Joachim Weischenfeldt

The paper establishes a multi-omic PDX resource linking GBM invasion phenotypes to molecular programs and therapeutic responses, identifying two invasion modes and a neurodevelopmental factor associated with tumor growth and survival.

QuickSeg improves copy number segmentation accuracy and efficiency using dynamic programming and median-based error function in cancer whole-genome sequencing data.

The paper identifies helicases as frequently mutated enzyme families in cancer, showing their role in genomic instability and DNA repair defects, with AQR as a novel hemizygous tumor suppressor.

This study identifies rare germline variants associated with metastatic prostate cancer using an extreme phenotype cohort and validates their functional impact.

This study investigates how 3D chromatin architecture influences and is influenced by somatic structural variants in cancer, showing an interplay between chromatin structure and SV formation.

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.

The paper analyzes somatic retrotransposition events in 2,954 cancer genomes, identifying L1 insertions as significant contributors to structural variations and oncogenesis.

SvABA detects structural variants and indels using genome-wide local assembly, showing improved sensitivity and specificity, especially for small variants and complex rearrangements in cancer genomes.

This paper identifies driver mutations across 2,500 tumors from 37 cancer types, revealing a whole-genome panorama of genomic events that underlie tumor development.

The paper analyzes somatic rearrangements in cancer genomes using whole-genome sequencing data, identifying recurrent breakpoints and their genomic features.

The paper identifies nine structural variation signatures in cancer genomes, revealing patterns of deletions, tandem duplications, and translocations linked to replication mechanisms and oncogenic activation.

The paper describes the PCAWG project's large-scale analysis of cancer whole genomes across multiple computing environments, producing validated consensus variants for downstream research.