PhD Position in Spatial Transcriptomics, Bioinformatics, and Mucosal Immunology at Karolinska Institutet Karolinska Institutet in Sweden

Karolinska Institutet, one of the world’s leading medical universities, is offering a fully funded PhD position in the Villablanca Lab, renowned for its research in mucosal immunology and spatial omics. The doctoral project is highly interdisciplinary, integrating spatial transcriptomics, bioinformatics, computational biology, and advanced models of inflammatory bowel disease (IBD) using mouse and zebrafish. The research aims to build functional spatial atlases of intestinal healing in ulcerative colitis by combining spatial transcriptomics, proteomics, and metabolomics, working with both pre-clinical models and clinical samples.

The successful candidate will analyze single-cell and spatial omics datasets, design experiments, and publish in top journals, collaborating within an international and interdisciplinary environment. The Villablanca Lab focuses on understanding the spatial organization of inflammation and healing in the gut, defining host–environment interactions that maintain intestinal homeostasis, and exploring how disruptions can lead to IBD. The lab employs cutting-edge technologies such as scRNA-seq, spatial transcriptomics, and system biology approaches, and maintains collaborations in host–microbe interactions and spatial technologies.

Applicants must hold a master’s degree in bioinformatics or computational biology, with documented experience in intestinal immunology, spatial transcriptomics, single-cell RNA sequencing, and bioinformatics. Proficiency in Python, R, and bash is essential, as is experience analyzing single-cell and spatial transcriptomics data in ulcerative colitis and IBD contexts. Familiarity with murine models for colitis and colorectal cancer is required, and mass spectrometry experience is advantageous. Candidates should demonstrate strong English skills, data analysis and presentation abilities, creativity, motivation, independence, and teamwork.

The position offers a contractual salary for up to 4 years full-time, access to fitness facilities, and reimbursement for medical care. Karolinska Institutet provides a creative, international research environment with opportunities for collaboration and exchange. Applications should be submitted via the Varbi recruitment system, including a personal letter, CV, degree certificates, publications, and documents demonstrating eligibility and skills. The deadline for applications is December 10, 2025.

For more information, visit the academic profile of Professor Eduardo Villablanca or the official job posting. This opportunity is ideal for candidates passionate about spatial omics, immunology, and computational biology, seeking to contribute to cutting-edge research in intestinal health and disease.