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Professor Kevin Tsia of the Department of Electrical and Electronic Engineering and his team worked on the research for the topic “StaVia: spatially and temporally aware cartography with higher-order random walks for cell atlases”. The research findings were recently published in Genome Biology on August 16, 2024
Details of the publication:
StaVia: spatially and temporally aware cartography with higher-order random walks for cell atlases
Shobana V. Stassen, Minato Kobashi, Edmund Y. Lam, Yuanhua Huang, Joshua W. K. Ho & Kevin K. Tsia
Article in Genome Biology,
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03347-y
Abstract
Single-cell atlases pose daunting computational challenges pertaining to the integration of spatial and temporal information and the visualization of trajectories across large atlases. We introduce StaVia, a computational framework that synergizes multi-faceted single-cell data with higher-order random walks that leverage the memory of cells’ past states, fused with a cartographic Atlas View that offers intuitive graph visualization. This spatially aware cartography captures relationships between cell populations based on their spatial location as well as their gene expression and developmental stage. We demonstrate this using zebrafish gastrulation data, underscoring its potential to dissect complex biological landscapes in both spatial and temporal contexts.