Postdoc in Intestinal Regeneration and Mucosal Immunology

1000scholars; Odense; On-site; DKK 314,000 - 448,000; Full time

Job summary

SDU - University of Southern Denmark invites applications for a Postdoctoral researcher in intestinal regeneration and mucosal immunology in Odense, Denmark. The role combines experimental biology with bioinformatics to study epithelial memory and mucosal healing in IBD.

The successful candidate will work with patient-derived organoids, co-cultures, and advanced molecular and computational methods, collaborating with clinicians and bioinformaticians to translate findings into clinically relevant

Qualifications

• Experience with organoid biology, especially intestinal or tissue-derived organoids.
• Strong background in tissue regeneration, epithelial biology, mucosal immunology, or inflammatory diseases.
• Experience analyzing single-cell or spatial-omics data using reproducible workflows.
• Proficient in R and/or Python; strong data analysis and documentation skills.
• Excellent English, ability to work independently in an international team.

Responsibilities

• Establish and manipulate patient-derived intestinal organoids and fibroblast-immune-cell co-cultures to investigate epithelial plasticity and regeneration.
• Generate and validate CRISPR-engineered organoids and perform engraftment studies to assess regenerative potential in vivo.
• Analyse scRNA-seq, scATAC-seq, spatial datasets with reproducible workflows for QC, differential analysis, cell-state annotation, trajectory analysis and integration.
• Apply molecular and cellular methods (qPCR, immunostaining, advanced microscopy, flow cytometry, ELISA) and validate pathways with perturbations.
• Collaborate with clinicians, experimental scientists and bioinformaticians to analyse patient-derived samples and data.
• Maintain records, present findings, prepare manuscripts and contribute to grant applications, teaching and supervision.

Skills

Organoid biology

Tissue regeneration

Mucosal immunology

Single-cell data analysis

R/Python

Education

PhD in molecular biology

Tools

R

Python

CRISPR

Job description

Postdoc in Intestinal Regeneration and Mucosal Immunology

SDU - University of Southern Denmark

Odense, Denmark

Research tasks

The position comprises research, teaching, professional development and supervision within intestinal tissue regeneration, epithelial biology, mucosal immunology and inflammatory bowel disease (IBD). The postdoc will join a translational research programme that investigates how inflammation reshapes the intestinal epithelium and its surrounding tissue niche, and how these changes can be targeted to promote safe and durable mucosal healing.

The successful candidate will combine patient-derived organoid and co-culture models with molecular biology, functional assays, and computational analysis of single-cell and spatial datasets. The position is particularly suited to a researcher who can connect experimental biology with bioinformatics and clinically relevant questions.

Research environment

The postdoc will be embedded in a dynamic and highly collaborative research environment spanning the Department of Clinical Research and the Department of Molecular Medicine at SDU. The project benefits from close interaction among basic scientists, clinicians, bioinformaticians and translational researchers, with strong links to Odense University Hospital and access to patient-derived material, advanced disease models and state-of-the-art molecular technologies.

The environment provides excellent opportunities to develop an independent research profile, contribute to clinically relevant discoveries in IBD and tissue regeneration, and build collaborations across experimental, computational and clinical disciplines.

Research project

The project investigates how inflammatory history establishes persistent epithelial and niche memory, shapes epithelial plasticity and influences intestinal regeneration in IBD. Using patient‑derived biopsies, intestinal organoids, fibroblasts and immune‑cell co‑cultures, we will determine how epithelial memory and injury‑induced cell‑state transitions influence regenerative capacity and distinguish effective from impaired mucosal healing.

Functional experiments will be integrated with single‑cell RNA sequencing, chromatin‑accessibility analysis, spatial transcriptomics and spatial epigenomics. CRISPR‑engineered patient‑derived organoids, including lineage reporters and targeted genetic perturbations, will be used to trace epithelial cell states and validate candidate mechanisms. Selected organoids will also be tested in engraftment models to determine whether regenerative phenotypes translate into improved tissue integration and repair in vivo.

Key responsibilities

• Establish and manipulate patient‑derived intestinal organoids and fibroblast‑immune‑cell co‑cultures to investigate epithelial plasticity, cell‑state transitions, regeneration, inflammatory responses and barrier function;
• Generate and validate CRISPR‑engineered organoids, including reporter lines and targeted genetic perturbations, and perform engraftment studies to assess regenerative potential in vivo;
• Analyse and integrate scRNA‑seq, scATAC‑seq, spatial transcriptomic and spatial epigenomic datasets using reproducible workflows for quality control, differential analysis, cell‑state annotation, trajectory analysis and multimodal integration;
• Apply molecular and cellular methods, including qPCR, immunostaining, advanced microscopy, flow cytometry and ELISA‑based assays, and validate candidate pathways using pharmacological and CRISPR‑based perturbations where appropriate;
• Collaborate with clinicians, experimental scientists and bioinformaticians to analyse and interpret patient‑derived samples and data;
• Maintain accurate and reproducible records, present findings, prepare manuscripts and conference contributions, and contribute to grant applications, teaching and supervision where relevant.

Expectations of qualifications

The successful applicant must hold a PhD in molecular biology, cell biology, immunology, bioinformatics, computational biology, regenerative medicine, biomedicine or a closely related discipline, with documented research experience relevant to the project.

Essential qualifications

• Documented experience in organoid biology, preferably involving intestinal or other tissue‑derived epithelial organoids, and in designing mechanistic studies of epithelial plasticity and regeneration;
• A strong background in tissue regeneration, epithelial biology, mucosal immunology, inflammatory disease or a closely related field;
• Demonstrated expertise in analysing single‑cell or spatial‑omics data, with proficiency in R and/or Python and experience developing reproducible computational workflows;
• Hands‑on experience in molecular and cell biology, with the ability to design, perform, troubleshoot and interpret experiments using a structured and careful approach to data analysis, documentation and responsible research practice;
• A strong publication record appropriate to career stage; excellent written and spoken English; and the ability to drive projects independently while collaborating effectively in a multidisciplinary and international environment.

Desirable qualifications

• Experience with intestinal organoids, patient‑derived material, fibroblast or immune‑cell culture, or epithelial‑stromal‑immune co‑culture models;
• Experience integrating scRNA‑seq, scATAC‑seq, spatial transcriptomic, spatial epigenomic or other multimodal datasets;
• Familiarity with advanced imaging, quantitative image analysis, flow cytometry, organoid phenotyping or high‑content screening;
• Demonstrated experience generating and validating CRISPR‑engineered organoids, including knock‑in reporters or targeted gene perturbations, and with intestinal organoid engraftment or transplantation and invivo assessment of epithelial regeneration is highly preferred;
• An interest in supervising junior researchers and contributing to collaborative teaching and research activities.