Postdoctoral Researcher in Single-Cell, Spatial, and Host-Microbiome Computational Biology Full-time

Postdoctoral Researcher in Single-Cell, Spatial, and Host-Microbiome Computational Biology

A postdoctoral position is available to study intestinal tissue regeneration, mucosal inflammation, and host-microbiome interactions using single-cell RNA-seq, spatial transcriptomics, and spatial metatranscriptomics combined with integrative computational biology. The position is based in the laboratory of Professor Eduardo Villablanca at Karolinska Institutet, a leading research environment in mucosal immunology and intestinal homeostasis. The successful candidate will join a collaborative program integrating experimental models, patient-derived material, and advanced transcriptomic technologies to investigate fundamental mechanisms relevant to inflammatory bowel disease (IBD), colorectal cancer (CRC), and tissue repair. The project offers strong opportunities for scientific development in computational method building, multi-omics integration, host-microbiome analysis, and translational research in close interaction with clinicians and experimental researchers.

Your Mission

We are seeking a postdoctoral computational biologist with strong expertise in single-cell, spatial, and host-microbiome transcriptomics. The main duties will focus on the analysis and integration of bulk RNA-seq, single-cell RNA-seq, spatial transcriptomics, and spatial metatranscriptomics datasets generated from intestinal experimental systems and human patient materials.

• Develop and apply reproducible computational pipelines for single-cell, spatial omics, and host-microbiome data analysis.
• Perform integrative analysis of host gene expression, microbial signals, tissue organization, and inflammatory states.
• Contribute to the analysis of intestinal regeneration, mucosal inflammation, and host-microbiome interactions.
• Support data QC, preprocessing, data management, annotation, visualization, and downstream statistical modeling.
• Participate in method development for multi-sample integration, spatial niche analysis, and host-microbiome computational frameworks.
• Contribute to manuscripts, grant applications, and presentations for both specialized and broader scientific audiences.
• Collaborate closely with wet-lab researchers, clinicians, and other computational scientists in the group.
• Help maintain and optimize the group's computational resources, data analysis servers, and storage workflows.
• Contribute to the setup, deployment, and maintenance of computational environments, including software installation, dependency management, and reproducible analysis configurations.
• Support workflow deployment and large-scale omics analyses in Linux and high-performance computing (HPC) environments.
• Help shape, develop, and maintain the current computing infrastructure of the group.

Your Profile

We are looking for a highly motivated researcher with strong quantitative, computational, and programming skills, a solid background in computational biology or bioinformatics, and a demonstrated research interest in intestinal biology, mucosal immunology, and host-microbiome interactions.

Required qualifications:

• A PhD in computational biology, bioinformatics, systems biology, immunology, genomics, computer science, computational medicine, or a closely related field.
• Documented experience in transcriptomics analysis, including single-cell RNA-seq, spatial transcriptomics, and spatial metatranscriptomics (SmT; see Saarenpää et al., Nature Biotechnology, 2024, “Spatial metatranscriptomics resolves host-bacteria-fungi interactomes”).
• Demonstrated hands-on experience in host-microbiome analysis, microbiome-integrated transcriptomics, and spatially resolved host-microbe data interpretation.
• Strong programming skills in R and/or Python, with experience in reproducible data analysis, workflow development, and code-based project organization.
• Experience working in Linux environments, large-scale omics data processing, and shared or high-performance computing (HPC) infrastructure.
• Excellent written and oral communication skills in English.
• Demonstrated experience in computational environment setup, software installation, dependency management, server maintenance, pipeline deployment, workflow automation, or support of shared computing resources.

Meritorious qualifications:

• Experience with intestinal biology, mucosal immunology, IBD, CRC, or tissue regeneration research.
• Experience with multi-omics integration, advanced statistics, machine learning, or high-quality biological data visualization.
• Prior postdoctoral or equivalent full-time research experience after the PhD is highly desirable.
• Experience in maintaining or developing research computing infrastructure for collaborative groups.
• A publication record in peer-reviewed journals relevant to the field.
• Experience contributing to collaborative projects involving both computational and experimental researchers.

To be eligible for employment as a postdoctoral researcher, a PhD or a foreign degree deemed to be equivalent to a Swedish PhD is required. This eligibility requirement must be fulfilled at the latest at the time of the employment decision. Completion of your doctoral degree within the last three years is considered an advantage. If there are special reasons, your degree may have been completed earlier.

What Do We Offer?

A creative and inspiring environment with wide-ranging expertise and interests. Karolinska Institutet is one of the world's leading medical universities. At Karolinska Institutet, we conduct successful medical research and hold the largest range of medical education in Sweden. At KI, you get to meet researchers working with a wide range of specialisms and methods, giving you ample opportunity to exchange knowledge and experience with the various scientific fields within medicine and health. It is the crossover collaborations, which have pushed KI to where it is today, at the forefront of global research. Several of the people you meet in healthcare are educated at KI. A close relationship with the health care providers is important for creating groundbreaking top quality education and research. Karolinska Institutet is also a state university, which entitles you to several benefits through our collective agreement.

Location

The position is located within the Department of Medicine, Solna. The department consists of ten divisions and each division consists of several research groups. The position is located within the research group led by Professor Eduardo Villablanca at the Division of Immunology and Respiratory Medicine. The group studies the molecular and cellular mechanisms that regulate intestinal homeostasis, tissue repair, and mucosal inflammation, using experimental models, patient materials, and advanced single-cell, spatial, and host-microbiome transcriptomic approaches.

Application

An employment application must contain the following documents in English or Swedish:

• PhD certificate
• A complete resumé, including date of the thesis defence, title of the thesis, previous academic positions, academic title, current position, academic distinctions, and committee work
• A complete list of publications
• A summary of current work (no more than one page)

The application is to be submitted through the Varbi recruitment system.