Bioinformatics Seminar
Time: 11AM
Venue: Davis Auditorium and Online
25 February 2025
This is a WEHI only event.Advancing Spatial Transcriptomics: Platform Benchmarking & Cell-Cell Communication Analysis
Lei QinWEHI Bioinformatics/ACRF CBSC
Spatial transcriptomics (ST) enables in situ gene expression profiling, overcoming the limitations of sc/snRNA-seq by preserving spatial context. Various ST technologies have been emerging and can be broadly categorized into imaging-based (iST) and sequencing-based (sST) methods. iST platforms like MERSCOPE and Xenium detect mRNA molecules with single-molecule resolution but are limited to targeted gene panels, whereas sST platforms like Visium capture whole transcriptomes at multi-cell resolution. Despite their potential, ST technologies differ in resolution, throughput, and applicability, posing challenges for experimental design and analysis. A key application of ST is improving cell-cell communication (CCC) analysis, which is critical for studying processes like tumor microenvironments and immune interactions. However, most CCC methods are adapted from scRNA-seq and fail to account for spatial proximity. Existing ST-based approaches are often simplistic or designed for sST data. My research focuses on i) benchmarking commonly used ST platforms, and ii) developing robust computational methods to study CCC in both iST and sST data more effectively.