PhD student to study gene expression variation in the brain

Department

Genetica

Working Enviroment

You will be working in the department of Genetics of the University Medical Center Groningen (UMCG) and the faculty of Medical Sciences of the University of Groningen. The University of Groningen is a research university with a global outlook, deeply rooted in Groningen. Quality has had top priority for four hundred years, and with success: the University is currently in or around the top 100 on several influential ranking lists. The faculty of Medical Sciences is the second oldest medical faculty in The Netherlands.
You will be working in the Functional genomics group which is embedded in the genetics department of the UMCG and consists of 300 people working in research, diagnostics and/or patient care. Our group consists of 15 highly skilled researchers focusing on better understanding diseases using genetic and genomic information. The group includes students, PhD students and post-docs, and is supervised by prof. dr. Lude Franke. We strongly believe in open science and the reuse of existing datasets and we are currently leading the international eQTLgen and sc-eQTLgen consortia for research in the genetic regulation of gene expression levels.

MetaBrain project
Recently, we have completed our first study on the genetics of gene expression in human brain, called MetaBrain, which combined genetic information and RNA-seq data from almost all published brain RNA-seq datasets in the brain (n>8,000 samples). This project is now entering the next phase, where we will expand upon the dataset by adding additional samples, and by performing new statistical analyses. Our goal is to delve deeper into the genetic regulation of gene expression in the brain and to compare the results with similar analyses in different tissues. We will also expand our dataset with single cell datasets, which will allow us to investigate gene expression patterns and networks in individual brain cell types. Since we are performing similar projects in blood, we have the opportunity to directly compare results to cell types other than the brain. This project is in close collaboration with a large US-based pharmaceutical company and aims to collect genetic variation and gene expression data in the brain. This will give you the opportunity to learn about the implications of research outside of academia. The research team at the UMCG consists of prof. Lude Franke and dr. Harm-Jan Westra.

Job description

You will investigate how genetic variants affect the expression of genes in thousands of samples from the human brain. To answer the main research questions, you will develop software and bioinformatics pipelines that efficiently perform millions of statistical tests on large genomic datasets. You will inspect different aspects of the genetic regulation of gene expression. For instance, you will determine if the effect of genetic variants on a gene is dependent on the expression of other genes through interaction effects. You will also investigate which genetic effects on gene expression levels are dependent on disease status or polygenic risk scores for diseases such as Alzheimer's disease and ALS. Furthermore, you will investigate the regulation of the expression of gene splice variants and their dependence on disease status. To investigate the cell type in which these effects operate you will then investigate these effects in large single cell RNA-seq datasets. You will summarize the results in articles for high impact scientific journals and clear presentations for (international) scientific conferences.

Requirements

You are expected to:
- have a master's degree (or are close to graduating) in bioinformatics, statistical genetics, molecular biology or a related field;
- have good communication and organizational skills (proficiency in English required);
- be willing to work in a team;
- have a good understanding of programming (Java, Python, R, Bash, etc) and data analysis;
- have affinity with statistics or are willing to learn.

The UMCG has a preventive Hepatitis B policy. The UMCG can provide you with the vaccination, should it be required for your position.
In case of specific professions a ‘Certificate of Good Conduct’ is required.

Conditions of employment

You will get a full-time appointment for a period of 4 years (32-36 hours a week) to be concluded with a PhD thesis. After 1 year, performance will be evaluated to decide whether there is sufficient progress to expect a successful completion of the PhD thesis within 4 years. Your salary will be a minimum of € 2.789,- gross per month in the first year and a maximum of € 3.536,- gross per month (scale PhD) in the final (4th) year, based on a full-time appointment. In addition, the UMCG will offer you 8% holiday pay, and 8.3% end-of-year bonus. The conditions of employment comply with the Collective Labour Agreement for Medical Centres (CAO-UMC).

Intended starting date: 1e of July 2023 or upon agreement.


Additional information

For more information about this vacancy you may contact:

dr. Harm-Jan Westra telefoonnummer +31(0)50 361 7100
h.j.westra@umcg.nl
prof. dr. Lude Franke telefoonnummer +31(0)50 361 7100
l.h.franke@umcg.nl

Applying for a job

Please use the the digital application form at the bottom of this page - only these will be processed. You can apply until 20 April 2023. Within half an hour after sending the digital application form you will receive an email- confirmation with further information.

Digital application form