Federal Project Grant Award Summary

The National Institute of General Medical Sciences (NIGMS) awarded the University of Chicago $1.73 million under the Biomedical Research and Research Training program (CFDA 93.859) for a four-year project running from July 1, 2026, through June 30, 2030. The project, titled "Spatially-Informed AI to Dissect Complex Cell-State Transitions in Tissue Niches," will develop quantitative computational tools and inference methods that integrate spatial transcriptomics (ST) and single-cell RNA-sequencing (scRNA-seq) data to analyze transcriptional dynamics within specific tissue microenvironments.

The project deliverables include three primary research aims: (1) development of methods to learn spatially aware gene programs that function across both ST and scRNA-seq modalities; (2) inference of process-specific dynamics and construction of sample- or context-specific transition matrices to model cell-state transitions; and (3) transformation of these matrices into rigorous quantitative evidence including effect sizes, confidence intervals, and reproducible group contrasts. These tools will enable detection of early transcriptional changes in cell-state trajectories and their dependence on tissue location, with applications to identifying tissue-state biomarkers, understanding homeostatic and pathogenic cell transitions, and discovering therapeutic targets in basic and translational biology research.