Florian M. Markowetz

scUnique measures ongoing chromosomal instability from single-cell whole genome sequencing data by identifying recent copy number aberrations in phylogenetic trees.

This paper identifies a chromosomal instability (CIN) biomarker that predicts response to PORCN inhibitors in cancers, validated through in vitro models, cell lines, and patient data.

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.

This paper introduces a Dirichlet-multinomial mixed model to analyze differential abundance of mutational signatures across clonal and subclonal mutations in cancer, finding significant differences in mutational processes between these groups.

The paper identifies pan-cancer evolutionary signatures linked to clonal expansion and immune microenvironment changes using TCGA data.

scAbsolute measures single-cell ploidy and replication status using single-cell DNA sequencing without prior knowledge of cell cycle phase.

The paper identifies persistent smoking-related immune alterations in airway tissues and links them to genetic risk factors and lung cancer risk using transcriptomic data and GWAS integration.

The paper evaluates tools for estimating absolute copy numbers from shallow whole genome sequencing data and introduces an improved tool called Rascal.

FrenchFISH improves DNA copy number quantification from FISH images by using Poisson models, outperforming manual and automated methods in ovarian cancer tissue sections.

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 quantifies low perfusion compartments in glioblastoma using MRI and correlates them with patient survival outcomes.

Ccube estimates cancer cell fractions and subclonal composition from whole-genome sequencing data using a probabilistic framework and variational inference.

This study uses joint histogram analysis of diffusion tensor imaging to identify tumor infiltration patterns in glioblastoma and their prognostic significance.

The paper introduces a novel normalization strategy for ChIP-seq to measure absolute fold-change in ER binding, validated using fulvestrant treatment and other experimental conditions.

This paper integrates multi-parametric and multi-regional MRI histogram features to identify patient subgroups with distinct survival outcomes in glioblastoma.

This study performs a meta-analysis of PDAC gene expression data to identify immunologic transcriptional subtypes with prognostic significance.

This paper introduces a method for allele-specific copy number segmentation across multiple samples, enabling the identification of shared and private segment boundaries for phylogenetic analysis.

This study uses causal modeling to identify directed interactions between cancer cells and the tumor microenvironment in breast cancer, proposing 11 novel genomic drivers of T cell phenotypes.