Projects

Our research aims to uncover the role of the epigenome in cancer development. 

Nearly all cancer types exhibit a global shift in DNA methylation, characterized by hypermethylation of specific promoters and a widespread decrease in DNA methylation levels. We are exploring whether these changes are a cause, consequence, or even a prerequisite of malignant transformation. 

Using advanced sequencing technologies, such as single-cell DNA methylation and long-read sequencing, we investigate the molecular mechanisms underlying cancer, with a focus on how DNA methylation and other epigenetic modifications differentiate in cancer.

During embryonic development, proliferating cells are directed toward specific fates through the coordinated action of cell type-specific transcription factors and widespread epigenetic machinery. 

While the molecular functions of these regulators are generally well understood, their direct roles in development are often obscured by complex mutant phenotypes that arise post-gastrulation. In collaboration with groups at the Max Planck Institute for Molecular Genetics, we employ advanced techniques such as combined zygotic perturbation and single-cell RNA sequencing to analyze multiple mutant mouse embryos simultaneously. 

This approach allows us to investigate the morphological and transcriptional data, providing insights into the precise roles of these regulators over time and space.

While we are interested in utilizing genomic data to gain biological insights, a key part of our work is focused on method development for DNA methylation processing and analysis to handle and interpret complex methylation data. 

We are developing robust algorithms to detect differentially methylated regions (metilene), capture and quantify DNA methylation stochasticity (RLM), and process Nanopore data. Additionally, we are improving real-time sequencing approaches, such as using Nanopore sequencing for live tumor classification (MethyLYZR). 

Through these innovations, we aim to provide more precise and actionable insights into the role of DNA methylation in health and disease.

In collaboration with Franz-Josef Müller from the University Hospital Schleswig-Holstein, we are developing a hybrid approach that combines wet-lab and computational techniques to sequence and classify tumor samples in real-time based on their genetic and epigenetic markers. 

To achieve this, we use Nanopore sequencing with library preparation times of under an hour, enabling us to directly assess the sequencing data for tumor class prediction as it is generated from the sequencer.