Yassine Souilmi

Dr Yassine Souilmi

ARC Postdoctoral Research Associate

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.

 

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  • Appointments

    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 Competencies

    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, speak and understand spoken
  • Education

    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
  • Research Interests

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  • Journals

    Year Citation
    2018 Ahmed, A., Mpangase, P., Panji, S., Baichoo, S., Botha, G., Fadlelmola, F., . . . Mulder, N. (2018). Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience. AAS Open Research, 1, 9.
    DOI
    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), 13 pages.
    DOI
    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 Scopus5 WoS2 Europe PMC1
    2015 Souilmi, Y., Allali, I., Badad, O., & Dwibedi, C. (2015). Highlights of the first ISCB Student Council Symposium in Africa 2015. F1000Research, 4.
    DOI Scopus1 Europe PMC2
    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 Scopus11 WoS11 Europe PMC11
    2014 Gafni, E., Luquette, L., Lancaster, A., Hawkins, J., Jung, J., Souilmi, Y., . . . Tonellato, P. (2014). COSMOS: Python library for massively parallel workflows. Bioinformatics (Oxford, England), 30(20), 2956-2958.
    DOI Scopus10 WoS11 Europe PMC7
  • Conference Items

    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. 

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  • Current Higher Degree by Research Supervision (University of Adelaide)

    Date Role Research Topic Program Degree Type Student Load Student Name
    2018 Co-Supervisor Using Pangenome-Graph to improve multiple population genetics inferences Doctor of Philosophy Doctorate Full Time Mr Adrien Oliva
    2018 Co-Supervisor Genomic Adaptation in Indigenous Populations of Sahul and Island Southeast Asia Master of Philosophy Master Full Time Miss Gina Lucille Guzzo
    2017 Co-Supervisor Paleo Population Genetic History of Australia and the Near East Doctor of Philosophy Doctorate Full Time Mr Matthew Williams
  • Position: ARC Postdoctoral Research Associate
  • Phone: 83135565
  • Email: yassine.souilmi@adelaide.edu.au
  • Fax: 8313 4364
  • Campus: North Terrace
  • Building: Darling, floor 2
  • Room: 2 05c
  • Org Unit: School of Biological Sciences

Connect With Me
External Profiles