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首頁 全所PI名錄
  • 吉喆
  • 研究員，研究組長，博士生導(dǎo)師
  • E-mail: zhe.ji@sibcb.ac.cn
  • 實驗室主頁: 
    個人簡介：

  • 2006年畢業(yè)于南京大學，獲生物技術(shù)專業(yè)學士學位。2012年畢業(yè)于新澤西醫(yī)科與牙醫(yī)大學（現(xiàn)新澤西州立羅格斯大學），獲得計算RNA基因組學博士學位。2012年至2017年在哈佛大學醫(yī)學院和麻省理工學院-哈佛B(yǎng)road研究所接受博士后訓(xùn)練。2018年至2025年在美國西北大學Feinberg醫(yī)學院和McCormick 工程學院擔任雙聘助理教授。2026年1月起任中科院分子細胞科學卓越創(chuàng)新中心(生物化學與細胞生物學研究所)研究員，研究組長，博士生導(dǎo)師。

    社會任職：
    研究方向：
  • RNA基因組學
    研究工作：

  • 本實驗室致力于整合計算與實驗基因組學，旨在揭示生理狀態(tài)和疾病狀態(tài)下RNA合成與翻譯的調(diào)控機制。課題組通過“干濕結(jié)合”的研究體系，系統(tǒng)性推進技術(shù)創(chuàng)新、基礎(chǔ)探索與臨床轉(zhuǎn)化。在技術(shù)創(chuàng)新方面，我們開發(fā)基于人工智能（包括機器學習與深度學習）的算法，實現(xiàn)對功能基因組學數(shù)據(jù)的整合分析，并建立基因表達流程的新型測序技術(shù)。在基礎(chǔ)研究方面，我們聚焦于RNA與蛋白質(zhì)代謝的多層級耦合機制，解析其在發(fā)育與疾病中的分子調(diào)控網(wǎng)絡(luò)。在臨床轉(zhuǎn)化方面，我們致力于發(fā)展靶向RNA翻譯過程及生成蛋白質(zhì)的治療方法。目前主要研究方向包括：

    1.開發(fā)深度學習模型，解析RNA生成與翻譯的動態(tài)過程，探究其在生理調(diào)控與疾病發(fā)生中的功能；

    2.發(fā)展核糖體圖譜分析技術(shù)，揭示RNA翻譯調(diào)控在癌癥與神經(jīng)退行性疾病中的作用；

    3.探索非經(jīng)典翻譯區(qū)及微蛋白的進化、功能及其在疾病中的調(diào)控機制；

    4.結(jié)合AI與測序技術(shù)，推動臨床個體化檢測與精準治療策略的發(fā)展。

    承擔科研項目情況：
    代表論著：
    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.
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    研究組成員：