个人简介

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 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。期间主要研究基因转录的表观遗传调控机制，发现果蝇染色质重塑酶的缺失广泛影响核小体排布并导致幼虫期发育迟滞（Nucleic acids research，2014），2014年获“博士生国家奖学金”，并受邀前往纽约纪念斯隆-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，从事人类复杂疾病的分子特性研究，开发新型计算生物学方法，在癌症表观遗传调节机制研究中取得一系列原创性发现，包括： (1) 提出“DNA甲基化并发率（methylation concurrence）”方法来衡量肿瘤表观遗传多态性，发现其与“甲基化-去甲基化”拮抗作用的显著关联，并证明它是抑癌基因的分子标记（Nature Communications，2021年9月） (2) 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 Communications，2021年1月） (3) 通过癌症基因组学、表观遗传组学、和转录组学的多角度分析，发现铁死亡蛋白调控癌症发生的表观遗传机制（Nature Cell Biology，2018） 2021年入选上海市海外高层次人才引进计划，并任同济大学特聘研究员。目前以第一作者（含共同）在Nature Cell Biology，Nature Communications，Cancer Research，Genes & Development等学术期刊上发表SCI论文30余篇。并担任生物信息学领域知名学术期刊Briefings in Bioinformatics和Genomics, Proteomics & Bioinformatics的特约审稿人。

研究领域

1、 表观遗传多态性的成因和对基因表达的调控 2、 早期发育和衰老过程中表观遗传多态性的动态变化 3、 肿瘤表观异质性在早期诊治中的应用 4、 多组学深度挖掘揭示疾病分子特征

计算生物学与表观遗传学

近期论文

查看导师新发文章 （温馨提示：请注意重名现象，建议点开原文通过作者单位确认）

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. 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. — Research reported by UC Irvine News 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 — Research highlighted by News & Views in Cancer of Nature Cell Biology 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. 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. 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. 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. 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. 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. 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. 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. Zheng ZY, Anurag M, Lei JT, …, Shi J, et al. (2020). Neurofibromin Is an Estrogen Receptor-α Transcriptional Co-repressor in Breast Cancer. Cancer Cell 37(3):387‐402.e7. 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. 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. 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. 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. 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. 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 (accepted). 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. 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. 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. Shi J*, Hu J*, Zhou Q, Du Y, and Jiang C. (2013). PEpiD: a prostate epigenetic database in mammals. PloS one 8, e64289. 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. 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. 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. 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. 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. 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. 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. 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. 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).