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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
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 Crohn’s 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 Crohn’s 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

Master’s 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
Working hours are part-time with 25,03 hours per week
The position is limited until 31.07.2029, as it is tied to the project duration
30 days of paid vacation per year
The application period ends on:
Position ID: 7189

Application

Everyone is welcome at the Charité, regardless of age, religion, gender, gender identity, sexual orientation, nationality, disability, ethnic or social background. We are committed to equal opportunities and inclusion.

For data protection reasons, we only accept applications via our application portal. The contact details provided below are intended solely for inquiries.

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If you have questions, please contact:

Dr. med. Malte Lehmann

malte.lehmann@charite.de

More information

Data protection information

The Charité would like to point out that personal data is stored and processed at various locations at the Charité premises (e.g. specialty department, personnel representatives, HR department) as part of and for the purposes of the application process. Furthermore, the data may be transferred or processed within the group and to external bodies (e.g. authorities) to protect legitimate interests. By submitting your application, you agree to our data protection policy and terms of use for application procedures, which you can find here.

Additional information

Charité – Universitätsmedizin Berlin makes its personnel decisions based on suitability, ability and professional performance. The Charité aims to increase the proportion of women in management positions and therefore strongly encourages women to apply. Women with equivalent qualifications will be given priority within the scope of legal possibilities. Applications from people with a migration background who meet the recruitment requirements are expressly encouraged. Severely disabled applicants with equal qualifications will be given preference. A police good-conduct certificate, in some cases an extended good-conduct certificate, is required at the time of recruitment. Unfortunately, application documents can be returned only if a sufficiently stamped envelope is enclosed. Any incurred travel expenses cannot be reimbursed.