Hammad Farooq

The paper shows that transcription factor activity depends on sequence context and partner availability, leading to different cell fates in various cell types.

The paper develops a polymer simulation framework to distinguish specific-folding interactions from polymer compaction in E. coli, revealing SFIs shape chromosome organization and gene expression.

This study uses 3D polymer models to show that LAD-lamin interactions influence chromatin organization and induce super long-range chromatin contacts in mouse cells.

ChromPolymerDB reconstructs single-cell 3D chromatin structures from bulk Hi-C data and provides a database for analyzing chromatin conformation across 50 human cell types.

The paper develops a method to analyze Hi-C and eQTL data to understand how 3D chromatin structures influence gene regulation through non-random interactions and ensemble modeling.

The paper introduces an algorithm that uses 3D chromatin interactions to identify functional non-coding regulatory variants and their target genes, reducing false positives in eQTL analysis.