Modeling chemically induced perturbation of spatiotemporal gene expression in the mammalian liver
Abstract: Single cell RNA-sequencing allows us to study the heterogeneity of cellular response to chemical perturbations. However, experimentally testing all relevant combinations of cell types, chemicals, and doses for regulatory purposes is a daunting task. We have developed scVIDR, a deep generative learning-based tool to predict single-cell gene expression perturbations induced by chemical pollutants and drugs. scVIDR is able to accurately predict dose-dependent gene expression changes across cell types in mouse liver, human blood cells, and cancer cell lines. I will also present our work on quantitative analysis of perturbations in spatiotemporal gene expression patterns in the mammalian liver induced under exposure to environmental pollutants and during liver disease.
Biography: Dr. Sudin Bhattacharya is an Associate Professor in the Departments of Biomedical Engineering and Pharmacology & Toxicology, as well as the Institute for Quantitative Health Science and Engineering, at Michigan State University. He leads a lab conducting research at the interface of computation and biology, studying the gene regulatory networks that underline cell fate choice and its perturbation by environmental pollutants. His current work focuses on single-cell and spatial transcriptomics analysis in the context of cell fate choice and tissue architecture. Dr. Bhattacharya earned his undergraduate degree at Jadavpur University, India; his master’s degree at the University of Kentucky; and his Ph.D. at the University of Michigan.