Doctoral Researcher (f/m/d) - “Dynamic simulation of immunological systems”

The advertised position is part of the NFDI4Immuno (https://www.nfdi4immuno.de/) consortium, involving experts from various areas including immunology, molecular and cellular biology, oncology, hematology, genetics, bioinformatics, machine learning, as well as data and software engineering. The NFDI4Immuno consortium aims to build the capability to combine data and metadata generated from immunological experiments, e.g. cytometry, immunoassays, sequencing, and imaging, providing its members with a federated infrastructure for all immunological data types. In addition, the consortium intends to develop tools and services to support its members with the adoption and utilization of interconnected and integrated data stored in its repositories. 

Our group focuses on the development of germinal centers (GCs) simulation tools. GCs are microanatomical structures within lymphoid organs with an important role in the development of antibodies and memory cells for the long-lasting immunity against pathogens. Using the HYPHASMA simulation tool, developed based on a discrete agent-based modeling approach, we can simulate and study the dynamics of GCs at subcellular level and the process of affinity maturation. The agent-based modelling approach allows for the integration with various data types, e.g. various levels of sparsity, scale and dimension, as well as mechanistic information. Based on immune data, e.g. AIRR-seq, transcriptomic sequences and cytometry data, we can study the dynamic of the immune response.

As part of the NFDI4Immuno consortium, we will focus on the delivery of agent-based models to the consortium as well as an user-friendly interface to our simulation tools. A central part of this endeavor would be to integrate the datasets and repositories of the consortium with our simulation tools.