Shu Zhang

The paper shows ecDNA localizes to the nuclear periphery in cancer, resisting silencing and enhancing transcriptional output through interactions with the nuclear lamina.

This study shows ecDNA copy number plasticity drives tumour evolution by generating functional heterogeneity and promoting drug resistance.

The paper introduces ec3D, a method to reconstruct 3D structures of ecDNA from Hi-C data, revealing spherical configurations and unique long-range interactions in cancer.

The paper introduces interSeg, a deep learning tool that accurately predicts oncogene amplification status from interphase FISH images, achieving high accuracy in detecting ecDNA and chromosomal amplifications.

This study shows that ecDNA mis-segregation leads to micronuclei formation, reduced oncogene transcription, and improved patient survival in neuroblastoma.

The paper shows that ecDNA-borne PVT1 fusions stabilize oncogenic mRNAs by interacting with SRSF1, enhancing RNA stability and supporting MYC dependency in cancer.

This paper identifies transcription-replication conflict as a vulnerability in ecDNA-containing cancers and demonstrates that CHK1 inhibition selectively kills these tumors.

This paper presents chromosome-scale genome assemblies and regulatory element annotations for planarians, revealing conservation of regulatory regions despite rapid structural divergence.

The paper investigates how 3D genome organization, specifically through Cohesin, influences gene co-expression in single cells and reveals its role in maintaining long-range chromatin interactions.

CoRAL improves ecDNA structure reconstruction using long-read sequencing, outperforming short-read methods in simulations and cell-line datasets.

The paper investigates the role of RNAPII in chromatin loop formation and shows that enhancer-promoter contacts are selectively lost upon RNAPII depletion, repressing gene expression.

The paper shows RNA polymerase II is necessary for spatial chromatin reorganization after mitosis, as demonstrated by Hi-C and in silico modeling.