Postdoctoral Researcher in single-cell and spatial omics of CNS development and disease

Do you want to contribute to improving human health?

The Li Research Group  at Karolinska Institutet investigates how the human central nervous system develops, how these programs are disrupted by injury and disease, and how they can be harnessed for regeneration and repair.

Our research integrates single-cell and spatial multi-omics, human developmental tissue, stem cell and organoid models, perturbation approaches, and in vivo models to uncover mechanisms controlling cell states and cell fate. Current directions include spinal cord development and regeneration, stem cell responses to spinal cord injury, neural stem cell transplantation, CNS organoids, and developmental mechanisms of brain tumours.

Our long-term goal is to move from mapping human CNS cell states to understanding and ultimately controlling them, creating new opportunities for regenerative medicine and neurological disease treatment. The group provides an interdisciplinary environment connecting experimental biology, computational science, and translational collaborations.

Your mission

The postdoctoral researcher will contribute to a research programme using large-scale single-cell, multi-omic, and spatial datasets to understand how cellular states and cell-fate decisions are regulated during CNS development and altered in disease. The duties will primarily involve datasets from human and rodent CNS development, brain tumors, and organoid models, with opportunities to connect computational discoveries to experimental perturbation and validation.

Key duties include

• Analysing single-cell and single-nucleus RNA-seq, spatial transcriptomics, and related omics datasets generated within the group and from complementary public resources.
• Integrating large datasets across samples, developmental stages, anatomical regions, experimental models, and disease conditions.
• Identifying and characterizing cell states, developmental trajectories, regulatory programs, and spatial organization relevant to CNS development and disease.
• Performing multi-omic and cross-modality analyses, including integration of transcriptomic, chromatin-accessibility, and spatial data where appropriate.
• Developing or adapting computational approaches for large-scale data integration, predictive modelling, gene-regulatory analysis, and cell-fate inference.
• Contributing to projects investigating how cell-intrinsic regulation and the cellular microenvironment jointly influence cell fate decisions.
• Working closely with experimental researchers to generate testable hypotheses, guide validation experiments, and interpret results in their biological context.
• Contributing to study design, reproducible analysis pipelines, data visualization, manuscript preparation, and development of new computational directions within the group.

The successful candidate will join an interdisciplinary research environment with access to extensive in-house single-cell, multi-omic, and spatial datasets spanning CNS development, regeneration, brain tumors, and organoid models. The position offers close interaction with experimental researchers, allowing computational discoveries to be directly connected to biological questions, perturbation experiments, and validation. There will also be opportunities to develop new analytical approaches and independent computational research directions, particularly in large-scale data integration, regulatory modelling, and cell-fate analysis.

The position is a fixed-term employment for two years, with a possibility of extension.

Your profile

We are looking for a highly motivated computational researcher with a strong background in bioinformatics, computational biology, genomics, or related quantitative fields, and a strong interest in CNS biology.

The successful candidate should have

• Documented experience in analysing single-cell or single-nucleus RNA-seq data.
• Documented experience in analysing spatial transcriptomics or other spatial omics data.
• Strong programming skills in R and/or Python.
• Experience with key analytical tasks including quality control, cell-type annotation, differential analysis, data integration, and biological interpretation.
• Experience handling large and complex biological datasets and applying appropriate statistical approaches across biological samples and replicates.
• Ability to independently develop and maintain reproducible computational workflows, troubleshoot analyses, and critically interpret results.
• Good communication skills in English and the ability to collaborate effectively with experimental biologists and other computational researchers.

Experience with large-scale data integration, high-performance computing, multi-omics, chromatin accessibility data, gene-regulatory network analysis, trajectory or cell-fate modelling, machine learning, or perturbation-data analysis is considered an advantage. Experience in CNS development, stem cell biology, brain tumors, or organoid research, as well as previous computational method development, is also highly meriting. Applicants are not expected to have expertise in all these areas.

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

Solna

Choose to work at KI – Ten reasons why

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)

KI applies individual and differentiated salary setting in accordance with our collective agreements RALS and RALS-T

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

Want to make a difference? Join us and contribute to better health for all!