Bauke Ylstra

The paper identifies DNA methylation changes during IDH-mutant glioma progression, links them to TET enzyme activity, and develops a methylation-based grading system that outperforms WHO grading.

The paper analyzes multi-omics data from IDH-mutant astrocytomas to identify molecular markers of malignant progression linked to cell cycling and DNA methylation changes.

This study tracks karyotype evolution in esophageal adenocarcinomas during chemoradiotherapy and recurrence, showing that treatment-induced copy number aberrations predict early recurrence and are partially reversed upon recurrence.

This study analyzes the epigenetic evolution of IDH1-mutant and IDH1-wildtype gliomas under treatment, showing IDHmut tumors undergo epigenomic changes resembling IDHwt tumors, with implications for treatment strategies.

The paper develops a computational framework to analyze spatial interactions in tumor microenvironments and shows that spatial context predicts survival in primary central nervous system lymphoma.

The paper compiles a comprehensive reference dataset of true somatic structural variations by analyzing melanoma and normal cell lines with multiple sequencing technologies and experimental validation.

This paper describes a CRISPR-Cas9 method to engineer arm-level chromosomal deletions in neuroblastoma cell lines to study their oncogenic role.

This study validates whole genome sequencing as a reliable single assay for detecting various cancer mutations with high sensitivity and precision.