Key Skills

Job Description

Join us in uncovering the complex biology of the lymph node by developing cutting-edge multiscale computational models to advance our understanding of immune function in health and disease. About The Project The immune system plays a central role in protecting the body against pathogens and detecting and eliminating abnormal cells, including cancer cells. Dysregulation of the immune system can lead to a wide range of autoimmune, inflammatory and immunodeficiency disorders. Lymph nodes are key organs of the immune system. They play a crucial role in immune cell activation and the initiation of adaptive immune responses. Despite their importance, many of the cellular and molecular processes that govern lymph node function remain poorly understood. As a postdoc in computational immunology, you will develop a mechanistic, spatio-temporal multiscale computational model of the lymph node. You will integrate agent-based modelling with differential equation-based approaches to better understand immune responses. This is a two-year postdoctoral position. You will have the opportunity to contribute to the development of this research line and use computational modelling to address fundamental questions in immunology. About The Role You will develop a mechanistic multiscale model of the lymph node, with a focus on understanding adaptive immune responses. You will work closely with principal investigators and fellow researchers at Amsterdam UMC and other institutes. You will also present and discuss your results in team meetings. Your Tasks Include Developing an initial model in the Julia programming language, focusing on T-cell activation at the cellular and molecular level, including cell motility and cell-cell interactions, gene regulatory and signalling networks, and chemokine gradients. Extending the model to include additional lymph node compartments or processes, such as the B-cell region and germinal centre dynamics, or stromal and fibroblast populations. Using single-cell omics and other datasets from public repositories and collaborators to define and parameterize the model. Ensuring that the model is well documented and accessible to other researchers by using our ENCORE framework (https://github.com/EDS-Bioinformatics-Laboratory/ENCORE/wiki). Contributing to teaching at Amsterdam UMC or the University of Amsterdam and writing a grant proposal to attract research funding and establish your own research line. Profile You are a computational scientist with a strong interest in biology, immunology and single-cell omics. You combine technical expertise with analytical thinking and clear communication. You are an ambitious researcher who enjoys working in an interdisciplinary environment and taking the lead in developing a research project. You Bring A PhD in computational science or a related field and experience in a previous postdoctoral research position. Experience with agent-based modelling and differential equations. Strong programming skills in Julia or Python and experience with tools such as Git, Visual Studio Code and CoPilot or Claude Code. Strong communication, presentation and scientific writing skills, with the ability to work independently and collaboratively. A good command of English, both spoken and written. Knowledge or experience with R, immunology and single-cell omics is an advantage. Our offer You will be employed by Amsterdam UMC Research BV. A contract for 12 months, with the intention to extend for a total of two years. Classification in salary scale 10: € 3.724 to € 5.867 gross for full-time employment (depending on experience). In addition to a good basic salary, we offer 8.3% end-of-year bonus. Calculate your net salary here (https://www.vismaraet.nl/bruto-netto-salaris-berekenen/). Holiday hours: 194.4 per year for full time and a possibility to save additional hours. 100% reimbursement for public transport travel costs. If you travel by foot, bicycle, or car, a mileage allowance of €0.21 per km applies (up to a maximum of 40 km one way by car). Do you prefer walking or cycling? Take advantage of our good bike scheme. Pension accrual with BeFrank, a modern, comprehensible and fairly priced pension. Watch this video (https://youtu.be/QO6mgb9R-sI) with more information about joining Amsterdam UMC Research BV. About The Workplace You will join the bioinformatics group within the department of Epidemiology and Data Science at Amsterdam UMC. The group develops bioinformatics methods for analysing single-cell and spatial omics data and computational multiscale models of biological systems, with a main focus on immunology and cancer. You will work closely with immunologists at Amsterdam UMC and other institutes. The interdisciplinary nature of the group brings together computational and biological expertise to address complex research questions. Amsterdam UMC Research BV Amsterdam UMC Research BV supports non-profit scientific research. In doing so, we provide researchers with everything they need to excel. Our principal investigators (PIs) and project leaders offer support in the field of project management, finance and human resources. In medical scientific research projects, legal support is also provided. Watch the video to find out more. Let's meet During the publication period, applications will be handled continuously. If the vacancy is filled, it will be closed prematurely. If you have any questions about this position, please feel free to contact prof. dr. Antoine van Kampen, at [email protected]. A reference check, screening and hiring assessment may be part of the procedure. Read here (https://werkenbij.amsterdamumc.org/nl/algemeen/medewerkerscreening) whether that applies to you. If you join us, we ask you for a VOG (Certificate of Good Conduct). Internal candidates will be given priority over external candidates in case of equal suitability. Acquisition in response to this vacancy will not be considered.

Core Responsibilities

Develop and extend a mechanistic, spatiotemporal multiscale computational model of lymph node function and adaptive immune responses, integrating agent-based modeling with differential equations. Use single-cell omics and other datasets to parameterize the model, document it through the ENCORE framework, collaborate with researchers, and contribute to teaching and grant writing.

Requirements

A PhD in computational science or a related field and experience in a previous postdoctoral research position are required, along with experience in agent-based modeling and differential equations. Applicants should have strong Julia or Python programming skills, effective communication and scientific writing abilities, and an interest in biology, immunology, and single-cell omics; R and relevant domain experience are advantageous.

Benefits

• End-Of-Year Bonus
• Paid Holiday Leave
• Public Transport Reimbursement
• Mileage Allowance
• Bicycle Scheme
• Pension