Postdoctoral fellowship: nucleosome repositioning in cancer for patient diagnostics
The project is devoted to cancer diagnostics based on nucleosomics analysis of cell-free DNA (cfDNA) extracted from blood plasma (so-called liquid biopsies). We aim to develop a method that can identify colorectal cancer at a very early stage by using a simple blood test. Our test is based on the analysis of DNA which is released from cancer cells into the blood stream. When cancer (and normal) cells die, their DNA is cut into pieces and released into the blood. This happens all the time and is a normal process. We will extract these DNA fragments from blood and with the help of powerful computer algorithms will detect changes in mathematical patterns that define whether someone has cancer.
We have recently applied this method to other types of cancer e.g. pancreatic, lung, prostate and breast cancer, and found that our approach is much more sensitive than alternative strategies. In this project we will apply this method, which is based on the use of machine learning/artificial intelligence, to colorectal cancer for the first time. The overall goal is to develop a test for the early detection of bowel cancer.
Postdoctoral candidate details:
Required skills: Computational NGS analysis (ChIP-seq, ATAC-seq, RNA-seq, Bisulfite sequencing, cfDNA and/or related); programming in R or Python.
Desired skills: knowledge of cfDNA or chromatin/gene regulation.
Project start: 1st April 2025.
Duration: 2 years.
Location: University of Essex, UK.
See below some of our recent publications in this direction:
- Takahashi et al (2024) bioRxiv 2024.06.02.59705
- Shtumpf et al (2024) Aging Cell 23, e14100.
- Jacob et al. (2024) Clinical Epigenetics 16, 50.
- Piroeva et al (2023) Genome Research 33, 1649-1661
More publications from our lab are available here.
If interested, please send your CV and cover letter to [email protected]