Two-year Postdoc position in Bioinformatics and Genomic Epidemiology Full-time

Two-Year Postdoc Position in Bioinformatics and Genomic Epidemiology

The Department of Animal and Veterinary Sciences (ANIVET), Aarhus University seeks applications from outstanding and interested candidates for a postdoctoral position in Multiomics, Bioinformatics and Genomic Epidemiology (MBE). The position is full-time, fixed term academic position with an expected start date of 1 October 2026 or shortly thereafter. We are seeking a highly skilled and experienced postdoc at ANIVET who will support the further development of research and educational activities in MBE-related areas applied to farm and companion animals.

The successful candidate will work in two related projects funded by the EU Partnership (EUP) Animal Health & Welfare (EUPAHW). Within the EUPAHW projects (SOA23 and SOA28), the candidate will integrate and analyze epidemiological, clinical and molecular data as well as genomic / metagenome sequence data including WGS datasets from mastitis bacteria and other select pathogens, using advanced bioinformatics pipelines.

Key Responsibilities

• In JIP2-SOA23, standardize the use of analysis tools for the mapping, annotation and analysis of whole genome sequences of hosts (e.g. cattle, pig) and pathogens (e.g. viral or bacterial or parasitic) as well as their metagenomic sequence datasets available within the EUPAHW- JIP2 – SOA23 consortium and/or in public databases with an overall aim of predicting and preventing infectious diseases outbreaks and for population-level surveillance.
• In JIP2-SOA28, identify key antimicrobial resistance (AMR) genes in mastitis pathogens and environmental samples in dairy systems, including their association with mobile genetic elements with the aim of devising a preliminary framework for risk factor analysis related to persistence of AMR, horizontal gene transfer, and dissemination between bacterial populations.
• Apply Artificial Intelligence (AI) methods including deep learning (DL) models and supervised and unsupervised machine learning (ML) methods for integration and for Genome-2-Phenome (G2P) and risk factor analysis.
• Develop robust, shareable bioinformatics pipelines for epidemio-genomic and phylogenomic analyses using genomic & metagenomic datasets and implement them in high performance computing (HPC) or cloud infrastructure.
• In both projects, actively participate in EU level network meetings, collaborate with other projects within the consortia and be responsible for writing, submitting and presenting reports.
• Contribute to project management, conference presentations and journal publications and assist with preparing grant applications to establish new projects in these areas for the team.
• Contribute to BSc and Master's courses.
• Contribute to MSc and PhD students' supervision, as requested and appropriate.

Qualifications

• Applicants must have a PhD in bioinformatics, genomic epidemiology, data science (AI/ML) or similar with a focus on animal health, microbiology and disease control and/or production traits.
• Proven experience in biostatistical and bioinformatic analysis of multiomics datasets with expertise in genomic (SNP genotype or WES/WGS), and metagenomic (16s rRNA and WGS) sequence data and relating them to animal health & disease and/or pathogens transmission / virulence / risk factors.
• Knowledge and prior use of Machine Learning and AI/deep learning for G2P or genomic epidemiology analyses will be considered an asset.
• Experienced user of various QA/QC tools and bioinformatics pipelines for 16s rRNA and WGS sequence data from pathogens.
• Advanced computer programming skills in R and Python and preferably also other languages and demonstrated proficiency in UNIX, shell scripting (Bash) for automation and workflow optimization.

The chosen candidate is expected to join and develop ongoing MBE – related research within the research group Management and Modelling (MAMO).

What We Offer

• A well-developed research infrastructure, laboratories and access to shared Equipment, HPC and animal-experimental facilities
• An informal and multicultural research environment with high professionalism and close collaboration and networking activities
• A workplace characterized by equality and a good work-life balance, and an open dialogue across different fields of research.

Who We Are

Department of Animal and Veterinary Sciences is well-known for its skilled and very innovative interdisciplinary research environments with high international impact. We perform world-class research, which contributes with solutions to solve essential societal challenges within the green transition: food production and veterinary medicine – nationally and globally. The department generates novel research at the highest international level within sustainable food production, environment, climate, and health and welfare for animals and humans. The activities form the basis for the research-based public sector consultancy and degree programs covering bachelor's, master's and PhD degree programs within animal science and veterinary medicine. We offer a lively, engaged and innovative learning and study environment, which is closely integrated in the research environment. ANIVET has unique and advanced animal experimental research facilities and technologies, situated in close connection to the research environment, and a comprehensive national and international research network and good industrial and professional collaboration. Please refer to Department of Animal and Veterinary Sciences (au.dk) for further information about the department.