Sofia A. Quinodoz

This paper introduces Deep-Phase, a deep learning framework that classifies and quantifies drug-induced changes in condensate morphology from microscopy images, revealing insights into nucleolar structure and function.

This study identifies late-stage processing bottlenecks in ribosome biogenesis caused by oncogene activation, which impair ribosome production and limit tumor growth.

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

The paper maps rRNA processing dynamics in the nucleolus and shows how rRNA processing affects nucleolar phase organization and structure.

The paper introduces RNA-SPRITE to map RNA-RNA spatial proximity genome-wide, revealing conserved mRNA organization and colocalization driven by shared motifs and functional relationships.

The paper shows that gene proximity to nuclear speckles increases spliceosome binding and co-transcriptional splicing efficiency, highlighting the role of 3D genome organization in mRNA splicing.

The paper uses CRISPR to live image Alu elements in euchromatin, revealing non-uniform dynamics linked to transcriptional activity.

The paper develops RD-SPRITE to map RNA-DNA and RNA-RNA interactions in 3D nuclear structures, revealing RNA's role in forming compartments that regulate nuclear functions.

The paper introduces SPRITE, a method for detecting higher-order DNA interactions, and shows that nuclear bodies act as inter-chromosomal hubs shaping 3D genome organization.