Software Engineer – Open Source Pathogen Data Platforms (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.

For the Epidemiology & Virus Evolution (EVE) group at Swiss TPH, we are seeking a

Software Engineer – Open Source Pathogen Data Platforms (80 – 100%)

to help shape the tools that underpin pathogen data generation and sharing in the 21st century. You will help expand Loculus, the software infrastructure powering Pathoplexus, and contribute to the ARTIC2 global surveillance toolkit.

Are you excited by the idea of building global infrastructure to make pathogen sequencing more accessible, interpretable, and equitable? This software developer position offers a unique opportunity to work at the intersection of two world-leading efforts:

• ARTIC2, the latest evolution of the renowned ARTIC project, enabling affordable, portable, and real-time genetic sequencing in low-resource settings
• Pathoplexus, a pioneering open-source platform redefining how viral sequence data is shared and governed globally, powered by the modular, federated backend database software Loculus

Fast and open sharing of pathogen genome data is critical to understand transmission and develop diagnostics and treatment. Loculus and Pathoplexus are part of a key effort to make such data sharing easier and more equitable. In this position, you’ll be part of an international team of scientists and developers working together to create real-world impact via programs and tools used by public health labs, outbreak responders, and researchers around the world. You will be embedded in the EVE group, led by renowned scientist Emma Hodcroft, named by Nature magazine as one of three 'Ones to Watch' in 2025, and lauded for her work on Enteroviruses, SARS-CoV-2, and open-source software.

How to apply:

Please submit your application online.

• CV
• Motivational letter, including your background and experience, any GitHub links or portfolio, and what you envision you could bring to the project
• Names and contact information (email) of 2-3 references
• Degrees and/or certifications achieved

Closing date for applications is 31 August 2025, but applications will be considered as soon as submitted.

We are proud to build inclusive and purpose-driven technology – applicants from all backgrounds are encouraged. Together, we can make the world a healthier place. We look forward to receiving your application.

Please note that we can only accept applications via our online recruiting tool. As long as the position is online on our company website, we are open for new applications. Applications via e-mail or external recruiter will not be considered.

Life in Basel/Allschwil/Switzerland:

Quality of life in Switzerland is consistently ranked as one of the highest in the world. Switzerland is a safe, stable country with relatively high pay, a temperate climate, and beautiful and accessible nature and mountains.

The Basel area is truly international, with many foreign national residents due to the universities and pharmaceutical industry. It boasts an international airport, almost 40 museums, numerous festivals (including the internationally-renowned Art Basel), and a river clean enough to swim right through town in (and we do!). The Basel area is nestled next-door to both France and Germany, further expanding its international feel and the opportunity for international exploration with a few minutes’ travel. The city and area are bike-friendly and offer excellent short- and long-range public transport.

Contact:

Please email to E-Mail schreiben for informal questions.