Research Interests

My research sits at the intersection of medical and evolutionary genomics. I use both modern and ancient DNA to understand past events that have shaped genetic fitness and human health. My work focuses on:

• Conservation Genomics: Working primarily with dingoes, understanding their genomic background using ancient DNA, building detailed admixture maps, modelling the impact of human activity on dingo admixture, and developing methods to improve genetic testing.
• Indigenous Genomics: Working on genomic research with Indigenous populations, with careful attention to ethical considerations and community engagement.
• Palaeo Population Genomics: Applying state-of-the-art population and quantitative genetic techniques to ancient human genomes to build detailed portraits of human genetic adaptation through time.
• Viral-Human Co-evolution: Investigating how ancient viral epidemics have shaped human genetics, including my work on coronavirus-interacting genes more than 20,000 years ago in East Asia.
• Bioinformatics and Computational Methods: Developing reproducible bioinformatics workflows for genomic analysis, particularly for ancient DNA and across heterogeneous computing environments.

Selected Publications

My research has been published in prestigious journals including Science, Current Biology, Nature Ecology & Evolution, NAR, AJHG, and PNAS. A live, complete record is available on my ORCID profile and in Research Outputs.

1. Kidd, J. M., Souilmi, Y. et al. Diploid dual assemblies reveal the telocentric structure and extensive allelic heterogeneity of canine genomes. NAR Genomics and Bioinformatics 8, lqag035 (2026). DOI.
2. Sinniah, E. et al. Conserved facultative heterochromatin identifies disease regulatory sequences. Nucleic Acids Research 53, gkaf971 (2025). DOI.
3. Souilmi, Y. et al. Lessons learned: recommendations for reproducible paleogenomic data analyses. American Journal of Human Genetics (2025). DOI.
4. Roca-Rada, X. et al. Genetic transitions in the Neolithic and Bronze Age at Mas d’en Boixos, Catalonia. iScience 28, 112871 (2025). DOI.
5. Souilmi, Y. et al. Ancient genomes reveal over two thousand years of dingo population structure. Proceedings of the National Academy of Sciences 121, e2407584121 (2024). DOI.
6. Ravishankar, S. et al. Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping. Briefings in Bioinformatics 26, bbae646 (2024). DOI.
7. Tobler, R. et al. The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa. Proceedings of the National Academy of Sciences 120, e2213061120 (2023). DOI.
8. Rogers, N. M. et al. The impact of the cytoplasmic ubiquitin ligase TNFAIP3 gene variation on transcription factor NF-κB activation in acute kidney injury. Kidney International 103, 1105–1119 (2023).
9. Roca-Rada, X. et al. A 1000-year-old case of Klinefelter’s syndrome diagnosed by integrating morphology, osteology, and genetics. The Lancet 400, 691–692 (2022).
10. Souilmi, Y. et al. Admixture has obscured signals of historical hard sweeps in humans. Nature Ecology & Evolution 6, 2003–2015 (2022).
11. Oliva, A., Tobler, R., Cooper, A., Llamas, B. & Souilmi, Y. Systematic benchmark of ancient DNA read mapping. Briefings in Bioinformatics 22, bbab076 (2021). DOI.
12. Lan, D., Tobler, R., Souilmi, Y. & Llamas, B. Genozip: a universal extensible genomic data compressor. Bioinformatics 37, 2225–2230 (2021).
13. Cooper, A. et al. A global environmental crisis 42,000 years ago. Science 371, 811–818 (2021).
14. Souilmi, Y. et al. An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia. Current Biology 31, 3704–3714 (2021).