I would like to advertise two PhD positions in ancient
pathogen genomics funded through my ERC project�EpidemioCene
<https://www.eva.mpg.de/press/news/article/reconstructing-the-long-term-dynamics-of-human-infectious-diseases/>.

The overall aim of the project is to better understand the
epidemiological history and the determinants of infectious diseases
since the end of the Last Ice Age. To this end, we will undertake
large-scale paleoepidemiological and phylodynamic analyses of ancient
pathogen genomic data generated from large cohorts of ancient human
individuals. The project is co-hosted by the Department of Archaeogenetics
at the Max Planck Institute for Evolutionary Anthropology in Leipzig,
Germany <https://www.eva.mpg.de/archaeogenetics/index/> (MPI-EVA)
and the Host-Pathogen Interaction Research Unit, Toulouse, France
<https://ihap.fr/en/> (UMR IHAP 1225 UT/INRAE/ENVT). In this context:

- PhD 1 will develop new methods to boost pathogen detection in
ancient metagenomic samples. 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. We are
looking for someone with a background in bioinformatics. Some
experience with machine learning or scientific software design
would be advantageous. See the complete description here
<https://www.eva.mpg.de/career/positions-available/job/680/Abteilung%20Arch%C3%A4ogenetik/en/?cHash=a8bc48c9fa6f3a7ee0baffc24e8af2a5>.

- PhD 2 will analyse ancient viral genomes using phylogenetic
and phylodynamic approaches to trace geographical spread and
transmission dynamics on large timescales. We are looking for someone
with a background in evolutionary biology, epidemiology or related
topics, and a specific interest in molecular epidemiology and viral
evolution. Bioinformatics skills are required, and some experience with
computational phylogenetics would be a plus. See the complete description
here <https://jobs.inrae.fr/en/ot-28863>.

Both positions are aimed at students excited to study the (pre)history
and evolution of pathogens using ancient DNA data, though specific
experience in this regard is not required. Candidates should have
proficient English skills and a strong motivation for teamworking in an
international context. PhD 1 will be based at MPI-EVA, starting ideally
in August 2026. PhD 2 will be based at IHAP, with regular visits to
MPI-EVA, starting ideally in October 2026. German or French skills are
not required.

Interested applicants should send their application via email to
arthur_kocher@eva.mpg.de by May 7th. The application should consist of
a single PDF document containing a cover letter (2 pages max.), a CV,
a proof of your most recent degree and up to two reference letters with
the names and contact information of the referees.

Don't hesitate to contact me at arthur_kocher@eva.mpg.de for further
questions.

Best,

Arthur Kocher 

arthur_kocher@eva.mpg.de

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