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Nucleosome footprints in cell-free DNA sequencing
We are currently looking for Master students in the field of Bioinformatics or Computational Biology for the analysis of cell-free DNA sequencing data. We have several topics which students can apply for depending on their previous expertise and proposed duration of the project (3 months or longer).
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.
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.
Depending on the experience and interest of the student we offer projects focusing on:
- Representation learning or
- Gene expression inference or
- Deconvolution of chromatin accessibility from cfDNA-sequencing data
Depending on the experience and interest of the student we offer projects focusing on: - Representation learning or - Gene expression inference or - Deconvolution of chromatin accessibility from cfDNA-sequencing data
If you want to know more about us, please visit https://krauthammerlab.ch/. To apply, you can either submit your application in the SiROP system or just e-mail your CV to zsolt.balazs@uzh.ch.
If you want to know more about us, please visit https://krauthammerlab.ch/. To apply, you can either submit your application in the SiROP system or just e-mail your CV to zsolt.balazs@uzh.ch.
