Doctoral Researcher in Bioinformatics: Quantifying quasispecies: Tool development and applications

Uni Jena; Jena; On-site; EUR 38,000 - 54,000; Part time

Benefits offered by this job

75% funded position

State-of-the-art equipment

Education and training programs

Job summary

University of Jena invites applications for a Doctoral Researcher in Bioinformatics focusing on quantifying quasispecies: tool development and applications. The role is 75% funded (30 hours/week) with a fixed-term four-year contract, starting Jan 1, 2027 or soon after.

The project will build a graph-based toolkit linking sequence data with genes, functions, and metadata to identify mutational hotspots and correlate variants with environmental data.

Qualifications

• 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.

Responsibilities

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

Skills

Python

Rust

C/C++

Education

BSc or MSc in bioinformatics

Tools

Graphs

Tool building

Job description

Vacancy ID: 268/2026

Closing date: 2026-10-19

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.

Your responsibilities:

• 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

Your profile:

• 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 bacteriophages is beneficial.


• Strong motivation, excellent organisational skills, and ability to contribute to a friendly and collaborative working environment in a cross-disciplinary scientific research group.


• Excellent communication in English is required, both written and spoken. Fluency in German and other languages is advantageous.

We offer:

• A 75% funded position (30 hours per week).


• Embedding in a highly collaborative, cross-disciplinary research group that is world-leading in viral and microbial ecology.


• Excellent equipment and infrastructure for both experimental and computational work.


• Affiliation to the Integrated Research Training Group VirusREvolution, offering a comprehensive education programme to train your hard and soft career skills, supported by the Jena School for Microbial Communication and the Jena Graduate Academy.


• Jena – City of Science: a young and lively town with a vibrant local cultural agenda. Jena is among the most liveable cities in Germany. Situated on the Saale River and surrounded by the famous Thuringian Forest, this city is ideal for lovers of nature and hiking.


• Remuneration based on the provisions of the Collective Agreement for the Public Sector of the Federal States (TV-L) up to salary scale E 13 (depending on the candidate’s personal qualifications), including a special annual payment in accordance with the collective agreement.


• 30 days of vacation per calendar year, plus two days off on December 24 and 31.

Candidates with severe disabilities will be given preference in the case of equal qualifications and suitability.

For further information for applicants and the information on the collection of personal data, please refer to Data privacy and information for applicants.