Bioinformatics Seminar
Time: 11AM
Venue: Davis Auditorium and Online
1 September 2026
This is a WEHI only event.Computational methods for spatial transcriptomics and their application to bone marrow plasma niches
Quoc Hoang NguyenWEHI
Spatial transcriptomics (ST) enables the study of gene expression in its spatial context and is rapidly being adopted. As ST datasets grow larger, span multiple samples, and are applied to increasingly complex tissues, robust and scalable methods are needed. To support this, our lab has been developing scider, a bioinformatics approach for cell type density-based spatial region analysis. In this work, I will present the scider workflow, my contributions towards making it an end-to-end analysis pipeline, and the underlying hexagonal kernel density estimation algorithm that I’ve developed. I will also describe an issue with permutation test implementations that I found in several popular statistical packages. This issue is widespread, can cause substantial statistical errors, but is straightforward to fix. Finally, I will report on my current analysis of a collaborative ST study investigating what environmental factors allow plasma cells to survive indefinitely in the bone marrow.