Research Interests:

Stem cells play key role in the development of the different tissues during morphogenesis and their maintenance during adult life. Stem cells have the unique capacity to self-renew and to differentiate into the different cell lineages that are also critical for regenerating tissue after injuries. We are trying to understand how stem cells give rise to the different tissues. We study how stem cells respond to different signals from their environment and orchestrate the changes in chromatin, transcription, translation, cell polarity, adhesion and cytoskeletal dynamics in normal tissue development, homeostasis, and tissue regeneration. We want to take lesions from the normal process of tissue dynamics to understand how these processes were disrupted or hijacked in aging and cancer. In our research approaches, we will utilize a broad range of techniques encompassing cell, molecular and developmental biology. Algorithms based on biological big data analysis and artificial intelligence reveal the mechanism and law of gene expression regulation within tumor cells, thereby infering the changes of tumor cell fate and predicting the trend of tumor development, providing a model for early diagnosis, treatment and intervention of tumors. Analyze the mechanism of tissue microenvironment in regulating stem cell behavior and fate decisions during tissue regeneration and aging based on human stem cells and cross-species model animals.

Awards and Honors:

Professional Activities:

Research Grants:

Selected Publications:

Xiaodong Yang,Guole Liu,Guihai Feng,Dechao Bu,Pengfei Wang,Jie Jiang,Shubai Chen,Qinmeng Yang,et al.,Xin Li*. GeneCompass: deciphering universal gene regulatory mechanisms with a knowledge-informed cross-species foundation model. Cell Research (2024). Xin Li*,Yu H C*. A new paradigm of life science research driven by artificial intelligence. Bulletin of Chinese Academy of Sciences (2024). 李鑫,于汉超. 人工智能驱动的生命科学研究新范式. 中国科学院院刊 (2024). Jiang H P,Gao C C,Liu W H,Yang Y G,Xin Li*. Advances in data-driven life sciences research. Bulletin of Chinese Academy of Sciences (2024). 江海平,高纯纯,刘文豪,杨运桂,李鑫*. 数据驱动的生命科学研究进展,中国科学院院刊（2024）。 Minsheng Hao,Lei Wei,Fan Yang,Jianhua Yao,Christina V. Theodoris,Bo Wang,Xin Li,Ge Yang,Xuegong Zhang. Current opinions on large cellular models. Quantitative Biology (2024). Chen Fang;Yidong Wang;Yunze Song;Qingqing Long;Wang Lu;Linghui Chen;Guihai Feng;Yuanchun Zhou*;Xin Li*. How do Large Language Models understand Genes and Cells. ACM Transactions on Intelligent Systems and Technology(2024). An J,Zhang S,Wu J,Chen H,Xu G,Hou Y,Liu R,Li N,Cui W, Xin Li,Du Y,Gu Q. Assessing bioartificial organ function: the 3P model framework and its validation. LAB ON A CHIP (2024). Guihai Feng, Xin Qin, Jiahao Zhang, Wuliang Huang, et al., Xin Li*. CellPolaris: Decoding Cell Fate through Generalization Transfer Learning of Gene Regulatory Networks. bioRxiv (2023). Xiaodong Yang, Guole Liu, Guihai Feng, Dechao Bu, Pengfei Wang, Jie Jiang, et al., Xin Li*. GeneCompass: Deciphering Universal Gene Regulatory Mechanisms with Knowledge-Informed Cross-Species Foundation Model. bioRxiv (2023). Yun Zhang, Joana Liu Donaher, Sunny Das, Xin Li, et al., Genome-wide CRISPR screen identifies PRC2 and KMT2D-COMPASS as regulators of distinct EMT trajectories that contribute differentially to metastasis. Nat Cell Biol (2022). Li X, Wang J, Wang L, Gao Y, Feng G, Li G, Zou J, Yu M, Li YF, Liu C, Yuan XW, Zhao L, Ouyang H, Zhu JK, Li W, Zhou Q, Zhang K. Lipid metabolism dysfunction induced by age-dependent DNA methylation accelerates aging. Signal Transduct Target Ther (2022). Xia HM*, Li Xin*, Gao WW*, Fu X, Ronnie H. Fang, Zhang LF, Zhang Kang. Tissue repair and regeneration with endogenous stem cells. Nat Rev Mater (2018). Zhang Y*, Zhang X*, Shi J*, Tuorto F*, Li Xin*, Liu Y, Liebers R, Zhang L, Qu Y, Qian J, Pahima M, Liu Y, Yan M, Cao Z, Lei X, Cao Y, Peng H, Liu S, Wang Y, Zheng H, Woolsey R, Quilici D, Zhai Q, Li L, Zhou T, Yan W, Lyko F, Zhang Y, Zhou Q, Duan E, Chen Q. Dnmt2 mediates intergenerational transmission of paternally acquired metabolic disorders through sperm small non-coding RNAs. Nature Cell Biology (2018). Li Xin*, Cui XL*, Wang JQ*, Wang YK, Li YF, Wang LY, Wan HF, Li TD, Feng GH, Shuai L, Li ZK, Gu Q, Hao J, Wang L, Zhao XY, Liu ZH, Wang XJ, Li W*, Zhou Q*. Generation and application of mouse-rat allodiploid embryonic stem cells. Cell (2016). Wang JQ*, Li Xin*, Wang L*, Li J, Zhao Y, Bou G, Li Y, Jiao G, Shen X, Wei R, Liu S, Xie B, Lei L, Li W, Zhou Q, Liu Z. A novel long intergenic noncoding RNA indispensable for the cleavage of mouse two-cell embryos. EMBO Rep (2016). Chen Q*, Yan M*, Cao Z*, Li Xin*, Zhang Y*, Shi J*, Feng GH, Peng H, Zhang X, Zhang Y, Qian J, Duan E#, Zhai Q, Zhou Q. Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder. Science (2016). Li Xin*, Wang J.*, Wang L.*, Wan H., Li Y., Li TD., Wang Y., Shuai L., Mao Y., Cui X., Wang L., Liu Z., Zhou Q. Co-participation of paternal and maternal genomes before blastocyst stage is not required for full-term development of mouse embryos. Journal of Molecular Cell Biology (2015). Wang J*, Li Xin*, Zhao Y., Li J., Zhou Q., and Liu Z. (2015). Generation of cell-type-specific gene mutations by expressing the sgRNA of the CRISPR system from the RNA polymerase II promoters. Protein & cell (2015). Shi J.*, Chen Q.*, Li Xin*, Zheng X.*, Zhang Y.*, Qiao J., Tang F., Tao Y., Zhou Q., and Duan E. Dynamic transcriptional symmetry-breaking in pre-implantation mammalian embryo development revealed by single-cell RNA-seq. Development (2015). Li Wei*, Li Xin*, Li TD*, Jiang MG*, Wan H, Luo GZ, Feng C, Cui X, Teng F, Yuan Y, Zhou Q, Gu Q, Shuai L, Sha J, Xiao Y, Wang L, Liu Z, Wang XJ, Zhao XY, Zhou Q. Genetic modification and screening in rat using haploid embryonic stem cells. Cell Stem Cell (2014). Li Xin*, Xia BL*, Li W, Zhou Q. Assessing reprogramming by chimera formation and Tetraploid complementation. Methods Mol Biol (2014).