I am an Assistant Professor at Mersin University, Department of Biotechnology. I use bioinformatics to recover biological signal from fragmented and noisy data.
Most of my work is ancient DNA and ancient metagenomics: reconstructing past microbial communities and past human demography from heavily damaged DNA. I follow that question across several archives:
- Dental calculus records the microbial species and diversity in the human mouth
- Lake and cave sediments record whole landscapes and the organisms that moved through them.
Each is the same problem at a different scale, recovering a community from low-biomass, heavily mixed, chemically degraded DNA.
I also work on systems biology. I analyze RNA-seq data and combine with genome-scale metabolic models to study how microbial metabolism responds to a series of genetic changes.
Selected publications
Full list on ORCID.
Ancient DNA
- Yüncü E, …, Kırdök E, …, Somel M. (2025) Female lineages and changing kinship patterns in Neolithic Çatalhöyük. Science. doi
- Kırdök E, et al. (2024) Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals. Scientific Reports. doi
- Bergfeldt N, Kırdök E, et al. (2024) Identification of microbial pathogens in Neolithic Scandinavian humans. Scientific Reports. doi
- Pochon Z, Bergfeldt N, Kırdök E, et al. (2023) aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow. Genome Biology. doi
- Koptekin D, …, Kırdök E, …, Somel M. (2023) Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean. Current Biology 33(1): 41–57.e15. doi
- Kılınç GM, …, Kırdök E, …, Götherström A. (2021) Human population dynamics and Yersinia pestis in ancient northeast Asia. Science Advances 7(2). doi
- Kashuba N*, Kırdök E*, et al. (2019) Ancient DNA from mastics solidifies connection between material culture and genetics of Mesolithic hunter-gatherers in Scandinavia. Communications Biology 2: 185. doi
Systems biology
- İlter İ, …, Kırdök E, …, Akkaya Ö. (2026) Comparative analysis of precursor supply and pathway reinforcement strategies for shikimic acid biosynthesis in Pseudomonas putida. Microbial Cell Factories. doi
* Equal contribution.
Experience
| Period | Position | Institution |
|---|---|---|
| 2019 – present | Assistant Professor | Mersin University, Dept. of Biotechnology |
| 2019 | Researcher | University of Oslo, Museum of Cultural History |
| 2018 – 2019 | Post-doctoral Researcher | Stockholm University, Archaeological Research Laboratory |
| 2017 | Post-doctoral Researcher | Bordeaux University Bioinformatics Center |
| 2016 – 2018 | Post-doctoral Researcher | İstanbul University, Molecular Biology and Genetics |
| 2013 – 2014 | Guest Researcher | Max Planck Institute for Plant Breeding Research |
| 2009 – 2016 | Research Assistant | Gebze Technical University |
Ph.D. Molecular Biology and Genetics, Gebze Technical University (2010 – 2016) · M.Sc. Biology, Gebze Institute of Technology (2006 – 2010)
Teaching
Courses at Mersin University, maintained openly as GitHub repositories — forks and contributions welcome.
- Data Analysis in Life Sciences (TR) — data analysis and statistical learning, undergraduate and graduate
- Bioinformatics (TR) — undergraduate and advanced graduate bioinformatics, focused on next-generation sequencing
I also taught Ancient Metagenomics at the Evolutionary Genomics summer school (Boğaziçi University, 2023) and co-organized the Evolutionary Genomics summer school at Mersin University in 2022, supported by TÜBİTAK 2237-A.
Talks
- What do ancient human microbes tell us? — 16th Aykut Kence Evolution Congress, 2022. For a general audience, in Turkish. video
- Ancient metagenomics and ancient pathogens — Palaeogenomics and Human Prehistory course, Centre for Palaeogenetics, Stockholm University, 2020
Grants
- Investigating the potential of lake sedimentary ancient DNA to understand Anatolia’s human and ecosystem history: a paleogenetic study of Lake Gölhisar — TÜBİTAK 1001 (principal investigator)
- Metagenomic investigation of the people who lived in thirteenth-century İznik: oral microbiota, opportunistic pathogens, and dietary habits — TÜBİTAK 1001 (principal investigator)
- An experimental investigation of burial traditions: human skeletal microbiome project — TÜBİTAK 1002 (principal investigator)
- Metabolic engineering of Pseudomonas putida for enhanced production of the antiviral precursor shikimic acid — TÜBİTAK 1001, 120Z407 (researcher)
- The metagenomic story of the Mary Rose and Kronan warships — Mersin University BAP, 2019-3-AP-3729 (principal investigator)