Frank Westermann

LACHESIS infers evolutionary trajectories of malignant transformation from whole-genome sequencing data and provides risk stratification for childhood and adult cancers.

The paper identifies genomic and transcriptomic features of telomere maintenance mechanisms in complex karyotype sarcomas, linking ALT status to therapeutic vulnerabilities.

This study compares ex vivo short-term, organoid, and PDX drug screening methods in neuroblastoma, finding ex vivo screens are faster and more consistent with in vivo results.

The paper introduces a PDX platform for pediatric cancers, providing in vivo drug testing models and molecular data to aid in therapy development.

The paper uses single-cell technologies to show that large-scale chromosomal aberrations drive medulloblastoma initiation, while single-gene oncogenic events like MYC contribute to progression and therapy resistance.

Pyjacker detects enhancer hijacking in AML, identifying MNX1 activation via 7q deletion as a novel oncogenic mechanism.

This paper shows that high MYCN levels in neuroblastoma reduce L1CAM expression, limiting CAR T cell efficacy, and that inhibiting MYCN with MLN8237 restores L1CAM and enhances CAR T cell activity.

The paper evaluates deconvolution methods for bulk RNA-Seq using scnRNA-Seq data, identifies biases, and introduces SQUID, a method that outperforms others in predicting cell mixtures and identifying cancer subclones.

The paper identifies PCF11 as a critical regulator of alternative polyadenylation in neuroblastoma, linking it to cell fate reprogramming and spontaneous tumor regression.

Synlet is an R package that provides a complete pipeline for analyzing synthetic lethal RNAi screen data, including quality assessment, normalization, and hit selection methods.