URAP

Peng He - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: Off Campus

This project focuses on applying and benchmarking state-of-the-art machine learning models—including foundation models like GeneFormer and SCimilarity—for automated cell type annotation using single-cell and spatial genomics data. The goal is to overcome the bottleneck of manual cell type labeling in large-scale datasets by...

Peng He - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

This project centers on the use of human lung organoids—three-dimensional miniature tissue models derived from stem cells—to study how stem cells make fate decisions. In particular, it investigates how stem cells commit to the neuroendocrine lineage, a process with direct relevance to understanding the development of neuroendocrine...

Peng He - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: Off Campus

This project investigates how cells behave and interact in their native environments by analyzing spatial gene expression data. Interns will use Visium and Xenium spatial transcriptomics datasets to identify tissue microenvironments, reconstruct 3D spatial maps, and apply computational tools like NicheFormer...

Peng He - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: On Campus

This project focuses on building robust and reusable computational pipelines to analyze bulk and single-cell transcriptomics data. Students will contribute to bioinformatics workflows for data processing, integration, and visualization across various tissues and disease contexts, including fibrosis and vascular diseases...