ESR 12: Bioinformatics analysis of T-cell and B-cell repertoires.

PhD research

Host:

Prof. dr. A.H.C. van Kampen (Antoine)

Bioinformatics Laboratory

Clinical Epidemiology, Biostatistics, and Bioinformatics

https://bioinformatics.amc.nl/

Amsterdam University Medical Centers (location AMC)

Meibergdreef 9

105AZ  Amsterdam

The Netherlands

Duration: 48 months

Background

AIRR-seq is used to determine the full repertoire of T-cell receptors (TCR) and B-cell receptors (BCR). These repertoires give insight in adaptive (auto)immune responses that aid to immunotherapeutics, vaccines, and immunodiagnostics. The last decade significant progress has been made with the pre-processing of AIRR-seq data to translate this data into meaningful information about receptors.  In this project we aim to make a next step and focus on the application and development of downstream analysis methods to examine complete repertoires in the context of autoimmune disorders. 

Approach 

The PhD candidate will get acquainted with existing pre-processing approaches. Subsequently, the candidate will use existing data analyses methods to investigate repertoire diversity, architecture, evolution, and convergence (see Miho et al (2018) Front Immunol.) for an excellent review and unresolved questions.  You will apply these methods to public and in-house generated repertoires obtained from patients with autoimmune disorders and compare them to repertoires obtained for other diseases and for healthy individuals. For specific questions you will develop new analyses methods using approaches from statistics, machine learning, and computational sciences.  

Our research team

The Bioinformatics Laboratory (Van Kampen) focusses on system genomics and systems medicine approaches to address biomedical questions. For more information see  (http://www.bioinformaticslaboratory.nl). The project is a close collaboration with prof. dr. Niek de Vries (MD) of the department Clinical Immunology and Rheumatology and other researchers.

Your profile

      • Candidates should have:
      • - a Master’s degree in bioinformatics, computer sciences, statistics, or similar. 
      • - Basic statistical knowledge and experience with R
      • - Basic knowledge of immunology and molecular biology
      • - Experience with the analysis of OMICS data
      • - Strong programming skills (for example in Phyton)
      • - Excellent higher education track record and strong scientific curiosity.
      • - Fluent spoken and written English skills
      • - Outstanding communication skills

       

    • In addition, the following experience would be helpful, but not essential:

      • - Experience with high performance computing.
      • - Experience in systems biology or systems medicine.

      We seek a highly motivated scientist who enjoys an interdisciplinary environment and in a interdisciplinary project. You are able to work independently but also as part of a team, and have strong communication skills.

Our offer

All ARCAID ESRs receive a full employment contract for 4 years, according to the Collective Employment Agreement (CAO) of the Dutch University Medical Centres. The monthly salary based on a 36-hour work starts from €2.422,- with yearly increments to a maximum of € 3.103,-. This 4-year PhD position is funded by the  Marie Skłodowska-Curie actions of the European Union's Horizon 2020 COFUND program under grant agreement No 847551. There is no separate budget available for mobility as it is already included in the ESR salary. ESRs may attend external courses, conferences or workshops. If applicable or required, additional expenses for training and conference participation and the travel to a Partner Organisation will be covered by the project. The ESR salary meets the requirements of the Dutch Immigration Department to allow family members to move to the Netherlands. It is at the convenience of the ESR to decide on this family movement since the Amsterdam UMC will not cover additional expenses regarding mobility of spouse nor for the required accompanying residence permits. In addition to their individual scientific projects, all fellows will have the opportunity to attend international progress meetings, scientific conferences and summer schools. Additionally, they benefit from further continuing education, which includes internships and secondments, a variety of training modules as well as transferable skills courses. See recruitment procedure.

Your application

See recruitment procedure. You can apply using the online application formFor more information about the position you can contact prof. dr. Antoine van Kampen (This email address is being protected from spambots. You need JavaScript enabled to view it.), telephone: +31 20 5667096.