Personal Introduction

Dr. Lingjie Li is a Principle Investigator of the Department of Histoembryology, Genetics, and Developmental Biology at Shanghai Jiao Tong University School of Medicine. He received his B.Sc. degree in Biotechnology from the Northwest University in China and a Ph.D. in Developmental Biology from the Chinese Academy of Science. In 2010, he became a Postdoctoral Fellow and then a Research Associate at Stanford University School of Medicine, where he worked in epigenomics and stem cell regenerative medicine. In late 2019, Dr. Li accepted the faculty position at Shanghai Jiao Tong University and started his independent research laboratory in 2020.  His lab has been studying the epigenetic regulation in stem cell, development, and disease.

Scientific Research Projects

• Epigenomic regulation of epithelial tissue development

• Mechanism of early ectodermal differentiation and development

• Skin tissue homeostasis and related disease

• Stem cell-based regenerative medicine

Publications

Selected publications as corresponding or first authors：

1. Wang Z, Yang C, Ma Z, He X, Li L, Wang Y, Wang Y, Cai X, Jiao H, Zhang M, Tong R, Zhang F, Li L. YAP-TEAD regulates the super-enhancer network to control early surface ectoderm commitment. Nucleic Acids Res. 2026;54(1):gkaf1285. doi: 10.1093/nar/gkaf1285.

2. Li L, He X, Zhang F, Cai X, Zhang Q, Yang T, Tong R, Li S, Ding X, Dong Y, Zhou J, Li L. Single-cell ATAC-seq analysis of human embryoid bodies reveals crucial transcription factor networks involved in early germ layer specification. Cell Biosci. 2026. Epub ahead of print. doi: 10.1186/s13578-026-01561-8. PMID: 41906160.

3. Zhang F, Jiao H, Wang Y, Yang C, Li L, Wang Z, Tong R, Zhou J, Shen J, Li L. InferLoop: leveraging single-cell chromatin accessibility for the signal of chromatin loop. Brief Bioinform. 2023;24(3):bbad166. doi: 10.1093/bib/bbad166.

4. Zhang F, Yang C, Wang Y, Jiao H, Wang Z, Shen J, Li L. FitDevo: accurate inference of single-cell developmental potential using sample-specific gene weight. Brief Bioinform. 2022;23(5):bbac293. doi: 10.1093/bib/bbac293.

5. Ma Q, Yang L, Tolentino K, Wang G, Zhao Y, Litzenburger UM, Shi Q, Zhu L, Yang C, Jiao H, Zhang F, Li R, Tsai MC, Chen JA, Lai I, Zeng H, Li L, Chang HY. Inducible lncRNA transgenic mice reveal continual role of HOTAIR in promoting breast cancer metastasis. eLife. 2022;11:e79126. doi: 10.7554/eLife.79126.

6. Wang Y, Shen Z, Li L, Shen J. DNA damage-induced nuclear STING translocation orchestrates innate immune activation and chromatin remodeling. Genes Dis. 2025;13(3):101851. doi: 10.1016/j.gendis.2025.101851. PMID: 41584859; PMCID: PMC12830200.

7. Gan C, Wu Q, Goronzy JJ, Zhang Y, Li L, Sheng H, Fang F. SNP rs10748643 determines CD39 expression in T and NK cells through altering NFIC binding affinity rather than interfering with RNA splicing. Front Immunol. 2025;16:1679064. doi: 10.3389/fimmu.2025.1679064.

8. Xia M, Zhang F, Ma J, Li Y, Jia G, Wu M, Lou Y, Liu Y, Li L, Li H, Li W. Single-nucleus profiling of mouse inner ear aging uncovers cell type heterogeneity and hair cell subtype-specific age-related signatures. Cell Rep. 2025;44(6):115781. doi: 10.1016/j.celrep.2025.115781. PMID: 40440168.

9. Wang Y, Ding X, Zhang F, Xie X, Yang C, Wang Z, Cai X, Li Q, Li L, Chen X, Dai F, Zhang S. Ultrasmall Cu₂I₂ nanoclusters trigger metabolic-epigenetic reprogramming and endogenous antioxidant systems for alleviating osteoarthritis. Chem Eng J. 2024;154568.

10. Lan L, Zhang X, Yang S, Li L, Mao X. Chromosome-level genome assembly of the Stoliczka's Asian trident bat (Aselliscus stoliczkanus). Sci Data. 2023;10(1):902. doi: 10.1038/s41597-023-02838-0.

11. Li L, Wang Y, Torkelson JL, Shankar G, Pattison J, Zhen H, Duren Z, Fang F, Melo S, Piekos S, Li J, Liaw E, Chen L, Li R, Wernig M, Wong WH, Chang HY, Oro AE. TFAP2C- and p63-dependent networks sequentially rearrange chromatin landscapes to drive human epidermal lineage commitment. Cell Stem Cell. 2019;24:271-284.

12. Li L, Chang HY. Physiological roles of long noncoding RNAs: insight from knockout mice. Trends Cell Biol. 2014;24(10):594-602.

13. Li L, Liu B, Wapinski OL, Tsai MC, Qu K, Zhang J, Carlson JC, Lin M, Fang F, Gupta RA, Helms JA, Chang HY. Targeted disruption of Hotair leads to homeotic transformation and gene derepression. Cell Rep. 2013;5(1):3-12.

14. Li L, Sun L, Gao F, Jiang J, Yang Y, Li C, Gu J, Wei Z, Yang A, Lu R, Ma Y, Tang F, Kwon SW, Zhao Y, Li J, Jin Y. Stk40 links the pluripotency factor Oct4 to the Erk/MAPK pathway and controls extraembryonic endoderm differentiation. PNAS. 2010;107(4):1402-1407.

Scientific Research Projects

• Epigenomic regulation of epithelial tissue development

• Mechanism of early ectodermal differentiation and development

• Skin tissue homeostasis and related disease

• Stem cell-based regenerative medicine

Publications

1.Computer Software Copyright:

Software for Predicting Cell Type-Specific 3D Chromatin Structure V1.0.

Feng Zhang, Lingjie Li

Reg. No.: 2023SR1619582; Cert. No.:12206755;

2. Computer Software Copyright:

Software for Predicting Single-Cell Developmental Potential Based on Sample Specific Gene Weights V1.0.

Feng Zhang, Lingjie Li

Reg. No.: 2022SR1050795; Cert. No.:10004994;
 
 
 

Lab Members: