Publications

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# Co-first authors; * Co-corresponding authors

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

Oliveira G, Egloff AM, Afeyan AB, Wolff JO, Zeng Z, Chernock RD, Zhou L, Messier C, ..., Adkins DR, Wu CJ, Uppaluri R. Preexisting tumor-resident T cells with cytotoxic potential associate with response to neoadjuvant anti-PD-1 in head and neck cancer. Science Immunology. 2023 Sep 8;8(87):eadf4968. doi: 10.1126/sciimmunol.adf4968. Epub 2023 Sep 8. PMID: 37683037.
[Abstract][Full Paper]
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 Metab. 2023 Sep 5;35(9):1580-1596.e9. doi: 10.1016/j.cmet.2023.07.001. Epub 2023 Jul 27. PMID: 37506695.
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Yang L, Wang J, Altreuter J, Jhaveri A, Wong CJ, Song L, Fu J, Taing L, Bodapati S, Sahu A, Tokheim C, Zhang Y, Zeng Z, Bai G, Tang M, Qiu X, Long HW, Michor F, Liu Y, Liu XS. Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA. Nature Protocol. 2023 Jun 30. doi: 10.1038/s41596-023-00841-8.
[Abstract][Full Paper]
Theodoris CV, Xiao L, Chopra A, Chaffin MD, Al Sayed ZR, Hill MC, Mantineo H, Brydon EM, Zeng Z, Liu XS, Ellinor PT. Transfer learning enables predictions in network biology. Nature. 2023 May 31. doi: 10.1038/s41586-023-06139-9.
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Zhang Y, Xiang G, Jiang AY, Lynch A, Zeng Z, Wang C, Zhang W, Fan J, Kang J, Gu SS, Wan C, Zhang B, Liu XS, Brown M, Meyer CA. MetaTiME integrates single-cell gene expression to characterize the meta-components of the tumor immune microenvironment. Nat Communications. 2023 May 6;14(1):2634.
[Abstract][Full Paper]
Sahu A, Wang X, Munson P, Klomp JPG, Wang X, Gu SS, Han Y, Qian G, Nicol P, Zeng Z, Wang C, Tokheim C, Zhang W, Fu J, Wang J, Nair NU, Rens JAP, Bourajjaj M, Jansen B, Leenders I, Lemmers J, Musters M, van Zanten S, van Zelst L, Worthington J, Liu JS, Juric D, Meyer CA, Oubrie A, Liu XS, Fisher DE, Flaherty KT. Discovery of Targets for Immune-Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha. Cancer Discovery. 2023 Mar 1;13(3):672-701.
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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.
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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]
Li Y#, Dennis S#, Hutch MR#, Li Y, Broad MS, Zeng Z*, Luo Y*. SOAR: a spatial transcriptomics analysis resource to model spatial variability and cell type interactions. bioRxiv. 2022:2022.04.17.488596.
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Li Y, Liu Q, Zeng Z, Luo Y. Using an Unsupervised Clustering Model to Detect the Early Spread of SARS-CoV-2 Worldwide. Genes(Basal). 2022;13(4):648.
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Yadav S#, Virk R, Chung CH, Eduardo MB, VanDerway D, Chen D, Burdett K, Gao H, Zeng Z, Ranjan M, Cottone G, Xuei X, Chandrasekaran S, Backman V, Chatterton R, Khan SA*, Clare SE*. Lipid exposure activates gene expression changes associated with estrogen receptor negative breast cancer. NPJ Breast Cancer. 2022 May 4;8(1):59.
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Zeng Z#, Li Y#, Li Yi#, Luo Y*. Statistical and machine learning methods for spatially resolved transcriptomics data analysis. Genome Biology. 2022. 10.02653
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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.
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2021

Wang X#, Tokheim C, Gu SS, Wang B, Tang Q, Li Y, Traugh N, Zeng Z, Zhang Y, Li Z, Shang B, Fu J, Xiao T, Li W, Meyer CA, Chu J, Jiang P, Cejas P, Lim K, Long H, Brown M*, Liu XS*.In vivo CRISPR screens identify the E3 ligase Cop1 as a modulator of macrophage infiltration and cancer immunotherapy target. 2021. Cell. 184(21):5357-5374.
[Abstract] [Full Paper]
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#, Wang J, Lindsay J, Vilimas T, Zhang J, Tokheim C, Sahu AD, Jiang P, Yan C, Y. Duose D, Cerami E, Chen L, Cohen D, Chen QR, Enos RA, Huang X, Lee JJ, Liu Y, Neuberg DS, Nguyen C, Patterson C, Sarkar S, Shukla SA, Tang M, Tsuji J, Uduman M, Wang X, Jason L Weirather, Jijun Yu, Joyce Yu, Zhang J, Zhang J, 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. Clin Cancer Res. Epub ahead of print.
[Abstract][Full Paper]
Li Y, Liu Q, Zeng Z, Luo Y. Unsupervised clustering analysis of SARS-Cov-2 population structure reveals six major subtypes at early stage across the world. In2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2021 Dec 9 (pp. 58-63). IEEE.
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Ranjan M, Lee O, Cottone G, Mirzaei Mehrabad E, Spike BT, Zeng Z, Yadav S, Chatterton R, Kim JJ, Clare SE, Khan SA. Progesterone receptor antagonists reverse stem cell expansion and the paracrine effectors of progesterone action in the mouse mammary gland. Breast Cancer Research. 2021 Dec;23(1):1-7.
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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.
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Gu SS, Zhang W, Wang X, Jiang P, Traugh N, Li Z, Meyer C, Stewig B, Xie Y, Bu X, Manos MP, Zeng Z, Sahu A, Brown M*, Liu XS*. Therapeutically increasing MHC-I expression potentiates immune checkpoint blockade. Cancer Discovery. 2021 Jun 1;11(6):1524-41.
[Abstract]
Cui Y, Cheng X, Chen Q, Song B, Chiu A, Gao Y, Dawson T, Chao L, Zhang W, Li D, Zeng Z, Yu J, Li Z, Fei T, Peng S, Li W. CRISP-view: a database of functional genetic screens spanning multiple phenotypes. Nucleic Acids Research. 2021 Jan 8;49(D1):D848-54.
[Abstract]

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.
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Gu S#, Wang X#, Hu X#, Jiang P, Li Z, Traugh N, Bu X, Tang Q, Wang C, Zeng Z, Fu J, Meyer CA, Zhang Y, Cejas P, Lim K, Wang J, Zhang W, Tokheim C, Sahu A,, Xing X, Kroger B, Ouyang Z, Long H, Freeman G*, Brown M*, Liu XS*. 2020. Clonal tracing reveals diverse patters of response to immune checkpoint blockade. Genome Biology. 2020 Dec;21(1):1-28.
[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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Lee O, Sullivan ME, Xu Y, Rogers C, Muzzio M, Helenowski I, Shidfar A, Zeng Z, Singhal H, Jovanovic B, Hansen N. Selective progesterone receptor modulators in early-stage breast cancer: a randomized, placebo-controlled Phase II window-of-opportunity trial using telapristone acetate. Clinical Cancer Research. 2020 Jan 1;26(1):25-34.
[Abstract][Full Paper]
Li, T#, Fu J#, Zeng Z, Cohen D, Li J, Chen Q, Li B, Liu, XS*. Nucleic Acids Research. 2020 Jul 2;48(W1):W509-14.
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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]
Chen N, Xie X, Zeng Z, Zhong X, Brenny-Fitzpatrick M, Liegel BA, Zheng L, Li J. Improving discharge process at the university of Wisconsin hospital: A system-theoretic method. IEEE Transactions on Automation Science and Engineering. 2019 Feb 20;16(4):1732-49.
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Zimmerman LP, Reyfman PA, Smith AD, Zeng Z, Kho A, Sanchez-Pinto LN, Luo Y. Early prediction of acute kidney injury following ICU admission using a multivariate panel of physiological measurements. BMC Medical Informatics and Decision Making. 2019 Jan;19(1):1-2.
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2018

Mao C, Pan Y, Zeng Z, Yao L, Luo Y. Deep generative classifiers for thoracic disease diagnosis with chest x-ray images. In2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2018 Dec 3 (pp. 1209-1214). IEEE.
[Abstract][Full Paper]
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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Zeng Z, Jiang X, Li X, Wells A, Luo Y, Neapolitan R. Conjugated equine estrogen and medroxyprogesterone acetate are associated with decreased risk of breast cancer relative to bioidentical hormone therapy and controls. Plos One. 2018 May 16;13(5):e0197064.
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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]
Luo Y, Thompson WK, Herr TM, Zeng Z, Berendsen MA, Jonnalagadda SR, Carson MB, Starren J. Natural language processing for EHR-based pharmacovigilance: a structured review. Drug Safety. 2017 Nov;40(11):1075-89.
[Abstract]

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.
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2015

Xie X, Zeng Z, Li J, Swartz CH, DePriest P. Analysis of multi-patient rapid response processes: An iterative approach. In2015 IEEE International Conference on Automation Science and Engineering (CASE) 2015 Aug 24 (pp. 740-745). IEEE.
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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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