Postdoctoral position in functional ancient microbial ecogenomics within the Ancient Environmental Genomics Initiative for Sustainability (AEGIS) Part-time NEW

Postdoctoral Positions in Functional Ancient Microbial Ecology

The Ancient Environmental Genomics Initiative for Sustainability (AEGIS) invites applications for three two-year postdoctoral positions in functional ancient microbial ecology, starting 1 November 2026, or as soon as possible thereafter. We seek one researcher in each of three areas: computational ancient metabolomics and natural products, carbohydrate-active enzymes and carbohydrate metabolism, and protein language models for ancient metagenomics.

AEGIS is a pioneering research centre headed by Prof. Eske Willerslev that brings together a highly interdisciplinary and international team of world-leading research groups with a shared vision of developing more robust, sustainable, and biodiverse crops and agricultural practices to mitigate the effects of climate change on global food production.

AEGIS combines ancient environmental DNA, genomics, metagenomics, informatics and biostatistics, evolutionary biology, ecology, geology, archaeology, plant engineering, and agricultural crop research. We will collect and work on geological sediments, bones, fossils, and material from contemporary species from more than 200 locations worldwide to generate and analyse vast amounts of ancient and contemporary environmental DNA and other ancient and modern biomolecular data, along with associated contextual data.

The advertised positions are within the Microbial EcoGenomics Group at the Center for Ancient Environmental Genomics. The group leverages ancient DNA (aDNA) to reconstruct past microbial ecosystems, understand long-term biodiversity dynamics, and innovate computational methods for analysing ancient microbial data.

We value diversity and inclusivity in our research community. We actively encourage applications from individuals of all backgrounds, identities, and experiences who share our commitment to addressing global environmental challenges through innovative research.

As a postdoctoral researcher, you will analyse large-scale ancient environmental DNA (aeDNA) datasets generated through high-throughput sequencing technologies. You will investigate how the functional potential of microbial communities has changed across time and space. The aim is to understand which microorganisms were present in past ecosystems, what functions they could perform, and how these functions changed through time. The three positions will address this by studying carbohydrate-active enzymes, biosynthetic gene clusters and natural products, and developing protein language models for functional annotation of ancient metagenomes.

Together, these areas will help us investigate how past microbial communities used organic matter and produced compounds involved in interactions among microorganisms, plants and their environments. Work on ancient metabolomics and natural products will focus on computational analysis of biosynthetic genes and pathways, with analysis of metabolomics datasets where available. Work on carbohydrate metabolism will examine CAZymes and associated pathways in ancient and modern metagenomes. Protein language models will be used to predict the functions of proteins recovered from ancient DNA, including incomplete and poorly characterised sequences, and support these analyses.

Your responsibilities will include developing computational and statistical methods to study microbial functions in ancient metagenomic data. You will work with the other postdoctoral researchers and colleagues across AEGIS to evaluate functional predictions and interpret them in an ecological and evolutionary context.

We are looking for three scientists with experience in ancient metagenomics and expertise relevant to one of the three research areas. Applicants are not expected to have expertise in all three areas.

Essential experience and skills:

• You have a PhD in bioinformatics, genomics, community ecology, computational biology, computational metabolomics or a related field.
• You have experience analysing large-scale ancient metagenomic datasets.
• You have experience investigating microbial genes, metabolic pathways, functional traits or community-level processes in an ecological or evolutionary context.
• You have experience with ancient or degraded DNA analysis, including authentication and the analysis of low-abundance and fragmented sequence data.
• For the protein language model position, you have experience implementing and evaluating machine learning models for protein sequences.
• Strong analytical skills and an interest in interdisciplinary research.
• Proficient communication skills and ability to work in teams
• Excellent English skills, written and spoken

Desirable experience and skills:

• Experience with computational metabolomics, natural product bioinformatics or biosynthetic gene cluster analysis; CAZyme annotation or microbial carbohydrate metabolism; or protein language models and protein function prediction, depending on the position applied for.
• Computational skills, including proficiency in R, Python, or other relevant programming languages.
• Experience working with high-performance computing (HPC) environments.
• Strong scientific track record with publications in peer-reviewed international journals as first author in the field of microbial community and/or bioinformatics, genomics, ecological modelling, ancient DNA or similar.
• Experience with startups, entrepreneurship, or innovation, particularly translating academic research and scientific findings into commercially relevant applications, or startup ventures

The place of employment is at the Globe Institute, Section for GeoGenetics (Øster Voldgade 5-7, 1350, Copenhagen), Faculty of Health and Medical Sciences, University of Copenhagen.

The Globe Institute is part of the Faculty of Health and Medical Sciences at the University of Copenhagen. The Institute's main purpose is to address basic scientific questions through interdisciplinary approaches. The institute operates at the intersection of natural and medical sciences and the humanities.

Globe Institute is committed to creating an inclusive and diverse environment where employees and students can belong and thrive. All qualified applicants will receive full consideration. Candidates who, through their research, teaching, and/or service, contribute to diversity and competencies of our Institute are encouraged to apply. The University of Copenhagen strives to offer a family-friendly and flexible working environment with a sustainable balance between work and private life, including parental leave schemes (up to 47 weeks for both parents) and up to six weeks of paid holidays per year. Researchers who have not been tax liable in Denmark for the last 10 years can apply for a special (reduced) tax scheme. The university offers a variety of services for international researchers and accompanying families.

The average weekly working hours are 37 hours per week.

The position is a fixed-term position limited to a period of 2 years. The starting date is on 1 November 2026, or as soon as possible thereafter.

The position is covered by the Memorandum on Job Structure for Academic Staff.

Terms of appointment and payment accord to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State.

There will be an opportunity to negotiate supplements based on qualifications. You can read more about salary levels in the state sector www.loenoverblik.dk (in Danish).

For further information, please get in touch with Antonio Fernandez-Guerra : antonio.fernandez-guerra@sund.ku.dk .

Foreign applicants may find this link useful: www.ism.ku.dk (International Staff Mobility).

Submit your online application in English by clicking 'Apply now' below. Furthermore, your application must include the following documents/attachments – all in PDF format:

1. Motivated letter of application (max. one page), stating which research area you are applying for and describing your relevant experience.
2. CV incl. education, work/research experience, language skills and other skills relevant for the position.
3. A certified/signed copy of a) PhD certificate and b) Master of Science certificate. If the PhD is not completed, a written statement from the supervisor will do.
4. List of publications.

Deadline for applications: 27 September 2026, 11.59 pm CET.

We reserve the right not to consider material received after the deadline, and not to consider applications that do not meet the above requirements.

After the deadline expires, the authorised recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor. Once the assessment work is complete, each applicant has the opportunity to comment on the part of the assessment that relates to the applicant.

You can read about the recruitment process at https://employment.ku.dk/faculty/recruitment-process/.

The applicant will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities.

The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background.