21 Months Single cell RNA sequencing is revolutionizing our possibilities to understand processes underlying development and disease. The analysis of the data is nevertheless challenging, both technically and at the level of obtaining meaningful biomedical insights from the data. Given the continued development of the experimental protocols it also provides ample opportunities to develop new analysis methods. We already have ample experience in the analysis of scRNA data in the context of vaccine research.

In this project we aim to expand our expertise to analyze scRNAseq data from two projects, 1) the DETECTIVE: in this project scRNAseq will be used to detect and analyze pathogenic T-cells in blood and tissues of patients with systemic autoimmune disease. The goal is to assist development of pathogenic T-cell targeting treatments by identifying T-cell populations specific to disease. 2) the HNF1B switch: in this project scRNAseq will be applied to kidneys of HNF1B KO mice to determine the effects of this transcription factor on kidney cyst formation and electrolyte disorders. The goal is to determine which pathways drive cyst formation. You will first work on the T-cell project and then on the kidney cysts formation project. Besides the primary analysis of the data for the primary research questions there will be ample opportunity for in depth analysis of the scRNAseq datasets to e.g. determine the transcription factors relevant to the clinical and experimental contrasts.

Your job includes, besides the scientific research, also regular communication with the scientific partners in the project. To ensure good transfer of knowledge, data and software, the Radboud Technology Center Bioinformatics (part of the CMBI) will aid with pipeline development, data management and project cooperation.

Tasks and responsibilities

• Analyze scRNA data from the DETECTIVE project and the HNF1B projects to identify cell types and genes associated with the clinical and experimental contrasts.
• Develop and implement new methods to allow functional interpretation of scRNA data.
• Communicate and collaborate with the experimental groups involved in the project.
• Reporting your results in the form of publications and presentations.
• Apply data management and open source/science principles to software development.

Working at Radboud university medical center means that you are ahead of the curve and working together on the healthcare of the future. And there is more. Our secondary terms of employment are impressive. These are fully tailored to you thanks to our Employment Conditions Selection Model. At Radboud university medical center, you will be given trust, and you will take the responsibility to handle everything together. We provide annual courses, both professional and personal.

• In addition to your monthly salary and an annual vacation allowance of 8%, you will receive an end-of-year bonus of 8.3%.
• If you work irregular hours, you will receive an allowance.
• As a full-time employee (36 hours per week), you are entitled to approximately 168 vacation hours (over 23 days) per year.
• Radboud university medical center pays 70% of the pension premium. You pay the rest of the premium with your gross salary.
• You get a discount on health insurance as well: you can take advantage of two group health insurance plans. UMC Zorgverzekering and CZ collectief.

In addition to our terms of employment, we also offer employees various other attractive facilities, such as childcare and sports facilities. Want to learn more? Take a look at the CAO UMC. The Centre for Molecular and Biomolecular Informatics (CMBI) fosters a lively, international and interactive scientific culture and aims to have a significant impact on health care by applying and developing methods for the analysis of biomedical data. We strive for excellence through critical, in depth data analysis, innovation and intense collaborations to identify and answer the relevant research questions. We collaborate in this project with Rogier Thurlings (Rheumatology) and Jeroen de Baaij (Physiology) in the analysis of scRNA data.

Radboudumc
Radboud university medical center is a university medical center for patient care, scientific research, and education in Nijmegen. Radboud university medical center strives to be at the forefront of shaping the healthcare of the future. We do this in a person-centered and innovative way, and in close collaboration with our network. We want to have a significant impact on healthcare. We want to improve with each passing day, continuously working towards better healthcare, research, and education. And gaining a better understanding of how diseases arise and how we can prevent, treat, and cure them, day in and day out. This way, every patient always receives the best healthcare, now and in the future. Because that is why we do what we do.

Read more about our strategy and what working at Radboud university medical center means. Our colleagues would be happy to tell you about it. #weareradboudumc You have obtained a PhD in computational biology/bioinformatics or in experimental molecular biology with a documented experience in computational analysis of ‘omics types of data. You are enthusiastic for understanding and developing of scRNA data analysis methods. You have strong communication skills and a collaborative mindset. All additional information about the vacancy can be obtained from Prof. Dr. Martijn Huijnen. Use the Apply button to submit your application.

See for more information the website about the CMBI.