Peter Halmos will present his General Exam "DeST-OT: Alignment of Spatiotemporal Transcriptomics Data" on Friday, May 17, 2024 at 3:00 PN in CS 301 and via zoom.

Zoom link: https://princeton.zoom.us/s/5942235413

Committee Members: Ben Raphael (advisor), Ellen Zhong, Olga Troyanskaya

Abstract:

Spatially resolved transcriptomics (SRT) measures mRNA transcripts at thousands of locations within a tissue slice, revealing spatial variations in gene expression and distribution of cell types. In recent studies, SRT has been applied to tissue slices from multiple timepoints during the development of an organism. Alignment of this spatiotemporal transcriptomics data can provide insights into the gene expression programs governing the growth and differentiation of cells over space and time. We introduce DeST-OT (Developmental SpatioTemporal Optimal Transport), a method to align SRT slices from pairs of developmental time points using the framework of optimal transport (OT). DeST-OT uses semi-relaxed optimal transport to precisely model cellular growth, death, and differentiation processes that are not well-modeled by existing alignment methods. We demonstrate the advantage of DeST-OT on simulated slices. We further introduce two metrics to quantify the plausibility of a spatiotemporal alignment: a growth distortion metric which quantifies the discrepancy between the inferred and the true cell type growth rates, and a migration metric which quantifies the distance traveled between ancestor and descendant cells. DeST-OT outperforms existing methods on these metrics in the alignment of spatiotemporal transcriptomics data from the development of mouse kidney and axolotl brain.  Moreover, DeST-OT shows better correlation with the expression of annotated proliferation and apoptosis genes.

Reading List:

https://docs.google.com/document/d/1vYk8ZLMaOgIiMaQpQSIBh-z0KIotPOcMa6p8Nh2CZvY/edit

Everyone is invited to attend the talk, and those faculty wishing to remain for the oral exam following are welcome to do so.