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

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.