PhD position in Unravelling B cell differentiation

Are you intrigued by the functioning of the human adaptive immune system? Do you want to understand the regulation of B cell differentiation, so this knowledge can be used to either induce better antibody responses, or to prevent unwanted antibodies responses, such as against auto-antigens or therapeutic proteins? We invite enthusiastic and dedicated candidates to join our passionate research team as a PhD candidate to study human B cell development using a combination of state-of-the-art B cell analysis methods with cutting-edge methodology for the analysis of single-cell sequencing.

Join us!
In our team we investigate the regulation of human T cell-dependent B cell differentiation into long-lived antibody secreting cells and memory cells. We investigate the role of antigen, Thelper skewing and B-T cell interactions in the B cell differentiation process using advanced in vitro B and T cell differentiation assays, deep B and T cell profiling, single cell RNA seq and BCR repertoire analyses. We combine this with direct ex vivo investigation of antigen-specific B and T cell differentiation upon in vivo antigen exposure.
The PhD candidate on this project will be part of both the Biosystems Data Analysis group (BDA) of the Swammerdam Institute for Life Sciences (SILS) and the B cell immunology group at Sanquin. Sanquin is a knowledge-driven not-for-profit organization that supplies life-saving products and services, as well as involved in blood transfusion medicine- and immunology- related research. The B cell Research group at Sanquin specializes in research on the regulation of human T cell-dependent B cell differentiation into antibody secreting cells and memory cells. The BDA group works on the development of methodology for data mining, machine learning/deep learning, data fusion, and modelling and application of these methods to answer biological questions. Novel methodology for the analysis of single-cell sequencing data using deep learning based approaches will be applied on the single cell data acquired in this project.

What are you going to do?
You will work on elucidating early human B cell differentiation by

1. analysing already available single cell RNA sequencing (Rhapsody) dataset of recently induced antigen-specific B cells in collaboration with computational researchers in the BDA group;
2. generating additional multi-omics datasets of B cell populations of interest;
3. study regulation of B cell differentiation in established 2D cultures and novel 3D lymph node organoid-like cultures.

Tasks and responsibilities
You will:

• perform in vitro B cell differentiation cultures, generate new ex vivo datasets of human B cells, and analyze these datasets;
• collaborate with both experimental researchers as well as with computational researchers (at UvA and Sanquin;
• be an active member of the research group and take responsibility for shared tasks; incorporate feedback and give input to others;
• take a leading role in writing manuscripts and complete a PhD thesis within the official appointment duration of four years;
• participate in the Faculty of Science PhD training program;
• supervise Bachelor and Master theses.

Your profile
You are passionate about immunology and have a particular interest in B cells. You have a creative mind and look forward to combine state-of-the art single cell analysis technologies and in vitro B cell cultures. Finally, you are a team player and a pleasant colleague who enjoys being part of an interdisciplinary team of experimental researchers and computational researchers.

You have/are

• an MSc in Biomedical sciences or similar;
• interested in cellular immunology;
• experience with cell culture and multi-parameter flowcytometry;
• motivated to learn and apply big-data analysis, such as single cell analysis;
• professional command of English.

Our offer
We offer a temporary contract for 38 hours per week for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years). The preferred starting date is as soon as possible. This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students.

Based on a full-time appointment (38 hours per week) the gross monthly salary will range from €2.901 in the first year to €3.707 (scale P) in the last year. This does not include 8% holiday allowance and 8,3% year-end allowance. The UFO profile PhD candidate applicable The Collective Labour Agreement of Universities of the Netherlands is applicable.

Besides the salary and a vibrant and challenging environment at Science Park and Sanquin we offer you multiple fringe benefits:

• 232 holiday hours per year (based on fulltime employment);
• multiple courses to follow from our Teaching and Learning Centre;
• a complete educational program for PhD students;
• a pension at ABP for which UvA pays two third part of the contribution;
• the possibility to follow courses to learn Dutch;
• help with housing for a studio or small apartment when you’re moving from abroad.

Are you curious to read more about our extensive package of secondary employment benefits, take a look here.

About us
The Swammerdam Institute for Life Sciences (SILS) is located at the vibrant Amsterdam Science Park. SILS is one of eight institutes of the University of Amsterdam's Faculty of Science (FNWI). With around 240 employees, SILS carries out internationally high-quality life science research and provides education within various university programs. Research is also carried out in close cooperation with the medical, biotech, chemical, flavor, food & agricultural, and high-tech industries, and revolves around 4 main themes, Cell & Systems biology, Neurosciences, Microbiology and Green Life Sciences. Want to know more about our organisation? Read more about working at the University of Amsterdam.

If you feel the profile fits you, and you are interested in the job, we look forward to receiving your application. You can apply online via the button below. We accept applications until and including 09 March 2025. Applications should include the following information (all files besides your cv should be submitted in one single pdf file):

• a detailed CV including the months (not just years) when referring to your education and work experience;
• a letter of motivation;
• the names and email addresses of two references who can provide letters of recommendation.

A knowledge security check can be part of the selection procedure (for details: national knowledge security guidelines). Only complete applications received within the response period via the link below will be considered. The interviews will be held in the second half of March 2025.

Do you have any questions or do you require additional information? Please contact:

• dr. Anja ten Brinke
• Email: a.tenbrinke@sanquin.nl
• T: +31 610914389

38 hours per week

Science Park 904