PhD position bioinformatics and immunogenomics

PhD position bioinformatics and immunogenomics

Published Deadline Location
3 Apr 21 Apr Groningen

Job description

The overall project aim is to identify infectious disease (ID) triggers that can potentially cause immune-related noncommunicable diseases (IR-NCDs) like inflammatory bowel disease, multiple sclerosis, rheumatoid arthritis and post-COVID-19-condition. In this project, we aim to 1) identify IDs triggering IR-NCDs by screening for antibody responses against >500,000 ID antigens from infections, microbiome and environment, and 2) to disentangle environmental and genetic factors affecting the transition from IDs to IR-NCDs. We will combine novel multi-omics approaches and technologies for personalized genotyping of HLA and adaptive immune receptor genes to deeply profile samples of patients at time of diagnosis as well as before diagnosis. This project will represent the largest and most deeply profiled systematic study of multiple IR-NCDs in a large population cohort Lifelines. The analysis of antibodies will take into account other multi-omics measurements available for participants, such as genetics and gut microbiome. The project is part of EU-funded grant Dark Matter, and will be performed in UMCG in collaboration with partners from Austria, Germany, Hungary and other countries.

The candidate will work on the generation and analysis of wide-scale antibodies data in pre- and post-disease samples from individuals with several non-communicable diseases (such as rheumatoid arthritis, chronic fatigue and post-COVID19), who are part of Lifelines population cohort. The antibodies profile will be linked with host environment, genetics and microbiome data. The work will be performed in close collaboration with colleagues from Groningen Microbiome Hub (https://groningenmicrobiome.org/)

Papers describing the methods of antibody analysis and the Lifelines population:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9558073/
https://pubmed.ncbi.nlm.nih.gov/37164013/
https://www.sciencedirect.com/science/article/abs/pii/S1074761323001851

Specifications

University Medical Centre Groningen (UMCG)

Requirements


Required Expertise
- Master’s degree with a focus on bioinformatics expertise ..
- A collaborative spirit to work effectively within an international interdisciplinary team and with clinical partners
- Excellent organizational skills to manage complex workflows and data collection processes
- Strong communication skills, both written and verbal, with the capability to present research findings to both a specialist and non-specialist audience
- Team player with excellent communication and collaborative skills

Additional experience in the following areas is highly desirable

- Experience handling large databases
- Knowledge of developing and debugging in Java/Python/R.
- Knowledge of immunology

Conditions of employment

The PhD student position is for a duration of 3.5 years, with an initial contract of one year followed by an extension, based on performance. The candidate will be provided with a stimulating work environment and opportunities for professional development within the field of infectious disease diagnostics. Your salary will be a minimum of € 2.901,- gross per month in the first year and a maximum of € 3.677,- gross per month (scale PRO) 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).

We are looking forward to your application and the possibility of you joining our team to contribute to this groundbreaking research endeavour.

For questions about the position
Any questions? Do contact us.

Department

proMaag-Darm-Leverziekten

The position will be embedded at the department of Gastroenterology and Hepatology and the department of Genetics at the University Medical Center Groningen, The Netherlands and will be conducted within an international consortium working on the EU Horizon funded Dark-Matter-NCD project.
The University of Groningen is a top 100 University that has built a reputation for world-class research. You will follow courses and do research in small groups where personal interaction with your supervisor is an important part of your education. As a result, our students design their research and their program to meet their own personal interests.

Additional information

Prof. Dr. R.K. Weersma
(050) 361 2620
r.k.weersma@umcg.nl

Prof. Dr. A.P. Zhernakova
sashazhernakova@gmail.com

Specifications

  • Research, development, innovation; Research, development, innovation
  • Health
  • max. 36 hours per week
  • max. €2901 per month
  • University graduate
  • 240308

Employer

University Medical Centre Groningen (UMCG)

Learn more about this employer

Location

Hanzeplein 1, 9713 GZ, Groningen

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Application procedure

Prof. Dr. R.K. Weersma, r.k.weersma@umcg.nl, telefoonnummer: (050) 361 2620
Prof. Dr. A.P. Zhernakova, sashazhernakova@gmail.com

Application procedure

Application procedure

Prof. Dr. R.K. Weersma, r.k.weersma@umcg.nl, telefoonnummer: (050) 361 2620
Prof. Dr. A.P. Zhernakova, sashazhernakova@gmail.com

Make sure to apply no later than 21 Apr 2024 23:59 (Europe/Amsterdam).