Research
Gene regulation is a classical and fundamental problem in biology. It explains how the same genetic code can give rise to diverse cellular phenotypes and how cells adapt to different external and internal perturbations. Conceptually, it can be viewed as a complex regulatory network in which thousands of molecular interactions jointly control cellular behavior. Historically, reconstructing gene regulatory network (GRN) is a classfical and challenging task in bioinformatics/computational filed. More recently, the emerging single-cell sequencing technologies are producing high-dimensional biological data, and deep learning approaches can be applied to model these data at the systems level and to GRNs. This transformation illustrates the shift of AI from a supporting tool to a core methodology for uncovering regulatory principles. .
One of the main directions of our research is the reconstruction of GRNs using single-cell sequencing data. Unlike conventional GRNs that use genes as nodes, we propose to develop deep-learning models for RNA-centric GRNs, which may provide deeper insights into gene regulation and offer more precise resources for RNA-based drug screen.
Biological processes involve interactions among multiple macromolecules to carry out specific cellular functions. For instance, antigen presentation is an essential process in immunology. Our research focuses on applying transformer-based deep learning models to model—and ultimately design—such essential biological processes by integrating multi-omics data, with the goal of facilitating the discovery of novel therapeutic targets.
With over a decade of research experience in RNA biology, we actively explore the potential of applying AI models to accurately predict RNA structures both in vivo and in vitro. In addition, we are developing methods to model interactions between small molecules and RNA, with the aim of facilitating RNA-based therapeutics.
Resources
The Human Phenotype Project is a landmark initiative, powered by Pheno.AI, that set out to deeply profile hundreds of thousands of participants from around the world, in an effort to unlock the information researchers need to improve human health.
The Emirati Genome Program is a significant national project that aims to draw a comprehensive genetic map for UAE citizens to accelerate the development of advanced preventive and personalised healthcare solutions for the nation’s present and future generations.