Browsing by Author "Aron, Shaun"

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    Designing a course model for distance-based online bioinformatics training in Africa: the H3ABioNet experience
    (Public Library of Science, 2017) Gurwitz, Kim T.; Aron, Shaun; Entfellner, Jean-Baka Domelevo; Saunders, Colleen J.; Cloete, Ruben
    Africa is not unique in its need for basic bioinformatics training for individuals from a diverse range of academic backgrounds. However, particular logistical challenges in Africa, most notably access to bioinformatics expertise and internet stability, must be addressed in order to meet this need on the continent. H3ABioNet (www.h3abionet.org), the Pan African Bioinformatics Network for H3Africa, has therefore developed an innovative, free-of-charge "Introduction to Bioinformatics" course, taking these challenges into account as part of its educational efforts to provide on-site training and develop local expertise inside its network. A multiple-delivery±mode learning model was selected for this 3-month course in order to increase access to (mostly) African, expert bioinformatics trainers. The content of the course was developed to include a range of fundamental bioinformatics topics at the introductory level. For the first iteration of the course (2016), classrooms with a total of 364 enrolled participants were hosted at 20 institutions across 10 African countries. To ensure that classroom success did not depend on stable internet, trainers pre-recorded their lectures, and classrooms downloaded and watched these locally during biweekly contact sessions. The trainers were available via video conferencing to take questions during contact sessions, as well as via online "question and discussion" forums outside of contact session time. This learning model, developed for a resource-limited setting, could easily be adapted to other settings.
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    High-depth African genomes inform human migration and health
    (Choudhury, A. et al. (2021). Author correction: High-depth African genomes inform human migration and health (nature, (2020), 586, 7831, (741-748), 10.1038/s41586-020-2859-7). Nature, 592(7856), E26. doi:10.1038/s41586-021-03286-9, 2021) Choudhury, Ananyo; Aron, Shaun; Botigué, Laura R; Botha, Gerrit
    The African continent is regarded as the cradle of modern humans and African genomes contain more genetic variation than those from any other continent, yet only a fraction of the genetic diversity among African individuals has been surveyed1. Here we performed whole-genome sequencing analyses of 426 individuals— comprising 50 ethnolinguistic groups, including previously unsampled populations— to explore the breadth of genomic diversity across Africa. We uncovered more than 3 million previously undescribed variants, most of which were found among individuals from newly sampled ethnolinguistic groups, as well as 62 previously unreported loci that are under strong selection, which were predominantly found in genes that are involved in viral immunity, DNA repair and metabolism. We observed complex patterns of ancestral admixture and putative-damaging and novel variation, both within and between populations, alongside evidence that population from Zambia were a likely intermediate site along the routes of expansion of Bantuspeaking populations. Pathogenic variants in genes that are currently characterized as medically relevant were uncommon—but in other genes, variants denoted as ‘likely pathogenic’ in the ClinVar database were commonly observed. Collectively, these findings refine our current understanding of continental migration, identify gene flow and the response to human disease as strong drivers of genome-level population variation, and underscore the scientific imperative for a broader characterization of the genomic diversity of African individuals to understand human ancestry and improve health.
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    Ten simple rules for developing bioinformatics capacity at an academic institution
    (Public Library of Science, 2021) Aron, Shaun; Jongenee, Victor; Kumuthini, Judit
    Bioinformatics is an applied interdisciplinary field whose primary purpose is to develop and deploy computational techniques to store, organize, and aid in the analysis and interpretation of large-scale data obtained from biological systems. While rooted in the analysis of nucleotide and protein sequences, it now encompasses techniques targeting multiple data acquisition modalities and seeks to comprehend the functioning of biological systems at many different levels. Bioinformaticians need to be cognizant of diverse scientific fields: basic and molecular biology, genetics, mathematics, statistics, and computer science at a minimum, thus requiring a thoroughly interdisciplinary set of skills to successfully carry out their duties. Due to the growing importance of bioinformatics in enabling modern biomedical research, programs and core facilities have been established in most academic institutions in the developed world over the last 30 years.