Merve Şahin

The paper shows that TAD hierarchy restricts LTR activation, and its loss in cancer allows LTRs to act as alternative promoters, driving oncogene activation and transcriptional diversity.

This study identifies TET2-mutant clonal hematopoiesis in thyroid cancer microenvironments and shows that TGFβ signaling from these macrophages mediates resistance to BRAF/MEK inhibition, with TGFβ inhibition restoring sensitivity.

This paper introduces GraphReg, a deep learning model that uses graph attention networks to predict gene expression from epigenomic data and genomic sequences, outperforming existing methods in modeling gene regulation and identifying functional enhancers.

HiC-DC+ is a tool for Hi-C/HiChIP interaction calling and differential analysis, showing improved performance in HiChIP benchmarking and revealing 3D organization changes during cohesin perturbation and differentiation.

The paper defines a shared differentiation trajectory of CD8 T cell dysfunction across cancer and infection using ATAC-seq and RNA-seq data from multiple studies.