We are looking for Masters Students in Bioinformatics!

We are currently looking for Master’s students in the field of Bioinformatics for the topic of

Nucleosome footprints in cell-free DNA sequencing data

Cell-free DNA (cfDNA) is released by dying cells into the surrounding tissues and also to the bloodstream. As nucleosomes protect DNA from degradation, plasma cfDNA carries information about the nucleosome organization in the cells of origin. Different characteristics of cfDNA are increasingly being used in the diagnostics of genetic diseases and the monitoring of cancer. We discern nucleosome footprints at transcription binding sites and DNase hypersensitivity sites from cfDNA-sequencing data and infer the contribution of different cell / tissue types to cfDNA. In doing so, we aim to quantify cancer-derived cfDNA and detect inflammation in various tissue types.

We are looking for students who have some experience with Unix systems, proficiency in at least one scripting language (e.g. Python or R), a strong understanding of biostatistics and a basic understanding of machine learning algorithms. Depending on the experience and interest of the student we offer projects focusing on:

• Gene expression inference or
• Batch effect correction or
• Deconvolution of chromatin accessibility from cfDNA-sequencing data

You can apply by sending a CV to this e-mail along with a short description of your motivation to join our lab.

References

1 Snyder, M. W. et al. Cell 164, 57–68 (2016)

2 Peneder, P et al. Nat Comms 12, 3230 (2021)

3 Rao, S. et al. Sci Adv 8, 34 (2022)