Biostatistics Dept. Seminar: Comparative Spatial Transcriptomics Analysis Identifies Evidence of Off-Target Probe Binding
Biostatistics Department Seminar
Title: Comparative Spatial Transcriptomics Analysis Identifies Evidence of Off-Target Probe Binding
Abstract: Recent advances in high-throughput spatial transcriptomics (ST) technologies now enable high-throughput molecular profiling of cells while maintaining their spatial organization within tissues. New statistical approaches and scalable computational tools are needed to connect these molecular states and spatial-contextual differences.
This talk will provide an overview of the latest ST technologies and computational analysis methods developed by my lab. Specifically, to facilitate spatial molecular comparisons across structurally matched tissue sections from replicates, case-control settings, and within and across technologies, we develop STalign to align ST datasets in a manner that accounts for partially matched tissue sections and other local non-linear distortions using diffeomorphic metric mapping. Likewise, to enhance the scalability of ST data analysis, we developed a rasterization preprocessing framework called SEraster that aggregates cellular information into spatial pixels. Finally, I will provide an example of how we applied these two tools to compare spatial gene expression profiles for two different ST technologies to identify evidence of off-target probe binding. Overall, we anticipate that such computational methods for analyzing ST data will offer the potential to contribute to important biological insights regarding spatial molecular changes across comparative axes of interest.
Speakers
Jean Fan is an associate professor of Biomedical Engineering in the Center for Computational Biology at Johns Hopkins University. Her research team, the JEFworks lab, is interested in understanding the molecular and spatial-contextual factors shaping cellular identity and heterogeneity.
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2025-2026 Monday Seminar Series
All seminars are held at 12:05 PM via Zoom and onsite. View all seminar information here.