Shan Li, Ph.D.
Shan Li's research focuses on deciphering the encryption of the gene regulatory code in eukaryotes, and identify the linkage between regulatory element sequence variations and diseases, especially cancer.
1) computational biology, 2) gene regulation, 3) genomics, 4) machine learning, 5) cancer genomics
The vast landscape of the human genome hosts elements that orchestrate the dynamics of proteins in every human cell, establishes cell identity, and safeguards the defense mechanisms. These elements, known as gene regulatory elements, are encrypted in a different genomic language known as the second language of genomes. As this second language of genomes remains largely unknown, my research mainly focuses on developing novel artificial intelligence methods to understand the genomic encryption of gene regulatory elements and studying the evolution of the gene regulatory code in eukaryotes. Specifically, I'm interested in prioritizing the regulatory variants of non-coding genomic regions to identify the linkage between sequence variation of the regulatory elements and disease, and that between regulatory elements sequence variation and phenotypic divergence across species. In the context of cancer, I'm interested in developing mechanism-based models to identify functional, and potentially causative ‘driver’ regulatory mutations in cancer.
Selected Key Publications
Stable enhancers are active in development, and fragile enhancers are associated with evolutionary adaptation.Genome Biol. 20(1): 140, 2019. [ Journal Article ]
- Nucleic Acids Res. 45(5): 2307-2317, 2017. [ Journal Article ]
- Mol Biol Evol. 32(8): 2161-80, 2015. [ Journal Article ]
- Genomics. 112(3): 2261-2270, 2020. [ Journal Article ]
SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genome.Bioinformatics. 34(2): 289-291, 2018. [ Journal Article ]
Dr. Li received her B.S. in mathematics from Shandong University, China, and obtained a Ph.D from UNC Charlotte (mentor: Dr. Zhengchang Su). At UNC Charlotte, she studied gene regulation in bacteria at department of bioinformatics and genomics. After graduation, she joined Ivan Ovcharenko’s research group at NCBI as a research fellow. During her tenure at NCBI, her research focused on identifying causative regulatory variants in the human genome, and exploring the mechanism underlying the different densities of deactivating mutations in human enhancers. Dr Li joined Dr. Sridhar Hannenhalli’s research group at Cancer Data Science Laboratory at NCI in Aug, 2020. There she continued her research on deciphering the gene regulatory code in human and bridging the gap between genomic sequence and disease, especially in the context of cancer.