Tom L. Kaufmann

This study uses single-cell and spatial multi-omics to analyze a malignant peripheral nerve sheath tumor, revealing chromosomal instability drives phenotypic diversity and spatial-temporal evolution.

PhytClust partitions rooted phylogenetic trees into monophyletic clusters without user-defined thresholds, achieving optimal and reproducible results across diverse biological datasets.

This paper introduces SPICE, a framework to infer copy-number events and model selection in cancer genomes, revealing 460 loci under selection and expanding the known cancer-related loci.

The paper analyzes paired breast carcinomas to determine if recurrences are clonal or new tumors, finding 7% are non-clonal by whole exome sequencing.

This study shows that ongoing whole-genome doubling in ovarian cancer promotes cell diversity and immune dysregulation through chromosomal instability and quiescent states.

The paper identifies gene dosage effects on telomere maintenance and disease pathways in neuroblastoma using genomic and transcriptomic data from 115 tumors.

Refphase uses multi-sample reference phasing to infer haplotype-specific copy numbers and reveal intra-tumour heterogeneity in cancer samples.

SMITH simulates cancer evolution with spatial constraints, showing that confinement mechanisms can reproduce clonal dynamics efficiently.

MEDICC2 infers cancer phylogenies from copy-number data, accounting for whole-genome doubling and parallel evolution, and performs well on simulated and real datasets.