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:

Fang, C., Cui, W., Hu, Z., Liu, W., Chen, S., Chang, S., ... & Li, X. (2025). Cell-GraphCompass: Modeling Single Cells with Graph Structure Foundation Model. National Science Review. Wang, P., Liu, W., Wang, J., Liu, Y., Li, P., Xu, P., ... & Li, X., Zhou, Y. (2025). scCompass: An Integrated Multi‐Species scRNA‐seq Database for AI‐Ready. Advanced Science. Zhang, J., Zhang, J., Han, L., Wu, S., Li, J., Eaton, E. N., ... & Li, X., Weinberg, R. A. (2025). Inflammation awakens dormant cancer cells by modulating the epithelial–mesenchymal phenotypic state. Proceedings of the National Academy of Sciences. Wu, W., Liu, W., Liu, Z., & Li, X. (2025). Construction of a Genetic Prognostic Model in the Glioblastoma Tumor Microenvironment. Genes. Li, P., Ying, S., Zou, Y., Wang, X., Zhang, R., Huang, C., Dai, M., Xu, K.,.Li, X., ... & Zhou, Q. (2025). NSun2‐Mediated tsRNAs Alleviate Liver Fibrosis via FAK Dephosphorylation. Cell Proliferation. Yang, X., Liu, G., Feng, G., Bu, D., Wang, P., Jiang, J., ... & Li, X. (2024). GeneCompass: deciphering universal gene regulatory mechanisms with a knowledge-informed cross-species foundation model. Cell Research. Fang, C., Wang, Y., Song, Y., Long, Q., Lu, W., Chen, L., ... & Li, X. (2024). How do large language models understand genes and cells. ACM Transactions on Intelligent Systems and Technology. 李鑫, & 于汉超. (2024). 人工智能驱动的生命科学研究新范式. 中国科学院院刊 江海平, 高纯纯, 刘文豪, 杨运桂, & 李鑫. (2024). 数据驱动的生命科学研究进展. 中国科学院院刊. Zhang, Y., Donaher, J. L., Das, S., Li, X., Reinhardt, F., Krall, J. A., ... & Weinberg, R. A. (2022). Genome-wide CRISPR screen identifies PRC2 and KMT2D-COMPASS as regulators of distinct EMT trajectories that contribute differentially to metastasis. Nature cell biology. Li, X., Wang, J., Wang, L., Gao, Y., Feng, G., Li, G., ... & Zhang, K. (2022). Lipid metabolism dysfunction induced by age-dependent DNA methylation accelerates aging. Signal transduction and targeted therapy. Li, X., Wang, J., Wang, L., Feng, G., Li, G., Yu, M., ... & Zhang, K. (2020). RETRACTED: Impaired lipid metabolism by age-dependent DNA methylation alterations accelerates aging. Proceedings of the National Academy of Sciences. Xia, H., Li, X., Gao, W., Fu, X., Fang, R. H., Zhang, L., & Zhang, K. (2018). Tissue repair and regeneration with endogenous stem cells. Nature Reviews Materials. Zhang, Y., Zhang, X., Shi, J., Tuorto, F., Li, X., Liu, Y., ... & Chen, Q. (2018). Dnmt2 mediates intergenerational transmission of paternally acquired metabolic disorders through sperm small non-coding RNAs. Nature cell biology. Li, X., Cui, X. L., Wang, J. Q., Wang, Y. K., Li, Y. F., Wang, L. Y., ... & Zhou, Q. (2016). Generation and application of mouse-rat allodiploid embryonic stem cells. Cell. Wang, J., Li, X., Wang, L., Li, J., Zhao, Y., Bou, G., ... & Liu, Z. (2016). A novel long intergenic noncoding RNA indispensable for the cleavage of mouse two‐cell embryos. EMBO reports. Chen, Q., Yan, M., Cao, Z., Li, X., Zhang, Y., Shi, J., ... & Zhou, Q. (2016). Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder. Science. Li, X., Wang, J. Q., Wang, L. Y., Wan, H. F., Li, Y. F., Li, T. D., ... & Zhou, Q. (2015). Co-participation of paternal and maternal genomes before the blastocyst stage is not required for full-term development of mouse embryos. Journal of molecular cell biology. Wang, J., Li, X., Zhao, Y., Li, J., Zhou, Q., & 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. Shi, J., Chen, Q., Li, X., Zheng, X., Zhang, Y., Qiao, J., ... & Duan, E. (2015). Dynamic transcriptional symmetry-breaking in pre-implantation mammalian embryo development revealed by single-cell RNA-seq. Development. Li, W., Li, X., Li, T., Jiang, M. G., Wan, H., Luo, G. Z., ... & Zhou, Q. (2014). Genetic modification and screening in rat using haploid embryonic stem cells. Cell stem cell. Li, X., Xia, B. L., Li, W., & Zhou, Q. (2014). Assessing reprogramming by chimera formation and tetraploid complementation. In Nuclear Reprogramming: Methods and Protocols.