Abdullah Ozer

The paper investigates enhancer-promoter interactions in a native chromatin context, revealing transcription factor synergy and the role of facilitators and repressive promoters in regulating gene activation.

This paper introduces DeepDETAILS, a method to reconstruct cell-type-specific genomic signals from bulk data, outperforming traditional methods and providing insights into disease mechanisms.

This study evaluates multiple MPRA and STARR-seq datasets to identify enhancers, finding inconsistencies due to technical factors and proposing a unified pipeline to improve cross-assay agreement.

The paper introduces PReCIS-seq, a nascent RNA assay, to study lineage-specific Pol II activity in mouse skin, revealing mechanisms of gene regulation in adult homeostasis.

The paper identifies human RNA Polymerase II interactors at early transcription stages using biochemical purification and mass spectrometry, revealing new factors involved in PIC assembly and promoter-proximal pausing.

The paper develops a dual reporter assay to measure promoter and enhancer potential, finding that they share regulatory logic and can function reciprocally.

Femto-seq enables targeted DNA sequencing from specific nuclear regions in individual cells using nanoscale photobiotinylation and sequencing.

The paper compares RNA sequencing assays and introduces a tool to identify active enhancers, compiling a compendium of enhancer candidates across 120 cell types.

The paper identifies fundamental enhancer units defined by transcription start sites and shows adjacent units operate non-cooperatively.

This study shows that chromatin conformation remains stable during heat shock-induced transcriptional changes in human and Drosophila cells.