School of Biological Sciences
Faculty of Sciences
Eligible to supervise Masters and PhD (as Co-Supervisor) - 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 applying 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 improve population genomics inferences.
Date Position Institution name 2016 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
Awards and Achievements
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 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.
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.
2020 Roca-Rada, X., Souilmi, Y., Teixeira, J. C., & Llamas, B. (2020). Ancient DNA studies in pre-Columbian Mesoamerica. Genes, 11(11), 1-19.
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.
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.
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.
DOI Scopus4 WoS4 Europe PMC1
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.
DOI Europe PMC1
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.
DOI Scopus6 WoS7 Europe PMC6
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.
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.
DOI Scopus7 WoS3 Europe PMC1
2015 Souilmi, Y., Allali, I., Badad, O., & Dwibedi, C. K. (2015). Highlights of the first ISCB Student Council Symposium in Africa 2015. F1000Research, 4, 569.
DOI Scopus3 Europe PMC4
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.
DOI Scopus12 WoS11 Europe PMC10
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.
DOI Scopus14 WoS14 Europe PMC9
— Tobler, R., Johar, A., Huber, C., & Souilmi, Y. (n.d.). PolyLinkR: A linkage-sensitive gene set enrichment R package. — Souilmi, Y., Lauterbur, M. E., Tobler, R., Huber, C. D., Johar, A. S., & Enard, D. (n.d.). An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia.
Year Citation 2015 Souilmi, Y., Jung, J. -Y., Lancaster, A., Gafni, E., Amzazi, S., Ghazal, H., . . . Tonellato, P. (2015). COSMOS: cloud enabled NGS analysis. Poster session presented at the meeting of BMC BIOINFORMATICS. Boston, MA: BIOMED CENTRAL LTD.
DOI WoS1 Europe PMC1
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.
Current Higher Degree by Research Supervision (University of Adelaide)
Date Role Research Topic Program Degree Type Student Load Student Name 2019 Co-Supervisor Genetic History of Pre-Columbian Mesoamerica Doctor of Philosophy Doctorate Full Time Mr Xavier Roca Rada 2019 Co-Supervisor Using Genomes to Unravel the Demographic and Evolutionary History of First Peoples of Sahul Master of Philosophy Master Full Time Mr Divon Mordechai Lan 2018 Co-Supervisor Using Pangenome-Graph to improve multiple population genetics inferences Doctor of Philosophy Doctorate Full Time Mr Adrien Oliva 2017 Co-Supervisor Paleo Population Genetic History of Australia and the Near East Doctor of Philosophy Doctorate Full Time Mr Matthew Williams
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