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  • 吉喆
  • 研究员,研究组长,博士生导师
  • E-mail: zhe.ji@sibcb.ac.cn
  • 实验室主页: 
    个人简介:
  • 2006年毕业于南京大学,获生物技术专业学士学位。2012年毕业于新泽西医科与牙医大学(现新泽西州立罗格斯大学),获得计算RNA基因组学博士学位。2012年至2017年在哈佛大学医学院和麻省理工学院-哈佛Broad研究所接受博士后训练。2018年至2025年在美国西北大学Feinberg医学院和McCormick 工程学院担任双聘助理教授。2026年1月起任中科院分子细胞科学卓越创新中心(生物化学与细胞生物学研究所)研究员,研究组长,博士生导师。

    社会任职:
    研究方向:
  • RNA基因组学
    研究工作:
  • 本实验室致力于整合计算与实验基因组学,旨在揭示生理状态和疾病状态下RNA合成与翻译的调控机制。课题组通过“干湿结合”的研究体系,系统性推进技术创新、基础探索与临床转化。在技术创新方面,我们开发基于人工智能(包括机器学习与深度学习)的算法,实现对功能基因组学数据的整合分析,并建立基因表达流程的新型测序技术。在基础研究方面,我们聚焦于RNA与蛋白质代谢的多层级耦合机制,解析其在发育与疾病中的分子调控网络。在临床转化方面,我们致力于发展靶向RNA翻译过程及生成蛋白质的治疗方法。目前主要研究方向包括:

    1.开发深度学习模型,解析RNA生成与翻译的动态过程,探究其在生理调控与疾病发生中的功能;

    2.发展核糖体图谱分析技术,揭示RNA翻译调控在癌症与神经退行性疾病中的作用;

    3.探索非经典翻译区及微蛋白的进化、功能及其在疾病中的调控机制;

    4.结合AI与测序技术,推动临床个体化检测与精准治疗策略的发展。

    承担科研项目情况:
    代表论著:
    1. Sundaram1, A.#, Li, Q.#, Wan, Y.#, Tang, J.#, Wu, H., Hegde, R.S., Ji, Z.*, and Keenan, R.J. * (2025). Global analysis of translocon remodeling during protein synthesis at the ER. Nature Structural & Molecular Biology 32, 2517–2525.
    2.  Yamsek, M., Ma, M., Jha, R., Wan, Y., Li, Q., Zhong, F., DeLong, K., Ji, Z., Rohatgi, R., & Keenan, R. J. (2025). Structural basis of regulated N-glycosylation at the secretory translocon. Nature.
    3. Stroup, E. K., Sun, T., Li, Q., Carinato, J., and Ji, Z.* (2025). The advances in deep learning modeling of polyadenylation codes. Wiley Interdisciplinary Reviews: RNA 16(3), e70017.
    4. Yang, H.#, Li, Q.#, Stroup, E.K., Wang, S., and Ji, Z.* (2024). Widespread stable noncanonical peptides identified by integrated analyses of ribosome profiling and ORF features. Nature Communications 15, 1932.
    5. Stroup, E.K., and Ji, Z.* (2024). Delineating yeast cleavage and polyadenylation signals using deep learning. Genome Research 34: 1066–1080.
    6. Wang, S., Stroup, E.K., Wang, T., Yang, R., and Ji, Z.* (2024). Comparative analyses of gene networks mediating cancer metastatic potentials across lineage types. Briefings in Bioinformatics 25(4): bbae357.
    7. Stroup, E.K., and Ji, Z.* (2023). Deep learning of human polyadenylation sites at nucleotide resolution reveals molecular determinants of site usage and relevance in disease. Nature Communications 14, 7378.
    8. Li, Q.#, Yang, H.#, Stroup, E.K., Wang, H., and Ji, Z.* (2022). Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation. Genome Research 32: 545–557.
    9. Ouspenskaia, T., Law, T., Clauser, K.R., Klaeger, S., Sarkizova, S., Aguet, F., Li, B., Christian, E., Knisbacher, B.A., Le, P.M., Hartigan, C.R., Keshishian, H., Apffel, A., Oliveira, G., Zhang, W., Chow, Y.T., Ji, Z., Jungreis, I., Shukla, S.A., Bachireddy, P., Kellis, M., Getz G., Hacohen, N., Keskin, D.B., Carr, S.A., Wu, C.J., and Regev, A. (2022). Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer. Nature Biotechnology 40 (2), 209-217.
    10. Prensner, J.R., Enache, O.M., Luria, V., Krug, K., Clauser, K.R., Dempster, J.M., Karger, A., Wang, L., Stumbraite, K., Wang, V. M., Botta, G., Lyons, N.J., Goodale, A., Kalani, Z., Fritchman, B., Brown, A., Alan, D., Green, T., Yang, X., Jaffe, J.D., Roth, J.A., Piccioni, F., Kirschner, M.W., Ji, Z., Root, D.E., and Golub, T.R. (2021). Non-canonical open reading frames encode functional proteins essential for cancer cell survival. Nature Biotechnology 39 (6), 697–704.
    11. Wang, X., Frederick, J., Wang, H., Hui, S., Backman, V., and Ji, Z.* (2021). Spike-in normalization for single-cell RNA-seq reveals dynamic global transcriptional activity mediating anti-cancer drug response. NAR Genomics and Bioinformatics 3(2): lqab054.
    12. Ji, Z.#, He, L.#, Regev, A. and Struhl, K. (2019). Inflammatory regulatory network mediated by the joint action of NF-kB, STAT3, and AP-1 factors is involved in many human cancers. Proc Natl Acad Sci U S A 116, 9453–9462.
    13. Ji, Z.#, He, L.#, Rotem, A., Janzer, A., Cheng, C.S., Regev, A. and Struhl, K. (2018). Genome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation. Nature Communications 9, 2068.
    14. Ji, Z., Song, R., Huang, H., Regev, A. and Struhl, K. (2016). Transcriptome-scale RNase-footprinting of RNA-protein complexes. Nature Biotechnology 34 (4), 410–413.
    15. Miotto, B.#, Ji, Z.# and Struhl, K. (2016). Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers. Proc Natl Acad Sci U S A 113, E4810–E4819. 
    16. Ji, Z.#, Song, R.#, Regev, A. and Struhl, K. (2015). Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins. eLife 4: e08890.
    17. Hoque, M.#, Ji, Z.#, Zheng, D., Luo, W., Li, W., You, B., Park, J.Y., Yehia, G., and Tian, B. (2013). Analysis of alternative cleavage and polyadenylation by 3′ region extraction and deep sequencing. Nature Methods 10, 133–139.
    18. Luo, W.#, Ji, Z.#, Pan, Z.#, You B., Hoque, M., Li, W., Gunderson, S., and Tian, B. (2013). The conserved intronic cleavage and polyadenylation site of CstF-77 gene imparts control of 3’ end processing by feedback autoregulation and U1 snRNP. PLoS Genetics 9, e1003613.
    19. Haenni, S.#, Ji, Z.#, Hoque, M., Rust, N., Sharpe, H., Eberhard, R., Browne, C., Hengartner, M.O., Mellor, J., McGhee, J., Tian, B. and Furger, A. (2012). Analysis of C. elegans intestinal nuclear gene expression using fluorescence-activated nuclei sorting and 3’ end-seq. Nucleic Acids Research 40, 6304–6318.
    20. Ji, Z.#, Luo, W.#, Li, W., Hoque, M., Pan, Z., Zhao, Y., and Tian, B. (2011). Transcriptional activity regulates alternative cleavage and polyadenylation. Molecular Systems Biology 7, 534. (Published as a featured article)
    21. Ji, Z., and Tian, B. (2009). Reprogramming of 3′ untranslated regions of mRNAs by alternative polyadenylation in generation of pluripotent stem cells from different cell types. PLoS One 4, e8419.
    22. Ji, Z.#, Lee, J.Y.#, Pan, Z.#, Jiang, B. and Tian, B. (2009). Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc Natl Acad Sci U S A 106, 7028–7033.
    获奖及荣誉:
    研究组成员: