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曾泽贤

 

曾泽贤

 

电子邮件: zexianzeng@pku(dot)edu(dot)cn

实验室主页http://cqb.pku.edu.cn/zenglab/

 

研究方向:

聚焦生物信息学与计算肿瘤免疫学,通过整合挖掘肿瘤基因组学与医疗数据,并结合机器学习方法研究肿瘤免疫及信号通路调控,揭示肿瘤免疫反应机理,旨在为临床免疫治疗成功率的提高提供新的靶向基因,为免疫调控基因的发现提供新的研究思路,为临床肿瘤用药提供新的方法。我们正在开发多种算法和工具来分析高通量基因组学数据,包括 RNA-seqWESCRISPR筛选、单细胞测序、空间转录组学、ATAC-seq 数据等。 通过数据整合和算法开发,我们尝试对肿瘤发展、进展、药物反应和耐药性的特异性和功能进行建模。 当我们在数据分析中得到意想不到但有趣的结果时,我们还会设计相应的实验进行验证和探索,以期了解潜在的机制。

 

  

代表性科研论文: 

1.      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 MHCII expression in melanoma. Cancer Immunology Research (2022) (in revision)

2.      Zeng Z*, Gu S*, Wong C, Li D, Lin Y, Wong C, Ouardaoui N, Zhang W, Brown M, Liu XS: A joint dimension reduction framework to model immunotherapy response for syngeneic mouse models. Science Advances (2022) (in revision)

3.      Zeng Z*, Li Y*, Li Yi*, Luo Y: Computational methods for spatially resolved transcriptomics data analysis. Genome Biology (2022) 10.02653

4.      Zeng Z*,#, Wong C*, Lin Y*, Li D, Zhang Y, Gu S, Zhang W, Kim S, Yates K, Freeman G, Brown M, Manguso R, Liu XS#: TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response. Nucleic Acids Research (2021) 10.1093

5.      Zeng Z*, Fu J*, Cibulskis C, Jhaveri A, Gumbs C, Das B, … & Liu XS#, Wu C#: Cross-site concordance evaluation of tumor DNA and RNA sequencing platforms for the CIMAC-CIDC network. Clinical Cancer Research. (2021).20.3251

6.      Kumar S*, Zeng Z*, Bagati A*, Tay Re*, Sanz L, Hartono SR, … & Liu XS#, Wucherpfennig K#: Carm1 inhibition enables immunotherapy of resistant tumors by dual action on tumor and T-cells. Cancer Discovery (2021). 20-1144

7.      Zhou L*, Zeng Z*, Egloff A, Zhang F, Guo F, Cambell K, Du P, … & Liu XS#, Uppaluri R#: Checkpoint blockade induced CD8+ T cell differentiation in responders in head and neck cancers. Journal for ImmunoTherapy of Cancer (2021). 10 (1), e004034

8.      Zeng Z, Vo A, Li X, Shidfar Ali, Saldana P, Xuei X, Luo Y, Khan AS, Clare SE: Somatic genetic aberrations in benign breast disease and the risk of subsequent breast cancer. npj Breast Cancer. (2020). 6(1),1-11

9.      Zeng Z, Amin A, Roy A, Pulliam N, Karavites L, Espino S, Li X, Luo Y, Khan AS: Preoperative magnetic resonance imaging and oncologic outcomes in premenopausal breast cancer patients. npj Breast Cancer. (2020). 6(1),1-8.

10.   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

11.   Zeng Z, Mao C, Vo A, Li X, Nugene J, Khan AS, Clare SE, Luo Y: Deep learning for cancer type classification and driver gene identification. BMC Bioinformatics. (2020) (18)1

12.   Zeng Z, Vo A, Mao C, Clare S, Khan S, Luo Y: Cancer classification and pathway discovering using non-negative matrix factorization. Journal of Biomedical Informatics. (2019): 103247

13.   Zeng Z, Yao L, Roy A, Li X, Espino S, Clare S, Khan S, Luo Y: Identifying breast cancer distant recurrence from electronic health records using machine learning. Journal of Healthcare Informatics Research. (2019). 1-17

14.   Zeng Z, Xie X, Menaker H, Sanford-Ring SG, Li J: Performance evaluation of operating room schedules in orthopedic surgery. Flexible Services and Manufacturing. (2018), 30(1-2):198-223.

15.   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):1-1

16.   Zeng Z, Espino S, Roy A, Li X, Khan S, Clare S, Jiang X, Neapolitan R, Luo Y: Using natural language processing and machine learning to identify breast cancer local recurrence. BMC Bioinformatics. (2018), 19(Suppl 17):498

17.   Zeng Z, Jiang X, Neapolitan R: Discovering causal interactions using Bayesian network scoring and information gain. BMC bioinformatics, (2016), 17(1):1.

 

 

 

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