Clarice KY Hong

The paper identifies 'matchmaker' cis-regulatory elements in erythropoiesis that strengthen loops between neighboring elements and are linked to gene expression and cohesin loading.

The paper introduces Cleopatra, a deep learning model that predicts high-resolution 3D genome maps across human cell types, revealing cell-type-specific loops and gene regulation patterns.

The paper develops MPIRE to assess insulator activity across the genome, finding that insulators function in specific genomic contexts and depend on transcription factor binding.

The paper introduces scMPRA, a single-cell assay to measure cis-regulatory activity across cell types, showing it detects cell-type specific effects of genetic variants in retinas.

The paper introduces SARGENT, a method to measure gene expression noise and mean expression across the genome, finding correlations between noise and histone modifications, and linking extrinsic noise to cell sub-states.

The paper measures core promoter activities across different genomic locations and finds that their intrinsic strengths are preserved, supporting the classical model of gene regulation.

The paper uses MPRA libraries to analyze cis-regulatory grammar in mouse ESCs, finding that synthetic and genomic elements share binding site quality as a key factor, but genomic activity is better explained by binding site affinity and spacing.