The Ye lab is focused on harnessing the power of single-cell and computational genomics to understand how immune cells sense and respond to their environment. Utilizing new experimental methods we have developed to enable multiplexed single-cell sequencing, I will describe results from sequencing 1.2M cells from ~250 samples to understand the cellular and molecular bases of systemic lupus erythematosus and COVID-19. I will also describe how population-scale single-cell sequencing can enable dissection of the genetic architecture of gene expression and annotation of disease-associated variants. Finally, I’ll touch on novel experimental workflows to further increase the throughput of single-cell genomics and for encoding orthogonal information into single-cell sequencing assays.
The Ye lab is interested in how the interaction between genetics and the environment affects human variation at the level of molecular phenotypes. To study these interactions, the lab couples high-throughput sequencing approaches that measure cellular response under environmental challenges with population genetics where such measurements are collected and analyzed across large patient cohorts. The lab develops novel experimental approaches that enable the large-scale collection of functional genomic data en masse and computational approaches that translate the data into novel biological insights. This approach is used to initially study primary human immune cells in both healthy and diseased patients to understand host-pathogen interactions and its role in autoimmunity.