Research Interests
Bioinformatics Bioinformatics Software Biological Evolutionary Biology Genetics Genomics Medical GeneticsDr Yassine Souilmi
NHMRC Grant-Funded Research Fellow
School of Biological Sciences
College of Science
Eligible to supervise Masters and PhD - email supervisor to discuss availability.
I am a postdoctoral researcher at the Australian Centre for Ancient DNA (ACAD). Prior to joining ACAD, I was trained as a bioinformatics researcher at the Department for Biomedical Informatics (DBMI) at Harvard University. I am a Fulbright alumnus and have played a significant leadership role in coordinating bioinformatics training and networks in Africa.
Currently, I lead an international team of researchers to data-mine the Online Ancient Genome Repository (OAGR)—a comprehensive centralized database containing all known ancient DNA specimens, genomes, and associated metadata. In this project, we use ancient DNA to uncover the genetic signatures of human adaptation to significant environmental, and socio-cultural changes over the last 20,000 years in Eurasia.
In addition, I am leading an effort to improve ancient DNA bioinformatic analyses and apply novel technological methods to address outstanding evolutionary questions. For instance, we are using pan-genome graphs to capture human genomic diversity omitted currently in linear reference genomes, early results using this approach showed major improvement in reducing reference bias, and improving population genomics inferences.
| Date | Position | Institution name |
|---|---|---|
| 2016 - ongoing | ARC Postdoctoral Researcher | University of Adelaide |
| 2014 - 2015 | Research and Teaching Assistant | Harvard University |
| 2014 - 2014 | Teaching Assistant | Harvard University |
| 2013 - 2013 | Adjunct Bioinformatics Instructor | Mohammed V University of Rabat |
| Date | Type | Title | Institution Name | Country | Amount |
|---|---|---|---|---|---|
| 2013 | Scholarship | Fulbright Joint Supervision Doctoral Grant | Harvard University | United States | - |
| Language | Competency |
|---|---|
| Arabic | Can read, write, speak, understand spoken and peer review |
| English | Can read, write, speak, understand spoken and peer review |
| French | Can read, write, speak, understand spoken and peer review |
| Spanish; Castilian | Can read and understand spoken |
| Date | Institution name | Country | Title |
|---|---|---|---|
| 2012 - 2016 | Mohammed V University | Morocco | PhD |
| 2008 - 2011 | Mohammed V University | Morocco | MS |
| 2004 - 2008 | Mohammed V University | Morocco | BS |
| Year | Citation |
|---|---|
| 2025 | Ravishankar, S., Perez, V., Davidson, R., Roca-Rada, X., Lan, D., Souilmi, Y., & Llamas, B. (2025). Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping. Briefings in Bioinformatics, 26(1), bbae646-1-bbae646-12. Scopus3 WoS2 |
| 2025 | Roca-Rada, X., Cuesta-Aguirre, D. R., Vinueza-Espinosa, D. C., Davidson, R., Ravishankar, S., Taufik, L., . . . Santos, C. (2025). Genetic transitions in the Neolithic and Bronze Age at Mas d’en Boixos (Catalonia, Spain). iScience, 28(7), 112871-1-112871-11. Scopus1 WoS1 Europe PMC1 |
| 2025 | Davidson, R., Ravishankar, S., Souilmi, Y., Roca-Rada, X., Sobek, C., Taufik, L., . . . Pérez, V. (2025). The necessity for authentication of ancient DNA from archaeological artefacts. Journal of Archaeological Science, 181, 9 pages. |
| 2025 | Roca-Rada, X., Davidson, R., Williams, M. P., Villalba-Mouco, V., Carvalho, A. F., Ravishankar, S., . . . Teixeira, J. C. (2025). The genetic history of Portugal over the past 5,000 years.. Genome Biology, 26(1), 248-1-248-39. Scopus2 WoS2 Europe PMC1 |
| 2025 | Souilmi, Y., Oliva, A., Davidson, R., Williams, M. P., Ravishankar, S., Roca-Rada, X., . . . Llamas, B. (2025). Lessons learned: Recommendations for reproducible paleogenomic data analyses. American Journal of Human Genetics, 112(12), 2830-2841. |
| 2025 | Sinniah, E., Mizikovsky, D., Shim, W. J., Yeung Chow, C. S., Souilmi, Y., Cheng, F. -F., . . . Palpant, N. J. (2025). Conserved facultative heterochromatin across cell types identify regulatory sequences underpinning cell identity and disease.. Nucleic Acids Res, 53(20), 23 pages. |
| 2024 | Souilmi, Y., Wasef, S., Williams, M. P., Conroy, G., Bar, I., Bover, P., . . . Mitchell, K. J. (2024). Ancient genomes reveal over two thousand years of dingo population structure. Proceedings of the National Academy of Sciences, 121(30), e2407584121-1-e2407584121-12. Scopus7 WoS6 Europe PMC6 |
| 2023 | Rogers, N. M., Zammit, N., Nguyen-Ngo, D., Souilmi, Y., Minhas, N., Meijles, D. N., . . . Grey, S. T. (2023). The impact of the cytoplasmic ubiquitin ligase TNFAIP3 gene variation on transcription factor NF-κB activation in acute kidney injury. Kidney international, 103(6), 1105-1119. Scopus11 WoS12 Europe PMC11 |
| 2023 | Tobler, R., Souilmi, Y., Huber, C. D., Bean, N., Turney, C. S. M., Grey, S. T., & Cooper, A. (2023). The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa.. Proc Natl Acad Sci U S A, 120(22), e2213061120. Scopus17 WoS13 Europe PMC12 |
| 2022 | Lan, D., Purnomo, G., Tobler, R., Souilmi, Y., & Llamas, B. (2022). Genozip Dual-Coordinate VCF format enables efficient genomic analyses and alleviates liftover limitations. |
| 2022 | Roca-Rada, X., Tereso, S., Rohrlach, A. B., Brito, A., Williams, M. P., Umbelino, C., . . . Teixeira, J. C. (2022). A 1000-year-old case of Klinefelter's syndrome diagnosed by integrating morphology, osteology, and genetics.. Lancet (London, England), 400(10353), 691-692. Scopus12 WoS10 Europe PMC5 |
| 2022 | Souilmi, Y., Tobler, R., Johar, A., Williams, M., Grey, S. T., Schmidt, J., . . . Huber, C. D. (2022). Admixture has obscured signals of historical hard sweeps in humans. Nature Ecology & Evolution, 6(12), 2003-2015. Scopus18 WoS18 Europe PMC26 |
| 2021 | Oliva, A., Tobler, R., Cooper, A., Llamas, B., & Souilmi, Y. (2021). Systematic benchmark of ancient DNA read mapping. Briefings in bioinformatics, 22(5), 1-12. Scopus30 WoS27 Europe PMC29 |
| 2021 | Roca-Rada, X., Politis, G., Messineo, P. G., Scheifler, N., Scabuzzo, C., Gonzalez, M., . . . Fehren-Schmitz, L. (2021). Ancient mitochondrial genomes from the Argentinian Pampas inform the early peopling of the Southern Cone of South America. iScience, 24(6), 1-18. Scopus20 WoS21 Europe PMC9 |
| 2021 | Souilmi, Y., Lauterbur, M. E., Tobler, R., Huber, C. D., Johar, A. S., Moradi, S. V., . . . Enard, D. (2021). An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia. Current Biology, 31(16), 3504-3514. Scopus61 WoS61 Europe PMC54 |
| 2021 | Oliva, A., Tobler, R., Llamas, B., & Souilmi, Y. (2021). BWA-mem is not the best aligner for ancient DNA short reads. Europe PMC1 |
| 2021 | Souilmi, Y., Lauterbur, M. E., Tobler, R., Huber, C. D., Johar, A. S., Moradi, S. V., . . . Enard, D. (2021). An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia.. Curr Biol, 31(16), 3704. Scopus5 WoS2 Europe PMC10 |
| 2021 | Tobler, R., Souilmi, Y., Huber, C., Bean, N., Turney, C., Cooper, A., & Grey, S. (2021). Genetic and climatic factors in the dispersal of Anatomically Modern Humans Out of Africa. |
| 2021 | Cooper, A., Turney, C. S. M., Palmer, J., Hogg, A., McGlone, M., Wilmshurst, J., . . . Zech, R. (2021). Response to Comment on "A global environmental crisis 42,000 years ago". Science New York N Y, 374(6570), eabi9756. Scopus2 WoS2 Europe PMC2 |
| 2021 | Cooper, A., Turney, C. S. M., Palmer, J., Hogg, A., McGlone, M., Wilmshurst, J., . . . Zech, R. (2021). Response to comment on “A global environmental crisis 42,000 years ago”. Science, 374(6570), 3 pages. Scopus1 |
| 2021 | Oliva, A., Tobler, R., Llamas, B., & Souilmi, Y. (2021). Additional evaluations show that specific BWA‐aln settings still outperform BWA‐mem for ancient DNA data alignment. Ecology and Evolution, 11(24), 18743-18748. Scopus16 WoS14 Europe PMC16 |
| 2021 | Cooper, A., Turney, C. S. M., Palmer, J., Hogg, A., McGlone, M., Wilmshurst, J., . . . Zech, R. (2021). A global environmental crisis 42,000 years ago. Science in China Series C: Life Sciences, 371(6531), 811-818. Scopus88 WoS81 Europe PMC23 |
| 2021 | Lan, D., Tobler, R., Souilmi, Y., & Llamas, B. (2021). Genozip - a universal extensible genomic data compressor. Bioinformatics, 37(16), 2225-2230. Scopus33 WoS27 Europe PMC24 |
| 2020 | Tobler, R., Johar, A., Huber, C., & Souilmi, Y. (2020). PolyLinkR: A linkage-sensitive gene set enrichment R package. |
| 2020 | Lan, D., Tobler, R., Souilmi, Y., & Llamas, B. (2020). genozip: a fast and efficient compression tool for VCF files. Bioinformatics, 36(13), 4091-4092. Scopus12 WoS10 Europe PMC11 |
| 2020 | Souilmi, Y., Tobler, R., Johar, A., Williams, M., Grey, S., Schmidt, J., . . . Cooper, A. (2020). Ancient human genomes reveal a hidden history of strong selection in Eurasia. Europe PMC1 |
| 2020 | Easteal, S., Arkell, R. M., Balboa, R. F., Bellingham, S. A., Brown, A. D., Calma, T., . . . Baynam, G. (2020). Equitable expanded carrier screening needs indigenous clinical and population genomic data. American Journal of Human Genetics, 107(2), 175-182. Scopus29 WoS26 Europe PMC23 |
| 2020 | Roca-Rada, X., Souilmi, Y., Teixeira, J. C., & Llamas, B. (2020). Ancient DNA studies in pre-Columbian Mesoamerica. Genes, 11(11), 1-19. Scopus8 WoS7 Europe PMC5 |
| 2020 | Souilmi, Y., Lauterbur, E., Tobler, R., Huber, C., Johar, A., & Enard, D. (2020). An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia. Europe PMC2 |
| 2019 | Jackson, S. M., Fleming, P. J. S., Eldridge, M. D. B., Ingleby, S., Flannery, T., Johnson, R. N., . . . Helgen, K. M. (2019). The Dogma of Dingoes—Taxonomic status of the dingo: A reply to Smith et al.. Zootaxa, 4564(1), 198-212. Scopus42 WoS37 Europe PMC16 |
| 2019 | Llamas, B., Narzisi, G., Schneider, V., Audano, P., Biederstedt, E., Blauvelt, L., . . . Busby, B. (2019). A strategy for building and using a human reference pangenome. F1000Research, 8, 1751. Scopus3 Europe PMC8 |
| 2019 | Llamas, B., Narzisi, G., Schneider, V., Audano, P., Biederstedt, E., Blauvelt, L., . . . Busby, B. (2019). A strategy for building and using a human reference pangenome. F1000research, 8, 1751. Scopus11 Europe PMC1 |
| 2019 | Ahmed, A., Mpangase, P., Panji, S., Baichoo, S., Souilmi, Y., Fadlelmola, F., . . . Mulder, N. (2019). Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience. AAS Open Res, 1, 9. |
| 2018 | Ahmed, A., Mpangase, P., Panji, S., Baichoo, S., Souilmi, Y., Fadlelmola, F., . . . Mulder, N. (2018). Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience. |
| 2018 | Baichoo, S., Souilmi, Y., Panji, S., Botha, G., Meintjes, A., Hazelhurst, S., . . . Mulder, N. (2018). Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics. BMC Bioinformatics, 19(1), 457-1-457-13. Scopus30 WoS29 Europe PMC29 |
| 2018 | Ahmed, A. E., Mpangase, P. T., Panji, S., Baichoo, S., Souilmi, Y., Fadlelmola, F. M., . . . Mulder, N. (2018). Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience.. AAS open research, 1, 9. Europe PMC11 |
| 2017 | Elshazly, H., Souilmi, Y., Tonellato, P., Wall, D., & Abouelhoda, M. (2017). MC-GenomeKey: A multicloud system for the detection and annotation of genomic variants. BMC Bioinformatics, 18(1), 1-14. Scopus12 WoS11 Europe PMC5 |
| 2015 | Souilmi, Y., Allali, I., Badad, O., & Dwibedi, C. K. (2015). Highlights of the first ISCB Student Council Symposium in Africa 2015. F1000Research, 4, ISCB Comm J-569. Scopus5 Europe PMC10 |
| 2015 | Souilmi, Y., Jung, J. -Y., Lancaster, A., Gafni, E., Amzazi, S., Ghazal, H., . . . Tonellato, P. (2015). COSMOS: cloud enabled NGS analysis. BMC BIOINFORMATICS, 16(Suppl 2), 1 page. WoS1 Europe PMC1 |
| 2015 | Souilmi, Y., Lancaster, A., Jung, J., Rizzo, E., Hawkins, J., Powles, R., . . . Wall, D. (2015). Scalable and cost-effective NGS genotyping in the cloud. BMC Medical Genomics, 8(1), 64-1-64-9. Scopus19 WoS18 Europe PMC17 |
| 2014 | Gafni, E., Luquette, L. J., Lancaster, A. K., Hawkins, J. B., Jung, J. Y., Souilmi, Y., . . . Tonellato, P. J. (2014). COSMOS: Python library for massively parallel workflows. Bioinformatics Oxford England, 30(20), 2956-2958. Scopus17 WoS14 Europe PMC12 |
| - | Souilmi, Y. (n.d.). Supplemental data for: Ancient Genomes Reveal Over Two Thousand Years Of Dingo Population Structure. |
| Year | Citation |
|---|---|
| 2024 | Deshpande, A., Rogers, N., Grey, S., Souilmi, Y., & Li, J. (2024). INVESTIGATING THE ROLE OF TNFAIP3 VARIATION IN KIDNEY DISEASE. In NEPHROLOGY Vol. 29 (pp. 11). WILEY. |
| Year | Citation |
|---|---|
| 2021 | Souilmi, Y., Lauterbur, E., Tobler, R., Huber, C., Johar, A. S., & Enard, D. (2021). An ancient coronavirus-like epidemic 25,000 years in ancestral populations from East Asia. Poster session presented at the meeting of AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY. WILEY. |
| Year | Citation |
|---|---|
| 2024 | Roca-Rada, X., Davidson, R., Williams, M., Ravishankar, S., Collen, E., Haarkötter, C., . . . Teixeira, J. (2024). The genetic history of Portugal over the past 5,000 years. DOI |
I have an extensive bioinformatics teaching experience, having participated in teaching activities at the University of Mohamed the Vth and at Harvard University (BMI 714) where I designed, taught and graded bioinformatics practicums between 2014 and 2016. Furthermore, I have trained, organised and ran over 25 different bioinformatics workshops in Africa, the United States, and Australia covering a wide range of basic to advanced topics.
| Date | Role | Research Topic | Program | Degree Type | Student Load | Student Name |
|---|---|---|---|---|---|---|
| 2025 | Principal Supervisor | A Study of Ancient Pandemics in Human History Based on Virus Interacting Protein Genes | Master of Philosophy | Master | Full Time | Ms Huize Gao |
| 2024 | Co-Supervisor | Genomic time travel: Unravelling the evolutionary history of fauna using paleogenomics | Doctor of Philosophy | Doctorate | Full Time | Mr Shyamsundar Ravishankar |
| Date | Role | Research Topic | Program | Degree Type | Student Load | Student Name |
|---|---|---|---|---|---|---|
| 2021 - 2022 | Co-Supervisor | Advances in Genomic Data Compression | Doctor of Philosophy | Doctorate | Full Time | Mr Divon Mordechai Lan |
| 2019 - 2022 | Co-Supervisor | Human demographic insights from paleogenetic studies of American and Iberian skeletal remains | Doctor of Philosophy | Doctorate | Full Time | Mr Xavier Roca Rada |
| 2018 - 2022 | Co-Supervisor | Quantifying and Reducing Biases in Paleogenomic Research | Doctor of Philosophy | Doctorate | Full Time | Mr Adrien Oliva |
| 2017 - 2022 | Co-Supervisor | Exploring the Genetic History of the Ancient Near East through the Bronze and Iron Ages |
Doctor of Philosophy | Doctorate | Full Time | Mr Matthew Peter Williams |
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