F. Markowetz

A Dirichlet-multinomial mixed model for determining differential abundance of mutational signatures

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.

Predicting response to cytotoxic chemotherapy

This study develops three precision biomarkers based on chromosomal instability signatures to predict response to different chemotherapies, showing improved progression-free survival in clinical trials.

In Breast Cancer ZMIZ1 Co-Regulates E2F2 as Part of the Estrogen Receptor-Mediated Cell-Cycle Response

This study identifies ZMIZ1 as a co-regulator of E2F2 in the estrogen receptor-mediated cell-cycle response in breast cancer, showing its role in tumor proliferation and patient prognosis.

High-grade serous ovarian carcinoma organoids as models of chromosomal instability

This study develops HGSOC patient-derived organoids to model chromosomal instability and its mutational processes, showing they represent different causes of instability and can be used for drug sensitivity testing.

The genomic landscape of early stage ovarian high grade serous carcinoma

This study compares genomic features of early and late stage high grade serous ovarian carcinoma, finding no unique mutations or focal copy number alterations but noting differences in ploidy and copy number signatures.

Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes

This study characterizes intra-tumor heterogeneity across 2,658 human cancer genomes, identifying subclonal mutations and evolutionary patterns across 38 cancer types.

3D-printed moulds for image-guided surgical biopsies: an open source computational platform

This paper develops an open-source computational platform to create 3D-printed moulds for image-guided surgical biopsies, achieving accurate co-registration of imaging and tissue samples.

SVclone: inferring structural variant cancer cell fraction

SVclone infers cancer cell fractions of structural variant breakpoints from whole-genome sequencing data and identifies subclonal copy-number neutral rearrangements linked to decreased survival in certain cancers.

VULCAN integrates ChIP-seq with patient-derived co expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer

The evolutionary history of 2,658 cancers

This study uses whole-genome sequencing of cancer samples to reconstruct the evolutionary history of 39 cancer types, identifying early and late-stage mutational patterns and driver genes.

Genome-wide Estrogen Receptor-alpha activation is sustained, not cyclical

This study shows that estrogen receptor-alpha binding is sustained, not cyclical, using genome-wide analysis with multiple replicates and a new method.

Neutral tumor evolution?

The paper explores tumor evolution through subclonal analysis and discusses the role of driver and passenger mutations in cancer progression.

Intra-tumor heterogeneity defines treatment-resistant HER2+ breast tumors

This study examines how intra-tumor heterogeneity in HER2 expression and copy number affects treatment outcomes in HER2+ breast cancer patients.

The small molecule KHS101 induces bioenergetic dysfunction in glioblastoma cells through inhibition of mitochondrial HSPD1

The paper shows KHS101 inhibits HSPD1 in glioblastoma cells, causing metabolic dysfunction and tumor growth reduction without affecting normal cells.

Copy-number signatures and mutational processes in ovarian carcinoma

This study identifies copy-number signatures in ovarian cancer and links them to mutational processes, showing that most cases involve multiple processes, suggesting therapeutic challenges.

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

BaalChIP corrects allele-specific ChIP-seq analysis for copy number variation in cancer genomes, improving detection of regulatory variants.