Yingqian Ada Zhan

SMARCA4, STK11, and KEAP1 co-inactivation associates with poor prognosis and upregulation of the TGF-β pathway in lung adenocarcinoma

The paper identifies SMARCA4/STK11/KEAP1 triple mutant lung adenocarcinoma as a poor prognosis subset and links it to TGF-β pathway activation.

TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer

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.

Altered chromatin accessibility mediated by somatic cohesin mutations amplifies FLI1-Menin output to promote leukemogenesis

This study shows that cohesin mutations alter chromatin accessibility, enhancing FLI1-Menin interaction and promoting leukemogenesis through therapeutic vulnerabilities.

Genetic variation modulates susceptibility to aberrant DNA hypomethylation and imprint deregulation in naive pluripotent stem cells

The paper identifies genetic variants that influence DNA methylation stability and imprint deregulation in naive pluripotent stem cells across different mouse strains.

Aging limits stemness and tumorigenesis in the lung by reprogramming iron homeostasis

This study shows aging reduces lung stem cell function and suppresses lung cancer by inducing iron deficiency through the NUPR1-lipocalin-2 pathway.

ChromaFold predicts the 3D contact map from single-cell chromatin accessibility

ChromaFold predicts 3D chromatin contact maps from scATAC-seq data, outperforming bulk-based methods and enabling cell-type-specific interaction analysis.

HiC-DC+: systematic 3D interaction calls and differential analysis for Hi-C and HiChIP

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.