Yingjie Zhu

The paper identifies MDF, a repair scar linked to POLQ-driven error-prone repair, as a marker of immune-responsive HRD pancreatic cancer with increased neoantigens and favorable clinical outcomes.

This study identifies APOBEC3 mutagenesis as a common driver of therapy resistance in breast cancer, associated with poorer clinical outcomes.

This study demonstrates that RNA transcripts can serve as templates for double-strand break repair in human cells, identifying DNA polymerase-zeta as a key enzyme and revealing genomic scars associated with this process.

The paper introduces iSeq, a tool for analyzing DSB-sequencing data, enabling identification and annotation of DSB-enriched regions across various resolutions.

The paper modifies Direct Coupling Analysis to predict interaction domains in large protein complexes, validated on known and unknown complexes.

qDSB-Seq quantifies absolute DNA double-strand break frequencies and their genomic coordinates across samples and organisms.