Software engineer; viral and bacterial sequence database

Software engineer (viral and bacterial sequence database) 100%, Basel, fixed-term

The Computational Evolution Group
, led by Prof. Dr. Tanja Stadler, in the Department of Biosystems Science and Engineering (D-BSSE) at ETH Zürich works at the interface of mathematics, computer science, and evolutionary biology. We develop methods to understand evolutionary, ecological, epidemiological, and developmental processes on different scales based on genetic data.

In our projects, we transfer cutting‑edge science to production‑ready software. Specifically, we develop genomic database, web applications, and APIs to facilitate real‑time monitoring of pathogen variants and answer epidemiological questions. Hereby, we collaborate closely with public health agencies and scientists around the globe.

We are recruiting a Junior
Software Engineer to join our interdisciplinary team. The position is fixed‑term for one year and starts in June 2026.

The projects are rooted in the SARS‑CoV‑2 pandemic. In response to the rapidly growing number of available genome sequences and the urgent need to track emerging variants of concern, we developed software to facilitate the detection and tracking of new variants and support management and sharing of pathogen sequencing data.

Our projects initially focused on virus data. This database system is written in Type Script, React, Kotlin and Python and part of the position is to extend this system. The other part of this position is to develop a novel database system for bacterial pangenome data based on a prototype developed in a research project. The backend of the prototype is written in Python (with some C++ bindings), and the frontend is written in Type Script and React.

We work closely with other research groups in Basel and other countries as well as with public health agencies, including the Federal Office of Public Health (FOPH) of Switzerland and the Centers for Disease Control and Prevention (CDC) of the United States.

We value good software engineering practices. We perform code reviews, have automated testing pipelines, and do our best to write modern, clean, and maintainable code. We also work in an agile fashion and are always open to suggestions to improve teamwork.

• You will work alongside other software engineers and research scientists from our group and collaborators.
• You will extend an existing database system for viral sequencing data.
• Based on an existing research prototype, you will design, implement, and test a new scalable database system for bacterial pangenome data.
• You will interact with other users and scientists to identify and refine needs and requirements.

We are looking for a motivated colleague with an interest in learning and contributing to public health and genomic epidemiology. The position requires:

• Experience with bacterial bioinformatics, specifically work with pangenome data (relevant publications are beneficial).
• Strong skills with Python. Experience with tools such as mypy, black, and ruff is beneficial.
• Experience with web development, ideally with Type Script and React.
• Experience with developing database engines and knowledge of core database properties and how they can be implemented. C++ experience is highly beneficial.
• Experience with phylogenetics and (Bayesian) phylodynamics.
• A Master degree in computer science, bioinformatics, or a related field.
• Interest in working with an interdisciplinary and international team. We value an open and inclusive group culture and you will be expected to help us maintain a positive team dynamic and a welcoming work environment.
• The working language in our group is English and no knowledge of German is required.

We are open to candidates from all experience level. In line with our commitment to an open and inclusive group culture, we welcome applications from individuals of all demographic groups and personal backgrounds.

• We offer a dynamic and supportive working environment with flexible working hours.
• We offer a very exciting project with direct contributions to public health.
• We value personal growth and career development opportunities and will support you with…