Ph.D. Student in Computational Biology (f/m/d)

Updated: about 2 months ago
Job Type: FullTime
Deadline: 30 Sep 2021

Project title/Context:

Mutations acquired during lifetime that lead to increased risk for human disease, with focus on cancer

The centre is funded within the International Research Agendas Programme of the Foundation for Polish Science. The 3P-Medicine Lab (Preventive, Personalized, Precision) International Research Agenda is joint unit of Medical University of Gdansk in Poland and Uppsala University in Sweden.

More about the center:

https://ira3p.mug.edu.pl/

https://www.fnp.org.pl/en/3p-medicine-preventive-personalized-precision/

More about participating universities:

https://www.uu.se/en

https://mug.edu.pl/


Project description:

The 3P-Medicine Laboratory (personalized, preventive, precision) is a new science center specializing in research on acquired genetic mutations as risk factors for cancer and other diseases. Our center is focused on somatic mutations that occur early in life in seemingly normal cells that eventually contribute to malignant transformation. Primary interest is in common malignancies that are etiologically related to environmental stimuli: breast cancer, colorectal cancer, urinary bladder cancer and prostate cancer. The ultimate goal is to develop genetic screening approach for non-hereditary cancer risk assessment, years before first clinical symptoms become apparent. Our unique collection of clinical samples includes not only primary and metastatic tumors, but also multiple biopsies of macroscopically normal tissue including frozen sections, peripheral blood, viable skin and stromal fibroblasts as well as cryopreserved primary cell cultures.


Research Group Description:

The Mieczkowski lab studies cell transitions, cell-cell communications and chromatin transformations. A key focus is the use of computational and experimental approaches to dissect, model, and interrogate the changes in chromatin structure triggered by genetic modifications and/or extracellular stimulations. The group pursues multi-disciplinary projects aiming to uncover patterns in chromatin and gene expression profiles relating to cell state. Members of the group will use state-of-the-art methodology to analyze molecular profiles obtained with genotyping microarrays, massively parallel sequencing of DNA (DNA methylation, ChIP, ATAC-seq etc.), bulk RNA- and single cell RNA-seq, as well as spatial transcriptomics.


Key responsibilities include:

1. Analysis of bulk ‘omic’ and genetic data  obtained with NGS.

2. Analysis of single-cell data.

3. Preparation of documented code.

4. Interactions with clinical partners, biobanking and bioinformatics teams.

5. Preparation of materials for scientific publications and patent applications.

6. Participation in collaboration with foreign partner (Uppsala University, Sweden).


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