RT Journal
A1 Song, Xiaoyu
A1 Shang, Yuqing
A1 Ehrlich, Michelle E.
A1 Roussos, Panos
A1 Yuan, Guo-Cheng
A1 Wang, Pei
T1 QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data
JF Genome Research 
JO Genome Research 
YR 2025 
FD August 01 
VO 35 
IS 8 
SP 1821 
OP 1831 
DO 10.1101/gr.279859.124 
UL http://genome.cshlp.org/content/35/8/1821.abstract 
AB Recent advances in spatially resolved transcriptomics (SRT) have provided valuable avenues for identifying cell–cell interactions and their critical roles in diseases. Here, we introduce QuadST, a novel statistical method for the robust and powerful identification of cell–cell interactions and their impacted genes in single-cell SRT. QuadST models interactions at different cell–cell distance quantile levels and innovatively contrasts signals to identify interaction-changed genes, which exhibit stronger signals at shorter distances. Unlike other methods, QuadST does not require the specification of interacting cell pairs. It is also robust against unmeasured confounding factors and measurement errors of the data. Simulation studies demonstrate that QuadST effectively controls the type I error, even in misspecified settings, and significantly improves power over existing methods. Applications of QuadST to real data sets reveal biologically significant interaction-changed genes across various cell types.