PhD Position at the Department of Gastroenterology, Infectious Diseases, and Rheumatology

PhD Position at the Department of Gastroenterology, Infectious Diseases, and Rheumatology

Specialty

Internal medicine

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Work time

part-time

Start date

01.08.2026

Employment period

limited

Application deadline (in weeks)

31.05.2026

Deployment location Charité

Campus Benjamin Franklin, Steglitz

Jobcode

7189

Salary group

E13

Working at Charité

Our research group focuses on the molecular characterization of chronic inflammatory bowel diseases, with a particular emphasis on fistulizing Crohns disease. The goal is to identify disease-specific cell–cell interactions and molecular programs and to translate these findings into novel therapeutic approaches.

Within a project funded by the Else Kröner-Fresenius Foundation, we combine state-of-the-art spatial multi-omics technologies (metabolic Imaging Mass Cytometry and 10x Xenium 5K spatial transcriptomics) to investigate the pathogenesis and progression of intestinal fistulas. In addition, patient-derived intestinal assembloid models are established to functionally validate identified mechanisms.

There is also the opportunity to contribute to a related project on the molecular characterization of fistula-associated carcinomas. We offer you a highly translational research environment with access to advanced core facilities, close integration into national and international collaborations (e.g., CRC-TRR241 / IBDome), structured supervision and PhD training opportunities and an interdisciplinary and international research team

Overview of the position

Establishment and further development of a multimodal analysis pipeline for Metabolic Imaging Mass Cytometry (IMC / mIMC) and Spatial transcriptomics (10x Xenium 5K)

Integration and analysis of multimodal datasets (protein + transcriptomic + spatial data)

Bioinformatic analysis (e.g., R-based pipelines, single-cell analyses, integration methods)

Analysis of cell–cell interactions and molecular networks in fistulizing Crohns disease

Contribution to the establishment and analysis of human intestinal assembloids

Functional validation of identified molecular candidates

Support in the collection, processing, and documentation of patient samples (biopsies, resections)

Close collaboration with clinicians, core facilities, and bioinformaticians

Presentation of results at conferences and lab meetings

Writing of scientific publications

In accordance with Section 110(4), third sentence, of the Berlin Higher Education Act (BerlHG), academic staff are allocated a reasonable amount of time during working hours for their own further academic development

What we are looking for

Masters degree in biology, biotechnology, bioinformatics, or a related life science field

Interest in translational research and human disease models

Experiences in Single-cell or spatial omics, Bioinformatics / data analysis (R, Python), or Cell culture / organoids / assembloids are advantageous

Immunology / molecular biology

Ability to work both independently and as part of a team

Structured and careful working style

Very good English skills

Charité offers you

Work in an innovative, translational research project with high clinical relevance

Access to unique patient cohorts and biobank data

Training in cutting-edge technologies (spatial omics, multimodal data integration)

Opportunities for scientific development and publication in high-impact journals

Integration into structured graduate programs

Information regarding the position

Paygrade E13 according to TVöD VKA-K. Your job grade depends on your job qualification whereas the experience level depends on the number of working years. The yearly gross salary is hereby provided based on a full time position excluding yearly bonus and additional pay. You may find further information here