Senior Scientist in Computational Biology (80%)

From June 1, 2027, or by agreement | initially fixed-term for 5 years, with the possibility of extension

The Department of Biomedical Engineering is part of the Faculty of Medicine at the University of Basel. It contributes to a better future in meeting health care needs through innovative biomedical research and engineering solutions, translating basic science into medical knowledge and healthcare innovations.

The Pediatric Disease Modeling Lab (https://dbe.unibas.ch/en/research/data-driven-modelling-analysis/pediatric-disease-modeling-lab/) is seeking a Senior Scientist to help lead a growing research group. Our mission is to understand how early-life exposures to the microbiome shape lifelong health through their impact on the developing immune system. We develop mathematical models of microbiome–immune co-development to quantify how early-life perturbations to the microbiome shape antimicrobial resistance, infectious disease dynamics, and non-communicable diseases, with the aim of translating our insights into actionable strategies for pediatric care. Our work combines statistical and mechanistic mathematical modeling, causal inference, and machine learning, applied to longitudinal multi-omics data from pediatric cohorts spanning diverse socio-economic and geographical contexts.

Our lab will be supported by two major grants starting in 2027. RESILIENT (ERC Starting Grant) asks why some infants recover from early-life perturbations-antibiotics, infections, feeding transitions-while others are set on a path toward chronic disease, by synthesizing existing longitudinal multi-omics data from several pediatric cohorts across Africa, Asia, and Europe; combining statistical analysis, causal inference, and mechanistic modeling. Restoring Homeostasis (SNSF Starting Grant) investigates how established gut dysbiosis drives immune dysregulation and disease progression in pediatric patients, generating new clinical multi-omics data and using deep learning, structural equation models, and causal inference to identify strategies for restoring immunological homeostasis. Together, these projects will bring a team of postdocs, PhD students, and technical staff to the lab, working with diverse clinical and academic partners.

We are looking for an experienced, scientifically active researcher to take on the operational leadership of the lab, working closely with the Principal Investigator. You will oversee the lab's research projects across both grants-timelines, milestones, and deliverables-act as the primary contact for collaborating cohorts, clinical partners, and their PIs, manage project budgets, procurement, and reporting to funders, and supervise the lab's technical staff. In this role, you will shape how the group operates and grows, and serve as a central point of contact for the team and its partners.

Alongside these responsibilities, you will remain scientifically active: contributing to the lab's research projects, coordinating and co-authoring manuscripts, and representing the lab at conferences. You will be part of a collaborative research environment with close interactions with the Basel Research Centre for Child Health (BRCCH), the University Children's Hospital Basel (UKBB), and the Swiss Tropical and Public Health Institute (Swiss TPH).

In line with our and Uni Basel values (https://www.unibas.ch/en/Research/Values-Ethics/Diversity-and-Inclusion.html), we are committed to sustain and promote an inclusive culture, ensure equal opportunities and value diversity and respect in our working and learning environment.

Your main tasks will include:

• Overseeing the lab's research projects: managing timelines, milestones, and deliverables across the ERC and SNSF grants, and preparing scientific and financial reports to the funders
• Managing project budgets, procurement, and contracts, including subcontracting and service agreements, in collaboration with the department's administration
• Coordinating collaborations with partner cohorts, clinical partners, and their PIs: organizing consortium meetings and site visits, and maintaining a regular flow of information between Basel and the partner sites
• Overseeing data- and material-transfer agreements, ethics approvals, and compliance with data-governance requirements, in collaboration with the lab's data manager / bioinformatics technician and the legal and research offices of the University of Basel
• Supervising the lab's data manager / bioinformatics technician and overseeing the pipeline that delivers analysis-ready datasets to the modeling team
• Contributing to the lab's research projects, and coordinating and co-authoring manuscripts across the team and partners
• Contributing to teaching and to the supervision of PhD and master's students
• Representing the lab at scientific conferences and supporting follow-up grant applications

Essential:

• PhD in computational biology, bioinformatics, epidemiology, or a related quantitative field, with postdoctoral experience
• Experience working in collaborative, multi-partner research projects, ideally involving clinical or cohort data
• Strong organizational skills and a track record of bringing research projects and publications to completion
• Proficiency in scientific programming (e.g., R or Python) and experience with the analysis of biomedical data
• Excellent written and spoken English, and the ability to communicate effectively with scientists, clinicians, and administrative partners

Desirable:

• Experience with data-transfer agreements, ethics applications, or data-protection processes
• Experience with project budgets, contracts, or reporting to funders
• Familiarity with microbiome, immunological, or multi-omics data, and / or with cohort studies
• Experience supervising technical or scientific staff
• Knowledge of German is an asset but not required
• A central role in expanding a research group funded by two major starting grants, with a five-year contract and the possibility of extension
• A scientifically active position with co-authorship on publications and support for conference participation
• A stimulating, interdisciplinary environment at the intersection of computational science and pediatric health, embedded in Basel's life-sciences ecosystem
• Close collaboration with clinical, epidemiological, and experimental partners across multiple continents
• A dynamic and supportive team culture that values diversity and inclusion
• Salary and social benefits according to the regulations of the University of Basel

Key References

• Tepekule, A.I. Lim, and C.J.E. Metcalf, "The ontogeny of immune tolerance: a model of early-life secretory IgA - gut microbiome interactions", PLoS Biology, 2025.

Link: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003263

• Tepekule, J. Bergadà-Pijuan, T. Scheier, H. F. Günthard, M. Hilthy, R. D. Kouyos, S. Brugger, "Computational and in vitro evaluation of probiotic treatments for nasal Staphylococcus aureus decolonization", Proceedings of the National Academy of Sciences (PNAS), 2025.

Link: https://www.pnas.org/doi/10.1073/pnas.2412742122

• Tepekule, P. Abel Zur Wiesch, R. Kouyos, S. Bonhoeffer, "Quantifying the impact of treatment history on plasmid-mediated resistance evolution in human gut microbiota", Proceedings of the National Academy of Sciences (PNAS), 2019.

Link: https://www.pnas.org/content/116/46/23106

Application / Contact

The position is available from June 1, 2027, or later by mutual agreement. The contract is initially limited to five years, with the possibility of extension thereafter. Review of applications will begin immediately and continue until the position is filled. Please submit your application via the University of Basel Recruiting-Portal, by submitting the following documents: (A) a cover letter describing your motivation and your experience, (B) a complete curriculum vitae including a list of publications, (C) contact details of at least two references willing to provide recommendation letters upon request.

For informal inquiries about the position, please contact Prof. Dr. Burcu Tepekule (burcu.tepekule@unibas.ch).

The University of Basel is an equal opportunity and family-friendly employer committed to excellence through diversity.ard to receipt of your complete online application.