Eric Herlenius

PhD position in Developmental Neuroscience at Karolinska Institutet, Sweden This doctoral position is hosted by Eric Herlenius’ research group at the Department of Women’s and Children’s Health and the Center for Molecular Medicine, Karolinska Institutet. Michael Hagemann-Jensen will serve as assistant supervisor. The project sits at the intersection of developmental neuroscience, molecular biology, bioinformatics, and cardiorespiratory physiology, with a special focus on how brainstem neural networks develop and how inflammation and birth-related transitions influence respiratory control. The research uses complementary patient, animal, and in vitro models, including rodent systems and organoid cultures, to study perinatal development and regulation of vital cardiorespiratory neural circuits. A major part of the work involves advanced transcriptomic and spatial genomics approaches, such as single-cell RNA sequencing, Smart-seq3xpress, spatial transcriptomics platforms (Xenium, MERSCOPE, TRISCO), and 3D RNA imaging. The project also includes computational integration and analysis of multimodal datasets, making it especially suitable for applicants with strong bioinformatics and programming skills. The successful candidate will formulate hypotheses, plan and perform experiments, analyse complex single-cell and spatial transcriptomics data, and contribute to scientific manuscripts and presentations. The environment is highly collaborative and interdisciplinary, with close interaction with doctoral students, postdocs, and researchers across the Herlenius and Hagemann-Jensen groups. The position is therefore attractive for candidates interested in computational biology, neurodevelopment, gene regulation, and translational biomedical research. Karolinska Institutet offers a creative, international, and well-resourced research setting. As a doctoral student, you will be enrolled in research education with an individual study plan, access to a broad course offering, and the opportunity to work in one of the world’s leading medical universities. The position is a salaried PhD employment, full-time for up to four years. Eligibility requires a second-cycle degree or equivalent academic qualifications, plus certified English skills equivalent to English B/English 6. Preferred experience includes transcriptomics or multi-omics analysis, differential expression analysis, cell type annotation, trajectory analysis, gene regulatory inference, Linux/Unix, large-scale sequencing data, organoid work, microscopy, and prior research experience. Applications are submitted via the Varbi recruitment system. The application should include a cover letter, CV, any thesis work and publications, supporting documents for eligibility, and any other material demonstrating relevant skills and experience. The deadline is 2026-09-09.

Karolinska Institutet is offering a doctoral (PhD) student position in developmental neuroscience within Eric Herlenius’ research group at the Department of Women’s and Children’s Health, Center for Molecular Medicine. The project is co-supervised by Michael Hagemann-Jensen and is based in Stockholm, Sweden. The research focuses on the development and dysfunction of cardiorespiratory and autonomic control, with particular attention to how brainstem neural networks, inflammation, and inflammatory signalling contribute to breathing disorders in newborns and children. The doctoral project aims to study perinatal development and regulation of vital cardiorespiratory brainstem neural networks, and to define cellular and molecular mechanisms governing respiratory development, including the effects of inflammation and birth-related transitions. The work combines rodent models with advanced molecular approaches, including single-cell RNA sequencing, Smart-seq3xpress, spatial transcriptomics, MERSCOPE, TRISCO, and computational integration of single-cell and spatial transcriptomic datasets. A key part of the project is the analysis of multi-modal datasets and the development of bioinformatics workflows using statistical and deep-learning-based approaches. The student will work in a collaborative, interdisciplinary environment with expertise in single-cell and spatial genomics, developmental neuroscience, and cardiorespiratory physiology. The doctoral student will formulate research questions and hypotheses, design and conduct experiments, analyze complex datasets, complete doctoral courses, write scientific manuscripts, and communicate results to specialist and non-specialist audiences. The position is particularly suitable for a candidate with strong bioinformatics and programming skills and an interest in computational biology, developmental neuroscience, and transcriptomic analysis. Eligibility requirements include a second-cycle/master degree or equivalent, along with English proficiency equivalent to English B/English 6. The ideal applicant should have a background in bioinformatics, computational biology, molecular biology, biomedicine, biotechnology, neuroscience, or a related field; solid knowledge of molecular and cellular biology; experience analysing biological or genomic data; and programming experience in R and Python. Helpful additional experience includes single-cell RNA-seq, spatial transcriptomics, transcriptomic or multi-omics analysis, Linux/Unix environments, large-scale sequencing datasets, developmental biology, cardiorespiratory physiology, microscopy, and prior research experience. The position is a doctoral studentship for up to 4 years full-time and includes a contractual monthly salary. Karolinska Institutet describes itself as a creative, internationally connected environment with access to courses, research infrastructure, and benefits such as a free gym and reimbursement for medical care. Application deadline: 2026-09-09. Applications should be submitted through the Varbi recruitment system and should include a personal letter, CV, degree projects and publications if available, proof of eligibility, and any other documents demonstrating the desired skills and qualities.