Bhavya Dhaka

The human RNA-DNA interactome is cell type-specific and dynamic

The paper maps RNA-DNA interactions in 16 human cell types, showing cell-type-specific and dynamic networks that correlate with gene regulation and disease traits.

Hepatobiliary Progenitor-like Reprogramming in Liver Metastases

This study identifies hepatobiliary progenitor-like reprogramming in liver metastases, driven by TGF-β and hypoxia, and shows its association with poor survival.

Pan-cancer discovery of driver mutations in long noncoding RNAs reveals widespread functional rewiring of RNA regulatory elements

The paper identifies 121 lncRNA driver mutations across 19 cancer types using 12,631 genomes, showing mutations disrupt RNA-binding protein interactions to promote oncogenesis.

HyperMap: An Efficient Framework for Transferring Perturbation Responses Across Diverse Biological Contexts

HyperMap transfers perturbation responses across biological contexts using a meta-learning framework, achieving accurate predictions with fewer parameters than typical models.

Functional identification of cis-regulatory long noncoding RNAs at controlled false-discovery rates

The paper introduces TransCistor, a framework to identify cis-regulatory lncRNAs with controlled false discovery rates, finding that only a minority of lncRNAs are cis-acting, primarily as activators.

Prognostic association of immunoproteasome expression in solid tumours is governed by the immediate immune environment

The paper examines the prognostic role of immunoproteasome expression in solid tumours, finding it correlates with immune infiltration and survival outcomes, but varies by tumour type and immune context.

Differential chromatin accessibility landscape of gain-of-function mutant p53 tumours

The paper identifies differentially accessible chromatin regions in mutant p53 tumours compared to wild-type p53 tumours in breast and colon cancers, revealing distinct transcription factor enrichments.