PhD position in ancient pathogen genomics Full-time

PhD Position In Ancient Pathogen Genomics

The Max Planck Institute for Evolutionary Anthropology (MPI EVA) brings together scientists from diverse backgrounds (natural sciences and humanities) with the aim of investigating the history of humankind from an interdisciplinary perspective using comparative analyses of genes, cultures, cognitive abilities, languages and social systems of past and present human populations, as well as those of primates closely related to humans.

The Max Planck Institute for Evolutionary Anthropology (MPI-EVA) in Leipzig, Germany, is a world-leading research institute that brings together scientists from a wide range of disciplines to gain new insights into the history, diversity and capabilities of the human species. The Department of Archaeogenetics, led by Johannes Krause, utilizes the recent advances in molecular approaches on biomolecules, such as genome-wide DNA sequencing, to uncover an entirely new spectrum of information that can be retrieved from sample repositories such as anthropological and archaeological collections. We are offering a

PhD Position (M/F/D) In Ancient Pathogen Genomics Starting Ideally In August 2026, Full-Time (39 H/Week)

The frequency of infectious disease emergence has increased over the last few decades, a phenomenon attributed to modern global sociodemographic and environmental changes. However, major transformations of human mobility, lifestyles and technologies associated with large-scale repercussions on the planet's ecosystems have occurred since prehistory. Recent advances in the field of paleogenetics have opened promising perspectives to measure the impact of these past dynamics on the epidemiology and evolution of pathogens by allowing the identification and genomic characterization of various disease-causing agents from archaeological remains. The ERC-StG EpidemioCene project, led by Dr Arthur Kocher, will leverage ancient DNA data generated from massive cohorts of ancient individuals to undertake large-scale paleoepidemiological investigations. In this context, the proposed PhD project will focus on the development of new methods to boost ancient pathogen detection in ancient metagenomic samples. More specifically, this will include a machine-learning algorithm to optimize the identification of pathogen DNA fragments in shotgun sequencing data and a hybridization capture system to enrich samples for a wide range of pathogen species before sequencing. The tools will be applied to a large collection of ancient human samples spanning the past ~12,000 years to uncover the past diversity of infectious diseases and reconstruct ancient pathogen genomes.

Supervision

• Dr Arthur Kocher is the PI of the EpidemioCene project. He studies infectious disease history, ecology and evolution using paleogenetics combined with bioinformatic approaches and Bayesian phylogenomics.
• Dr Alexander Herbig is the leader of the Computational Pathogenomics group at MPI-EVA. He has a strong expertise in the development of bioinformatic tools for ancient pathogen research, including the widely used Heuristic Operation for Pathogen Screening (HOPS) pipeline.
• Dr Megan Michel is a postdoctoral fellow in David Reich's lab at Harvard Medical School. She is an expert in pathogen genomics, with a specific interest in the application of AI algorithms.

Your qualifications

• Completed or close to completing a Master's degree in bioinformatics or related topics
• Previous experience with machine learning or scientific software design would be advantageous
• Strong interest in methodological development
• Strong interest in the study of ancient diseases using paleogenetic data (though previous experience in that regard is not mandatory)
• Proficient English skills and a strong motivation for teamworking in an international context (knowledge of German is not required)

Our offer

• A 3-year doctoral funding contract (65 percent of Pay Group E 13 of the Collective Wage Agreement for the Civil Service, TVöD; ~ €3,100 gross monthly), including social security.
• An exciting PhD position in a world-leading institution in the field of paleogenetics
• Access to state-of-the-art scientific infrastructure
• A collaborative and dynamic research environment
• Integration within the International Max Planck Research School The Leipzig School of Human Origins (IMPRS-LSHO)
• An excellent quality of life in the vibrant and green city of Leipzig
• Family-friendly working conditions and support

Key references

1. Kocher, A., Krause, J. & Spyrou, M. A. Insights into infectious diseases through ancient pathogen genomics. Nat. Rev. Microbiol. 1–15 (2025).
2. Hübler, R. et al. HOPS: automated detection and authentication of pathogen DNA in archaeological remains. Genome Biol. 20, 280 (2019).
3. Kocher, A. et al. A minimal hybridization capture system for the parallel enrichment and cost-effective detection of ancient human pathogens. BioRxiv 2025.06.02.657376.

How to apply

• By email to arthur_kocher@…
• Please send a single PDF document containing a cover letter (2 pages max.), a CV, proof of your most recent degree and up to two reference letters with the names and contact information of the referees
• Application deadline: May 7 2026
• Interviews: end of May 2026

If you have any questions, please feel free to contact Arthur Kocher at arthur_kocher@… The Max Planck Society and the Department of Archaeogenetics at the Max Planck Institute for Evolutionary Anthropology are committed to employing individuals with disabilities and especially encourage them to apply. Additionally, we seek to increase diversity of our workforce in areas where it is underrepresented and therefore explicitly encourage women and members of underrepresented groups to apply.