Full project description ESR 11

ESR 11: Understanding auto-immune disorders through computational modelling.

PhD research

Hosts:

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

Bioinformatics Laboratory

Clinical Epidemiology, Biostatistics, and Bioinformatics

https://bioinformatics.amc.nl/

Dr. E.G.M. van Baarsen (Lisa)

Experimental Immunology

Internal Medicine: Clinical Immunology and Rheumatology

Amsterdam University Medical Centers (location AMC)

Meibergdreef 9

105AZ  Amsterdam

The Netherlands

Duration: 48 months

Background

To ultimately cure or prevent rheumatoid arthritis, it is critical to understand the earliest changes in the immune system that cause rheumatoid arthritis (RA). Using computational modelling and (single cell) genome-wide expression profiling we aim to delineate the role of stromal cells in bone marrow, lymph node and synovial tissue in arthritis development. Results from these studies may provide innovative drug targets for preventive intervention in pre-clinical RA and identify the immunological processes that initiate RA and possibly other related chronic inflammatory diseases.

Approach 

The PhD candidate will develop computational models that contribute to the understanding of cellular and/or molecular mechanisms underlying RA with a particular focus on stromal cells. Depending on the precise questions and data available, the candidate will develop computational models using approaches such as differential equations, agent-based modelling, (Gillespie) stochastic modelling, etc. These approaches will be used to describe cellular mechanisms and gene regulatory networks in order to gain further insights in the mechanisms underlying RA. The candidate aims to integrate models developed at the cellular level with models at the molecular level (i.e. multi-scale modelling). These models will partially be based on (single cell) omics data (e.g., RNAseq). Therefore, the candidate will be involved in the exploitation of such data for defining the gene regulatory networks and the parameterization of the computational models.

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 department of Experimental Immunology and the department of Internal Medicine: Clinical Immunology and Rheumatology (Van Baarsen) focus on the development of new approaches to delineate (auto)immune disorders and to translate findings to the clinic.

Your profile

    • Candidates should have:
    • – a Master’s degree in computer sciences, bioinformatics, or similar with a strong interest in immunology and (molecular) biology. 
    • – Experience with differential equations and/or agent-based modelling
    • – Knowledge of or experience with (single cell) RNAseq and omics
    • – Basic statistical knowledge and experience with R
    • – Strong programming skills (for example in Phyton or c++)
    • – Excellent higher education track record and strong scientific curiosity.
    • – Fluent spoken and written English skills
    • – Outstanding communication skills

We seek a highly motivated computational scientist with interest in life sciences, who enjoys an interdisciplinary working environment as wells as an interdisciplinary research 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. 

Your application

The position is filled. For more information about the position you can contact prof. dr. Antoine van Kampen (a.h.vankampen@amsterdamumc.nl), telephone: +31 20 5667096.