID profile (0009-0005-7811-8425 · 1 paper)Unclaimed ORCID profile · follow to get notified of new preprints

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Same name, identified by ORCID

Ziqi YangiD1 paper · McGill University

Biology Disciplines

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Bioinformatics· 3 Immunology· 1

Signature Assays, Organisms & Methods

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Research Focus:differential expression· 3 Organism:human· 3 Approach:statistical model· 3 Research Focus:benchmarking· 2 Research Focus:cell type annotation· 2 Research Focus:gene regulatory network inference· 2 Assay:scRNA-seq· 2 Research Focus:software / tool· 2

Frequent Co-Authors

Hailong HuiD· 4 shared Julia Fleming· 4 shared Mingyao PaniD· 4 shared Yuhao TaniD· 4 shared Bo Li· 3 shared Jing HuiD· 2 shared Tong Wang· 2 shared Yizhou Tracy Wang· 2 shared

Activity by Year

2025-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 40 mutual co-author links

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4 shared papersBioinformatics

Hailong HuORCID

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Author profile →

4 papers

Recent·Most cited

Cancer cells hijack mitochondria from Bhlhe40+ T cells for immune evasion

Hailong Hu, Yuhao Tan, Irina S. Shkundina, Richard Madnick, Jing Hu, Hongyi Zhang, Ziqi Yang, Tong Wang, Xuexin Yu, Julia Fleming, Mingyao Pan, Yizhou Wang, Yuanyuan Pang, Drew Weissman, Bo Li

The paper identifies the Bhlhe40-S100a4 cascade as a key regulator of cancer cell mitochondrial transfer from T cells, offering a target for immunotherapy.

bioRxiv · Oct 28, 2026 · PreprintImmunology

Antigen-aware TCR embeddings reveal conserved immune patterns for personalized immune monitoring

Mingyao Pan, Jing Hu, Yizhou Tracy Wang, Yuhao Tan, Hailong Hu, Ziqi Yang, Julia Fleming, Yuanyuan Pang, Bo Li

TCRmeta integrates antigen specificity with TCR repertoires to enable cross-individual and longitudinal immune monitoring by revealing conserved patterns and technical variation robustness.

bioRxiv · Oct 16, 2026 · PreprintBioinformatics

AI-enabled virtual immunopeptidomics links quantitative neoantigen presentation to immunogenicity

Yuhao Tan, Ziqi Yang, Tong Wang, Hailong Hu, Julia Fleming, Mingyao Pan, Laurence Crane Eisenlohr, Bo Li

The paper develops epiVIP, a deep learning framework to predict HLA-I peptide abundance from (sc)RNA-seq data, showing that peptide abundance and non-selfness jointly determine antigenicity and predict tumor reactivity and survival.

bioRxiv · May 10, 2026 · PreprintBioinformatics

Quantitative and large-scale investigation of human TCR-HLA Cross-Reactivity

Mingyao Pan, Yuhao Tan, Yizhou Tracy Wang, Jing Rong Hu, Julia Fleming, Hailong Hu, Ziqi Yang, Xiaowei Zhan, Bo Li

The paper introduces THNet, a method to analyze HLA-TCR cross-reactivity, revealing new disease associations and improving transplantation outcomes.

Science Advances · Oct 24, 2025Peer-reviewedBioinformatics