Computational Immunologist
The Grieshaber-Bouyer Lab is seeking a highly motivated scientist with strong expertise in systems immunology, bioinformatics and machine learning interested in continuing their scientific development in our department.
In your new role, you will lead projects to integrate multi-omics data (transcriptomics, proteomics, high dimensional flow cytometry) with clinical data (demographics, medication, laboratory values) and drive forward our development of bioinformatic methods to better integrate different data modalities.
The overarching goal of these efforts is to identify new drivers of autoimmune disease heterogeneity, predictors of treatment response, relapse and resistance.
Information about the lab:
We are a systems immunology group at the Department of Internal Medicine 3 – Rheumatology and Immunology at Erlangen University Hospital. Our group investigates the mechanisms driving immune cell heterogeneity in tissues and inflammatory conditions and how this affects disease variation across individuals. In particular, we perform systems scale analyses of the immune system in patients with autoimmune disease in the context of cutting-edge immunotherapies, such as CAR T-cell therapy and T cell engager therapy.
Previous work:
Using single cell RNA sequencing, we demonstrated that neutrophils in homeostasis are organized a chronologically ordered main sequence, termed neutrotime. In experimental inflammation, neutrophils deviate from neutrotime and reach distinct polarization states driven by timepoint, tissue, stimulus and other factors. We extended this approach to inflammatory arthritis and identified a transcriptional program which characterizes neutrophils in the arthritic joint in both mice and humans. Functionally, this program was highly enriched for interferon gamma response genes. We identified a hallmark phenotype of joint neutrophils and then modeled the response of neutrophils to the joint environment in vitro using a culture system of primary human neutrophils.
We developed an approach to perform an integrative analysis of leukocyte gene expression across species. We found that overall, lineage identity was stronger than species differences. Using this method, we identified that human and mouse neutrophils share a core inflammation program across various inflammatory conditions. Chromatin accessibility revealed increased accessibility of core inflammation genes in cells migrating from blood to tissue, indicating that neutrophils are pre-programmed to express these core inflammation genes even before the onset of inflammation. Furthermore, this cross species method can be used to improve the translatability of findings between mice and humans.
Key References:
1. Hagen … Grieshaber-Bouyer. BCMA-Targeted T-Cell–Engager Therapy for Autoimmune Disease. N Engl J Med 2024
2. Bucci …Grieshaber-Bouyer. Bispecific T cell engager therapy for refractory rheumatoid arthritis. Nature Medicine 2024
3. Hackert …Grieshaber-Bouyer. Human and murine neutrophils share core transcriptional programs in both homeostatic and inflamed contexts.Nature Communications2023
4. Grieshaber-Bouyer et al. Ageing and interferon gamma response drive the phenotype of neutrophils in the inflamed joint.Ann Rheum Dis2022
5. Grieshaber-Bouyer et al. The neutrotime transcriptional signature defines a single continuum of neutrophils across biological compartments.Nature Communications2021
Current mission and your tasks:
We combine high dimensional discovery in patient samples with in vitro systems, CRISPR-mediated genetic perturbations and murine models to dissect how immune cells adapt to different tissues and inflammatory conditions. Furthermore, we develop novel analysis tools for high dimensional data.
Qualification requirements:
* Doctoral degree in the life sciences / immunology / bioinformatics or computer sciences
* Publication track record in computational immunology (peer-reviewed articles on PubMed)
* Fluent coding skills in R
* Extensive experience analyzing several of the following: bulk and single cell RNA-seq, CITE-seq, CyTOF, flow cytometry data – please see our published references for examples
* Experience with code management and version control, e.g. using github
* Experience with molecular biology methods
* Fluent knowledge of English, able to communicate effectively with other research groups and at conferences
* Enthusiasm for translational research bridging basic immunology and human disease
* Willingness to work in a team environment and to collaborate with other people
* Strong theoretical knowledge of immunology and autoimmunity
* Coding skills in Python not required but advantageous
What we offer:
* The position is initially fixed for 24 months with the possibility for extension
* Intended classification is according to TV-L, E13 100 %
* Starting date: May 1, 2025
* We offer an inspiring, dynamic and interdisciplinary research environment with state-of-the-art research facilities and comprehensive support. The work program of this project includes the application of advanced techniques that ensure a high level of scientific education. We care about qualified training and support with the new challenge.
* Health promotion offered by University Hospital Erlangen
* All civil service benefits incl. supplementary provision of the Federal and State Pension Institution (VBL)
* Additional training and mentoring programs are available through FAU
* Support to present their work at national and international conferences and gain experience in writing grant applications
Applications should be directed to:
Professor Dr. med. Ricardo Grieshaber-Bouyer
Department of Internal Medicine 3 –Rheumatology and Immunology
Friedrich-Alexander-Universität Erlangen-Nürnberg and University Hospital Erlangen
ricardo.grieshaber@fau.de
www.rgb-lab.de
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