姓名：史偈君

导师情况：博士生导师

邮箱：shij@tongji.edu.cn

研究方向：计算表观修饰组学

1、 新型表观修饰检测方法开发

2、 表观多态性对细胞命运和疾病的调控

3、表观修饰大模型与药物发现 

教育及工作经历

2019.09–2021.09，加州大学尔湾分校，博士后/助理研究员

2016.08–2019.09，休斯顿贝勒医学院，博士后，导师：Wei Li教授

2013.11–2014.04，纽约纪念斯隆-凯特琳癌症中心，访问学者，导师：Li-Xuan Qin博士

2011.09–2016.03，同济大学，博士，导师：江赐忠教授

2007.09–2011.06，内蒙古大学，学士

个人简介

2011年于内蒙古大学获得生物技术学士学位，后被免试保送同济大学并于2016年获得生物学博士学位，2014年前往纽约纪念斯隆-凯特琳癌症中心进行访学交流。2016-2021年，先后在美国贝勒医学院和加州大学尔湾分校Wei Li实验室任博士后和助理研究员。2021年底入选上海市海外高层次人才引进计划，2022年获聘同济大学“百人计划B类”特聘研究员。目前以通讯或第一作者（含共同）在Nature Methods, Nature Cell Biology, Nature Communications, Nucleic Acids Research, Cancer Research, Genes & Development等学术期刊上发表SCI论文40余篇，累计他引4000余次。担任中国生物信息学会表观遗传学委员会委员，上海市生物信息学会青委会委员，法国国家健康与医学研究院inserm外审专家，并担任知名学术期刊Genome Biology, Briefings in Bioinformatics和Genomics, Proteomics & Bioinformatics等的特约审稿人。

研究领域为计算表观修饰组学，成果包括：构建纳米孔直接RNA测序检测RNA修饰的算法重训练和评估平台NaRMBench（Nature Methods，2025）；开发RNA和DNA修饰通用比对算法BASAL，发现大量被忽视的修饰位点，并拓展了单细胞RNA修饰数据的解读（Nucleic Acids Res，2025）；提出DNA甲基化并发率方法衡量肿瘤表观多态性，并证明它是抑癌基因的新型分子标记（Nature Commun，2021a）；校正甲基化测量方法的细胞异质性，大幅改善其与基因表达水平的相关性，并利用其鉴定出癌症恶化相关基因（Nature Commun，2021b）；癌症多组学研究发现调控铁死亡的表观遗传机制（Nature Cell Biology，2018）。

实验室主页   https://junlab.netlify.app/ 

已发表论文：  

1. Luo T, Xu M, Wang M, Chen F, Shi J#. (2025). Systematic evaluation of computational tools for multitype RNA modification detection using nanopore direct RNA sequencing. Nature Methods, online.

2. Xu M, Liu X, Wang M, Luo T, Gao Y, Liu J#, Shi J#. (2025). BASAL: a universal mapping algorithm for nucleotide base-conversion sequencing. Nucleic Acids Research, 53(2):gkae1201.

3. Wang M, Shi J#, Xu K, et al. (2025). T cell exhaustion and dendritic cell-mediated tertiary lymphoid structures (TLSs) modulation affect response to neoadjuvant chemoradiotherapy in microsatellite stable rectal cancer. Advanced Science, e14332.

4. Lin J, Yang X, Jiang C#, Liu X#, Shi J#. (2026). Enhancing cancer susceptibility to disulfidptosis by inducing cell cycle arrest and impairing DNA repair. Theranostics, 16: 637–50.

5. Wang Z-X, Chen F, He B-D, ..., Hou Y#, Shi J#, Xue J#. (2025). Direct sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution unravels their distinct roles in alzheimer’s disease. Advanced Science, 12: e07843.

6. Wang H, Wu A, Yang M-C, ..., Liu X#, Shi J#, Gao S#, Zhang J#. (2025). Genome-wide investigation of transcription factor footprints and dynamics using cFOOT-seq. Protein & Cell, 16: 932–52.

7. Fan K, Zhou S, Ren Y, ..., Shi J#, Ding C#, Zhang Y#. (2025). Epigenetic regulation of ACSL4 via H2A monoubiquitylation connects lipid metabolism to BAP1-mediated ferroptosis. Cell Death & Differentiation, online.

8. Hu X, He Y, Li S, …, Lin C, Shi J, Li HB, Gao Y. (2025). Acute inflammation induces acute megakaryopoiesis with impaired platelet production during fetal hematopoiesis. Development, DOI: 10.1242/dev.204226

9. Cheng ZL, Zhang SY, Wang Z, …, Wang Z, Chen F, Xue J, Shi J, …, Xiong Y, Ye D. (2025). Pathogen-derived glyoxylate inhibits Tet2 DNA dioxygenase to facilitate bacterial persister formation. Cell Metabolism

10. Yang L, Chen X, Lee C, Shi J, et al. (2023). Functional characterization of age-dependent p16 epimutation reveals biological drivers and therapeutic targets for colorectal cancer. Journal of Experimental & Clinical Cancer Research 42(1):113.

11. Shi J, Xu J, Chen EY, Li SJ, Cui Y, Shen L, Li JJ, and Li W. (2021). The Concurrence of DNA Methylation and Demethylation is Associated with Transcription Regulation. Nature Communications 12:5285.

12. Xu J*, Shi J*, Cui X, Cui Y, Li JJ, Goel A, Chen X, Su J, Issa J-P, and Li W. (2021). Cellular heterogeneity–adjusted clonal methylation (CHALM) provides better prediction of gene expression. Nature Communications 12(1):1-9.

13. Zhang Y*, Shi J*, Liu X, Feng L, Gong Z, et al. (2018). BAP1 links metabolic regulation of ferroptosis to tumour suppression. Nature Cell Biology 20(10), 1181-1192. (ESI highly cited paper)

14. Zhang Y*, Shi J*, Liu X, Xiao Z, et al. (2020). H2A monoubiquitination links glucose availability to epigenetic regulation of the endoplasmic reticulum stress response and cancer cell death. Cancer Research 80(11):2243-2256.

15. Hsu CC*, Shi J*, Yuan C*, Zhao D*, Jiang S, et al. (2018). Recognition of histone acetylation by the GAS41 YEATS domain promotes H2A.Z deposition in non-small cell lung cancer. Genes & Development 32, 58-69.

16. Hsu CC*, Zhao D*, Shi J*, Peng D, et al. (2018). Gas41 links histone acetylation to H2A. Z deposition and maintenance of embryonic stem cell identity. Cell discovery 4, 28.

17. Shi L*, Shi J*, Shi X, Li W, and Wen H. (2018). Histone H3. 3 G34 Mutations Alter Histone H3K36 and H3K27 Methylation In Cis. Journal of molecular biology 430, 1562-1565.

18. Xi Y*, Shi J*, Li W*, Tanaka K*, Allton KL*, et al. (2018). Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes. BMC genomics 19, 150.

19. Shi J*, Zheng M*, Ye Y, Li M, Chen X, et al. (2014). Drosophila Brahma complex remodels nucleosome organizations in multiple aspects. Nucleic acids research 42, 9730-9739.

20. Koronowski KB, Kinouchi K, Welz PS, Smith JG, Zinna VM, Shi J, et al. (2019). Defining the independence of the liver circadian clock. Cell 177(6):1448-1462.e14.

21. Zhang Y, Xue Y, Shi J, Ahn JW, Mi W, et al. (2018). The ZZ domain of p300 mediates specificity of the adjacent HAT domain for histone H3. Nature structural & molecular biology 25(9), 841–849.

22. Liu X, Olszewski K, Zhang Y, Lim EW, Shi J, et al. (2020). Cystine transporter regulation of pentose phosphate pathway dependency and disulfide stress exposes a targetable metabolic vulnerability in cancer. Nature Cell Biology 22(4):476‐486.

23. Zheng ZY, Anurag M, …, Shi J, et al. (2020). Neurofibromin Is an Estrogen Receptor-α Transcriptional Co-repressor in Breast Cancer. Cancer Cell 37(3):387‐402.e7.

24. Greco CM, Koronowski KB, Smith JG, Shi J, et al. (2021). Integration of Feeding Behaviour by the Liver Circadian Clock Reveals Network Dependency of Metabolic Rhythms. Science Advances 7(39): eabi7828.

25. Greco CM, Cervantes M, …, Shi J, et al. (2020). S-adenosyl-l-homocysteine hydrolase links methionine metabolism to the circadian clock and chromatin remodeling. Science Advances 6 (51), eabc5629.

26. Koppula P, Lei G, …, Shi J, et al. (2022). A targetable CoQ-FSP1 axis drives ferroptosis- and radiation-resistance in KEAP1 inactive lung cancers. Nature Communications 13:2206.

27. Gates LA, Shi J, Rohira AD, Feng Q, Zhu B, et al. (2017). Acetylation on histone H3 lysine 9 mediates a switch from transcription initiation to elongation. Journal of Biological Chemistry, jbc. M117. 802074.

28. Koppula P, Zhang Y, Shi J, Li W, and Gan B. (2017). The glutamate/cystine antiporter SLC7A11/xCT enhances cancer cell dependency on glucose by exporting glutamate. Journal of Biological Chemistry, jbc. M117. 798405.

29. Cui Y, Cui Z, Xu J, Hao D, Shi J, et al. (2020) NG-Circos: next-generation Circos for data visualization and interpretation. NAR Genomics and Bioinformatics 2 (3), lqaa069.

30. Shi J, and Qin L-X. (2014). CORM: An R Package Implementing the Clustering of Regression Models Method for Gene Clustering. Cancer informatics 13, CIN. S13967.

31. Qin L-X, Zhou J, Shi J, et al. (2020). Statistical Assessment of Depth Normalization for Small RNA Sequencing. JCO Clinical Cancer Informatics 4, 567-582.

32. Chen Y, Zhang H, …, Shi J, et al. (2019). A PARP1-BRG1-SIRT1 axis promotes HR repair by reducing nucleosome density at DNA damage sites. Nucleic Acids Research 47(16): 8563-8580.

33. Shi J*, He J*, Lin J, Sun X, Sun F, et al. (2016). Distinct response of the hepatic transcriptome to Aflatoxin B₁ induced hepatocellular carcinogenesis and resistance in rats. Scientific reports 6, 31898.

34. Shi J*, Hu J*, Zhou Q, Du Y, and Jiang C. (2013). PEpiD: a prostate epigenetic database in mammals. PloS one 8, e64289.

35. Huang K*, Zhang X*, Shi J*, Yao M, Lin J, et al. (2015). Dynamically reorganized chromatin is the key for the reprogramming of somatic cells to pluripotent cells. Scientific reports 5, 17691.

36. Li D*, Shi J*, Du Y, Chen K, Liu Z, et al. (2016). Profiling analysis of histone modifications and gene expression in lewis lung carcinoma murine cells resistant to anti-VEGF treatment. PloS one 11, e0158214.

37. Ye Y, Li M, Gu L, Chen X, Shi J, et al. (2017). Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos. Cell death and differentiation 24, 409.

38. Ye Y, Gu L, Chen X, Shi J, et al. (2016). Chromatin remodeling during the in vivo glial differentiation in early Drosophila embryos. Scientific reports 6, 33422.

39. Wang X*, Shi J*, Yang J, Liang Y, et al. (2012). Molecular Characterization and Expression Pattern of Gene IGFBP-5 in the Cashmere Goat (Capra hircus). Asian-Australasian journal of animal sciences 25, 606.

40. Yang J*, Shi J*, Liang Y, Zheng X, Zhang T, Qin Y, Wang Z, Liu D. (2011). Cloning and expression pattern of protein kinase B/AKT gene in Inner Mongolia Cashmere Goat. Scientia Agricultura Sinica 44 (13), 2787-2795.

41. Zheng X, Yang J, …, Shi J, et al. (2011). Molecular characterization and expression pattern of Rheb gene in Inner Mongolia cashmere goat (Capra hircus). Agric Sci China 10, 1452-1458.

42. Zhang T, Wang Z, Li B, Shi J, Qin Y, et al. (2010). Molecular cloning and characterization analysis of LEF-1 gene from Inner Mongolia Cashmere Goat. Paper presented at: Biomedical Engineering and Informatics (BMEI), 2010 3rd International Conference on (IEEE).