Our Research

We study the spatial organization of the genome within the Department of Genetics and Epigenetics Institute at the University of Pennsylvania School of Medicine.

We use a combination of cellular, molecular, genetic, and computational tools to elucidate how the structure and position of chromosomes within the nucleus is established and inherited across cell divisions, and how dysfunctional organization contributes to genome instability and disease. We also develop and utilize new technologies that use fluorescent in situ hybridization (FISH) to interrogate chromosome structure at single-cell resolution. These include a new type of probe, called Oligopaints, which reduces the cost and increases the resolution of FISH and our recently developed pipeline for high-throughput DNA or RNA labeling with Oligopaints (HiDRO).

Chromosome Folding

Understanding how the genome becomes spatially organized and folded inside the nucleus is central to understanding how chromosomes function in normal development and in disease. Recent advances have shown that nuclear organization is driven by a complex collection of chromosome interactions at different genomic scales,

Disorders of chromatin looping

Cohesin plays a key role in regulating gene expression by forming DNA loops that connect genes to distal enhancers. Mutations in the structural and regulatory components of the cohesin complex lead to complex developmental disorders and cancers and are associated with chromatin misfolding and widespread gene misexpression.

High-throughput FISH

Although chromosome interactions are a fundamental aspect of nuclear organization little is known about how they are established, regulated, and inherited across cell divisions. To address this gap, we developed a fully automated imaging pipeline, called HiDRO (high-throughput DNA or RNA labeling with optimized Oligopaints).