Jonathan Karin

CRISP identifies and localizes interactions between biological signals in single-cell and spatial transcriptomic data, revealing their effects on tissue function and gene regulation.

The paper shows that dermal-epidermal junction geometry influences stem cell fate in mouse skin, with concave areas promoting proliferation and convex areas promoting differentiation.

CO_SCPLOWASEIC_SCPLOW identifies condition-specific cell-cell interactions in spatial omics data by modeling edges rather than cells, revealing spatial reorganization in disease states.

This paper introduces Annotatability, a method that uses deep network training dynamics to identify and correct ambiguous cell annotations in single-cell and spatial omics data.

scPrisma decouples and enhances periodic and linear biological signals in single-cell data using spectral template matching, demonstrating effectiveness across multiple biological systems.