Epigenetics & Epitranscriptomics
At the COMBINE Lab, we specialize in Oxford Nanopore long-read sequencing and the development of innovative bioinformatics pipelines designed to decode the complexities of the human methylome and epitranscriptome. These chemical modifications regulate gene expression and cellular identity without altering the underlying sequence. By combining our deep nanopore expertise with custom computational workflows, we are bypassing the strict limitations of traditional genomics to unlock entirely new dimensions in cancer research and precision medicine.
Traditional short-read sequencing methods struggle to capture these landscapes, relying heavily on harsh chemical treatments like bisulfite conversion or enzymatic amplification. These legacy workflows introduce severe genomic fragmentation, amplify experimental biases, and restrict the analysis of single-molecule methylation patterns (epialleles) to high-CpG-density regions, resulting in a significantly lower resolution.
Our laboratory overcomes these bottlenecks by leveraging the unique ability of nanopore technology to sequence native DNA and RNA molecules directly. As a strand passes through the pore, modified bases, such as 5mC and 5hmC, alter the ionic current in a highly distinctive manner. This native, real-time detection allows our pipelines to perform high-resolution profiling without any prior chemical conversion, seamlessly capturing full epigenetic landscapes across both high- and low-CpG-density regions.
By training our proprietary computational suites on this high-yield long-read data, we can precisely map molecular mechanisms across multiple biological fronts. Currently, we apply these pipelines to three primary areas: cancer genomics, to dissect intra-tumor heterogeneity and therapy resistance; neurological and rare diseases, to map tissue-specific dysregulations; and functional genome annotation, to link discovered epigenetic alterations directly to disease-driving regulatory networks.
Last update
05.06.2026