Jake June-Koo Lee

The paper analyzes the evolutionary trajectories of high-level copy-number amplifications in cancer cell genomes to distinguish between extrachromosomal and intrachromosomal amplification mechanisms.

This study tracks clonal evolution of drug resistance in ovarian cancer using structural variants in cfDNA, finding polyclonal resistance with dominant high-fitness clones and genomic features linked to drug resistance.

The paper develops Mosaic, a machine learning system that classifies tumors into detailed subtypes and identifies molecular phenotypes using histopathologic and genomic data from a large patient cohort.

This study identifies MAPK activation and cellular plasticity as complementary resistance mechanisms to EGFR TKI in lung adenocarcinoma using single-nuclei RNA sequencing and clinical data.

The paper identifies mutational signatures SBS26 and SBS54 in MMRD tumors that correlate with immune checkpoint blockade response and survival, suggesting their use as prognostic biomarkers.

The paper analyzes whole-genome sequencing data from cancer samples to identify genomic footprints of telomere maintenance mechanisms, finding specific telomere variant repeat patterns associated with ATRX/DAXX mutations.

The paper examines how somatic structural variations affect TAD boundaries and gene regulation in human cancers using whole genome sequencing data.

This study analyzes chromothripsis in 2,658 cancers using whole-genome sequencing, finding it prevalent across multiple cancer types with complex structural alterations.