Publications

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# Co-first authors; * Co-corresponding authors

2025

  • Tang K, Wu L, Hu Y, Xue T, Jin Y, Zhou X, Luo C, Zhao Y, Tong L, Dai J, Feng D, Zeng Z*, Pan D*.Perturbation of calreticulin potentiates CD8+ T cell-mediated antitumor immunity.Journal of Experimental Medicine.2025 Oct 6;222(10):e20242360. doi: 10.1084/jem.20242360. Epub 2025 Aug 20. PMID: 4083353.
    [Abstract][Full Paper]
  • Li Y, Ding Y, Dennis S, Hutch MR, Zhou J, Zhou Y, Li Y, Pillai M, Ghotbaldini S, Garcia MA, Broad MS, Mao C, Dulai PS, Cheng F, Zeng Z*, Luo Y*.SOAR elucidates biological insights and empowers drug discovery through spatial transcriptomics.Science Advances.2025 Jun 13;11(24):eadt7450.doi: 10.1126/sciadv.adt7450.Epub 2025 Jun 11.PMID: 40498826.
    [Abstract][Full Paper]
  • Zhan X,Liu Y,Guo Y,Zhou W,Yan Y,Zeng H,Dong X,Chen X,Ma R,Liu Z,Zhu F,Zheng X,Li X,Yin J,Chan FK,Liu C,Liu L,Xu X,Hou Y,Tao H,Dong Y,Zeng T,Li Y*,Zhou J*,Zeng Z*,Feng Y*.Single cell resolved spatial immune repertoire unveils spatial heterogeneity of lymphoid aggregates in human immune disorders.bioRxiv.2025.01.16.630222.
    [Abstract][Full Paper]
  • Ren P, Zhang R, Wang Y, Zhang P, Luo C, Wang S, Li X, Zhang Z, Zhao Y, He Y, Zhang H, Li Y, Gao Z, Zhang X, Zhao Y, Liu Z, Meng Y*, Zhang Z*, Zeng Z*. Systematic Benchmarking of High-Throughput Subcellular Spatial Transcriptomics Platforms. bioRxiv. 2024.2012.2023.630033.
    [Abstract][Full Paper]
  • Luo C, Zhang R, Guo R, Wu L, Xue T, He Y, Jin Y, Zhao Y, Zhang Z, Zhang P, Ye S, Li X, Li D, Zhang W, Wang C, Lai L, Pan-Hammarström Q, Wucherpfennig K, Gao Z*, Pan D*, Zeng Z*.Integrated computational analysis identifies therapeutic targets with dual action in cancer cells and T cells. Immunity. 2025 Mar 11;58(3):745-765.e9. doi: 10.1016/j.immuni.2025.02.007. Epub 2025 Feb 28. PMID: 40023158.
    [Abstract][Full Paper]
  • Zhou X, Xu T, Li C, He Y, Hu Y, Gong H, Li J, Jiang H, Wen L, Fu Y, Zeng Z*, Pan D*. Potentiating anti-tumor immunity by re-engaging immune synapse molecules.Cell Reports Medicine. 2025 Feb 14:101975. doi: 10.1016/j.xcrm.2025.101975.Epub 2025 Feb 24. PMID: 39999838.
    [Abstract][Full Paper]

2024

  • Xiong X, Yang C, Jin Y, Zhang R, Wang S, Gan L, Hou S, Bao Y, Zeng Z*, Ye Y*, Gao Z*. ABHD6 suppresses colorectal cancer progression via AKT signaling pathway. Mol Carcinog. 2024 Jan 10. doi: 10.1002/mc.23678. Epub ahead of print. PMID: 38197491.
    [Abstract][Full Paper]

2023

  • Wu L, Jin Y, Zhao X, Tang K, Zhao Y, Tong L, Yu X, Xiong K, Luo C, Zhu J, Wang F, Zeng Z*, Pan D*. Tumor aerobic glycolysis confers immune evasion through modulating sensitivity to T cell-mediated bystander killing via TNF-α. Cell Metabolism. 2023 Sep 5;35(9):1580-1596.e9. doi: 10.1016/j.cmet.2023.07.001. Epub 2023 Jul 27. PMID: 37506695.
    [Abstract][Full Paper]

2022

  • Fan T, Liao Q, Zhao Y, Dai H, Song S, He T, Wang Z, Huang J, Zeng Z*, Guo H*, Zhang H*, Qiu X*. Sialylated-IgG in epithelial cancers inhibits anti-tumor function of T cells via Siglec-7. Cancer Science (2022) 10.1111.
    [Abstract][Full Paper]
  • Zeng Z#, Gu S#, Wong C, Li D, Lin Y, Wong C, Ouardaoui N, Zhang W, Brown M, Liu XS*: Machine learning on syngeneic mouse tumor profiles to model clinical immunotherapy response. Science Advances (2022) 10.1126.
    [Abstract][Full Paper]
  • Zeng Z#, Gu S#, Yang L, Wong C, Ouardaoui N, Zhang W, Li D, Weirather J, Zhang Y, Meyer C, Rodig S, Hodi SF*, Brown M*, Liu XS*: Hippo signaling pathway regulates cancer cell-intrinsic MHC-II expression. Cancer Immunology Research (2022) 10.1158.
    [Abstract][Full Paper]
  • Zeng Z#, Li Y#, Li Yi#, Luo Y*. Statistical and machine learning methods for spatially resolved transcriptomics data analysis. Genome Biology. 2022. 10.02653
    [Abstract][Full Paper]
  • Zhou L#, Zeng Z#, Egloff AM, Guo F, Campbell KM*, Du P, Fu J, Zolkind P, Ma X, Zhang Z, Zhang Y, Wang X, Gu S, Riley R, Nakahori Y, Keegan J, Haddad R*, Schoenfeld JD, Griffith O, Manguso RT, Lederer JA, Liu XS, Uppaluri R*. Checkpoint blockade-induced CD+ Tcell differentiation in head and neck cancer responders. J Immunother Cancer (JITC). 2022. 10(1), e004034.
    [Abstract][Full Paper]
  • Zeng Z#*, Wong C#, Yang L#, Ouardaoui N, Li D, Zhang W, Gu SS, Zhang Y, Liu Y, Wang Z, Fu J, Zhou L, Zhang B, Kim S, Yates KB, Brown M, Freeman GJ, Uppaluri R, Manguso, Liu XS*. 2021. TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response.Nucleic Acids Research. 2022 Jan 7;50(D1):D1391-7.
    [Abstract][Full Paper]

2021

  • Kumar S#, Zeng Z#, Bagati A, Tay RE, Sanz LA, Hartono SR, Ito Y, Abderazzaq F, Hatchi E, Jiang P, Cartwright ANR, Olawoyin O, Mathewson ND, Pyrdol JW, Li MZ, Doench JG, Booker MA, Tolstorukov MY, Elledge SJ, Chedin F, Liu XS*, Wucherpfennig KW*. CARM1 inhibition enables immunotherapy of resistant tumors by dual action on tumor cells and T cells. Cancer Discovery. 2021. 11:2051-71.
    [Abstract][Full Paper]
  • Zeng Z#, Fu J#, Cibulskis C, Jhivari A, Gumbs C, Das B, Sanchez-Espiridion B, Janssens S, Taing L … Meerzaman D, Thurin M, Futreal PA, Karlovich C, Gabriel SB, Wistuba II, Liu XS*, Wu C. 2020. Cross-site concordance evaluation of tumor DNA and RNA sequencing platforms for the CIMAC-CIDC network. Clinical Cancer Research. Epub ahead of print.
    [Abstract][Full Paper]
  • Zeng Z, Mao C, Vo A, Li X, Nugent JO, Khan SA, Clare SE, Luo Y. Deep learning for cancer type classification and driver gene identification. BMC bioinformatics. 2021 Oct;22(4):1-3.
    [Abstract][Full Paper]

2020

  • Zeng Z, Vo A, Li X, Shidfar A, Saldana P, Blanco L, Xuei X, Luo Y, Khan SA, Clare SE. Somatic genetic aberrations in benign breast disease and the risk of subsequent breast cancer. NPJ Breast Cancer. 2020 Jun 12;6(1):1-1.
    [Abstract][Full Paper]
  • Zeng Z, Fan Z, Xie X, Swartz C, DePriest P, Li J: A two-level iteration approach for modeling and analysis of rapid response process with multiple deteriorating patients. Flexible Service and Manufacturing. (2020). 1-37
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  • Zeng Z, Amin A, Roy A, Pulliam NE, Karavites LC, Espino S, Helenowski I, Li X, Luo Y, Khan SA. Preoperative magnetic resonance imaging use and oncologic outcomes in premenopausal breast cancer patients. NPJ breast cancer. 2020 Oct 2;6(1):1-8.
    [Abstract][Full Paper]

2019

  • Zeng Z, Yao L, Roy A, Li X, Espino S, Clare SE, Khan SA, Luo Y. Identifying breast cancer distant recurrences from electronic health records using machine learning. Journal of healthcare informatics research. 2019 Sep;3(3):283-99.
    [Abstract][Full Paper]
  • Zeng Z, Zhao Y, Sun M, Vo AH, Starren J, Luo Y. Rich Text Formatted EHR Narratives–A Hidden and Ignored Trove. Studies in health technology and informatics. 2019 Aug 21;264:472.
    [Abstract][Full Paper]
  • Zeng Z, Vo AH, Mao C, Clare SE, Khan SA, Luo Y. Cancer classification and pathway discovery using non-negative matrix factorization. Journal of biomedical informatics. 2019 Aug 1;96:103247.
    [Abstract][Full Paper]

2018

  • Zeng Z, Espino S, Roy A, Li X, Khan SA, Clare SE, Jiang X, Neapolitan R, Luo Y. Using natural language processing and machine learning to identify breast cancer local recurrence. BMC bioinformatics. 2018 Dec;19(17):65-74.
    [Abstract][Full Paper]
  • Zeng Z, Deng Y, Li X, Naumann T, Luo Y. Natural language processing for EHR-based computational phenotyping. IEEE/ACM transactions on computational biology and bioinformatics. 2018 Jun 25;16(1):139-53.
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  • Zeng Z, Roy A, Li X, Sasa E, Clare S, Khan S, Luo Y. Using Clinical Narratives and Structured Data to Identify Distant Recurrences in Breast Cancer. In2018 IEEE International Conference on Healthcare Informatics (ICHI) 2018 Jun 4 (pp. 44-52). IEEE.
    [Abstract][Full Paper]
  • Zeng Z, Xie X, Menaker H, Sanford-Ring SG, Li J. Performance evaluation of operating room schedules in orthopedic surgery. Flexible Services and Manufacturing Journal. 2018 Jun;30(1):198-223.
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2017

  • Zeng Z, Li X, Espino S, Roy A, Kitsch K, Clare S, Khan S, Luo Y. Contralateral breast cancer event detection using nature language processing. InAMIA Annual Symposium Proceedings 2017 (Vol. 2017, p. 1885). American Medical Informatics Association.
    [Abstract][Full Paper]

2016

  • Zeng Z, Jiang X, Neapolitan R. Discovering causal interactions using Bayesian network scoring and information gain. BMC bioinformatics. 2016 Dec;17(1):1-4.
    [Abstract][Full Paper]

2014

  • Zeng Z, Xie X, Li J, Menaker H, Sanford-Ring SG. An analytical model for performance evaluation of operating room schedules in orthopedic surgery. In2014 IEEE International Conference on Automation Science and Engineering (CASE) 2014 Aug 18 (pp. 570-575). IEEE.
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2013

  • Zeng Z, Xie X, Zhong X, Liegel BA, Sanford-Ring S, Li J. Simulation modeling of hospital discharge process. In Stochastic Modeling and Analytics in Healthcare Delivery Systems 2018 (pp. 113-134).
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