Postdoctoral Scientific Collaborator (80-100%)

The Swiss Tropical and Public Health Institute (Swiss TPH) is a world-leading institute in global health with a particular focus on low- and middle-income countries. Associated with the University of Basel, Swiss TPH combines research, education and services at local, national and international levels. 950 people from 95 nations work at Swiss TPH focusing on infectious and non-communicable diseases, environment, society and health as well as health systems and interventions.
The Department of Medical Parasitology and Infection Biology (MPI) investigates the biology and transmission of pathogens. Findings from this research inform the development of new diagnostics, treatments, and vaccines against malaria, tuberculosis, schistosomiasis, Chagas and other neglected tropical diseases.
This position is part of a project investigating how hospital-associated environments and patient compartments contribute to the evolution, persistence, and transmission of antimicrobial resistance (AMR) genes. By applying high-throughput sequencing and integrative data analysis in clinical and environmental settings across hospitals in Guinea-Bissau, Nigeria, and Côte d'Ivoire, the project aims to reconstruct AMR transmission pathways and identify microbial and environmental drivers of resistance hotspots at the patient-environment interface.

Your position
• Design and conduct longitudinal phylogenetic and ecological analyses of microbial communities to identify plausible AMR transmission routes across clinical and environmental reservoirs
• Perform sequencing experiments using short-read (Illumina) and long-read (Nanopore) platforms; implement hybrid metagenomics assembly strategies using high-performance computing infrastructure
• Coordinate/supervise sample collection (clinical and environmental); contribute to the design of the longitudinal sampling strategy and develop SOPs for multi-site harmonization
• Contribute to capacity building through local training workshops with partners in West Africa
• Publish high-impact scientific articles and participate in project reporting and dissemination activities

Your profile
• PhD in microbial ecology, molecular microbiology, microbiome research, or a related field is a must
• Proficiency in bioinformatics or clear motivation and prior exposure; HPC and metagenomics pipeline experience preferred
• Experience with next-generation sequencing; hands-on with Illumina and/or Nanopore and meta-omics is a plus
• Strong organizational skills, attention to lab detail, and ability to work independently
• Willingness to conduct short-term fieldwork in Guinea-Bissau, Nigeria, and Côte d'Ivoire
• Solid publication record for career stage, with recent first-author papers in relevant fields

We offer you
• Meaningful work in an international environment
• Being part of a committed and motivated team with short information and decision paths
• A state-of-the-art workplace in our new headquarters on the dynamic BaseLink site in Allschwil
• Inspiring encounters with people from diverse backgrounds
• Attractive employment conditions, versatile training opportunities and mentoring
Job conditions
• Start Date: as soon as possible
• Duration: 2 years
• Percentage: 80-100%
• Location: Allschwil, Switzerland
• Travel required: Possibly at the beginning of the project (10-20%)
• Internal job title: Postdoctoral Scientific Collaborator