Bioinformatiker (m/w/d) in Jena

The Friedrich Schiller University Jena is a dynamic and innovation-driven university centrally located in Germany. With a broad range of disciplines, it shapes the future through excellent research and teaching. Its scientific excellence is reflected in the profile areas Light - Life - Liberty, which provide pioneering insights and sustainable solutions for the society of tomorrow. Through close collaborations with leading research institutions, innovative companies, and renowned cultural organizations, it advances interdisciplinary developments. With around 17,000 students and approximately 10,000 employees, it defines Jena as a vibrant, internationally connected city of science and innovation.

The professorship of Viral Ecology and Omics (VEO) seeks to fill the position of a:

Doctoral Researcher in Bioinformatics:

Quantifying quasispecies: Tool development and applications

commencing on the 1st of January 2027 or as soon as possible thereafter. We offer a part-time position (75%, 30 hours per week) initially offered as a fixed-term position until the 30th of June 2030. A total contract term of four years is planned.

The project aims to develop a graph structure suited to represent viral quasispecies, together with tools to build and analyse them. The resulting toolkit will connect sequence data of different kinds with annotations of genes, functions, and experimental or environmental metadata. This connection between sequence and metadata will allow us to identify mutational hotspots in a virus, link mutations to the functions they modulate, and correlate virus variants with environmental metadata. Applying this tool suite to large sets of public data as well as to experimental data generated for the project will allow us to quantify quasispecies across different environments and to explore the hypothesis that a larger quasispecies is linked to better adaptability.

The Viral Ecology and Omics Group (veo.uni-jena.de) aims to study the role of viruses in the Microverse. To do this, we combine microbiological and eco/evolutionary experiments with molecular biology, microscopy, (meta-) genomics, bioinformatics, artificial intelligence, and computational modelling. Our wet lab manager oversees a level S1/S2 wet lab featuring a state-of-the-art laboratory automation system with a high-throughput automatic plate reader, microscopy, microbiology, and molecular biology facilities. Our dry lab manager supports access to bioinformatics tools and databases on the FSU high-performance compute cluster, which consists of ~100 CPU and 12 GPU nodes, dedicated interactive and visualization nodes, and five high-memory (up to 4TB) nodes with access to global genomic and metagenomic datasets on our 2+ petabyte storage disks.

You will be embedded in the newly founded Collaborative Research Centre VirusREvolution (virusrevolution.uni-jena.de), a multidisciplinary consortium that combines expertise in bioinformatics, virology and photonics to build and apply advanced omics and optical tools for the systematic study of viruses. The CRC offers many opportunities to collaborate with experimental and computational scientists and to do a PhD within a structured graduate programme.

• With your advisors, design and perform analyses to address the research questions.
• Analyse your results in the context of literature and public (meta-) ‘omics data.
• Develop web-integrated visualizations to gain scientific insights from virus -omics datasets.
• Take initiative to communicate and discuss your results with wet- and dry-lab group members.
• Report your findings in publications and presentations at international scientific platforms.
• Support Master's students and undergraduate project students.

• A BSc or MSc in bioinformatics with extensive coding experience (Python, Rust or C/C++).
• Experience with graphs in general, sequence variation graphs, and tool building.
• Specialist knowledge and hands-on expertise in metagenomics, genomics, viruses, or bacte...