Post-doctoral Researcher in Global Genomic Surveillance Infrastructure 80

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.

Are you excited by the idea of building global infrastructure to make pathogen sequencing more accessible, interpretable, and equitable? This post-doctoral 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

**Your position**
- Design and deployment of privacy-conscious, locally-hosted genomic data infrastructures using Loculus
- Extending Loculus to link seamlessly with the ARTIC2 sequencing pipeline for local storage, as well as enabling easy 'one-button' upload of viral sequence data to Pathoplexus
- Integration of analytical pipelines into Cephalopod, the offline research engine at the heart of ARTIC2
- Development of research outputs (talks, papers, tools) demonstrating the real-world utility of modular data platforms for outbreak response and routine surveillance

Potential additional Research directions include:

- Evaluating how decentralized data sharing and analysis affects outbreak detection speed and data completeness
- Identifying the software needs of different research communities involved in sequence sharing in different settings
- Analyses of submission behaviour, metadata completeness, or global inequities in data availability using Pathoplexus datasets

**Your profile**
- PhD in bioinformatics, computer science, data science, public health, or a related field (must be awarded before starting)
- Strong skills in Python, Java, Kotlin, and/or other relevant languages; knowledge of or willingness to learn the languages used in Loculus (Typescript, Kotlin)
- Interest or experience in genomic data, open science infrastructure, or viral evolution
- Self-motivated and comfortable working across interdisciplinary and international teams
- Experience with web-based data tools, GitHub-based development, or federated systems is a plus
- Excellent communication and interpersonal skills, with the ability to engage and collaborate effectively with stakeholders from diverse backgrounds
- Desired: Experience working with databases and data storage and access

**We offer you**
- Opportunities to generate publications, conference presentations, and/or community-facing tools. There is freedom to tailor these directions based on your interests and background, within the larger project.
- Meaningful work with real-world impact on the accessibility and ease of sequencing and data sharing
- A state-of-the-art workplace in our new building with its own canteen on the dynamic BaseLink site in Allschwil
- A diverse institute with people from a wide variety of backgrounds
- Being part of a world-leading team developing open-source public health software, with close links to other renowned research groups in the Basel area
- Attractive employment conditions, versatile further education opportunities and mentoring

**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

**Application / Contact**
- CV, including publication list
- Motivational letter, including your background & experience, and what you envision you could bring to the project
- Degrees achieved

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