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Introduction
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January 2013 - March 2017
Publications
Publications (34)
Bioinformatics training programs have been developed independently around the world based on the perceived needs of the local and global academic communities. The field of bioinformatics is complicated by the need to train audiences from diverse backgrounds in a variety of topics to various levels of competencies. While there have been several atte...
A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03286-9.
South Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong ev...
With more microbiome studies being conducted by African-based research groups, there is an increasing demand for knowledge and skills in the design and analysis of microbiome studies and data. However, high-quality bioinformatics courses are often impeded by differences in computational environments, complicated software stacks, numerous dependenci...
Dichapetalum cymosum produces the toxic fluorinated metabolite, fluoroacetate, presumably as a defence mechanism. Given the rarity of fluorinated metabolites in nature, the biosynthetic origin and function of fluoroacetate have been of particular interest. However, the mechanism for fluorination in D. cymosum was never elucidated. More importantly,...
Pancreatic cancer accounts for 2.8% of new cancer cases worldwide and is projected to become the second leading cause of cancer-related deaths by 2030. Patients of African ancestry appear to be at an increased risk for pancreatic ductal adenocarcinoma (PDAC), with more severe disease and outcomes. The purpose of this study was to map the proteomic...
South Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong ev...
Pancreatic cancer accounts for 2.8% of new cancer cases worldwide and is projected to become by 2030 the second leading cause of cancer-related deaths. Patients of African ancestry appear to be at an increased risk for pancreatic ductal adenocarcinoma (PDAC), with worse severity and outcomes. The purpose of this study was to map the proteomic and g...
South Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong ev...
The need for portable and reproducible genomics analysis pipelines is growing globally as well as in Africa, especially with the growth of collaborative projects like the Human Health and Heredity in Africa Consortium (H3Africa). The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for portable, reproducible pipelines ada...
Background:
The Pan-African bioinformatics network, H3ABioNet, comprises 27 research institutions in 17 African countries. H3ABioNet is part of the Human Health and Heredity in Africa program (H3Africa), an African-led research consortium funded by the US National Institutes of Health and the UK Wellcome Trust, aimed at using genomics to study and...
Genetic variation and susceptibility to disease are shaped by human demographic history. We can now study the genomes of extant Africans and uncover traces of population migration, admixture, assimilation and selection by applying sophisticated computational algorithms. There are four major ethnolinguistic divisions among present day Africans: Hunt...
The need for portable and reproducible genomics analysis pipelines is growing globally as well as in Africa, especially with the growth of collaborative projects like the Human Health and Heredity in Africa Consortium (H3Africa). The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for portable, reproducible pipelines ada...
The Southern African Human Genome Programme is a national initiative that aspires to unlock the unique genetic character of southern African populations for a better understanding of human genetic diversity. In this pilot study the Southern African Human Genome Programme characterizes the genomes of 24 individuals (8 Coloured and 16 black southeast...
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), th...
Detailed description of the different modules provided in the IBT_2016 course, including learning objectives and learning outcomes.
(PDF)
The H3ABioNet pan-African bioinformatics network, which is funded to support the Human Heredity and Health in Africa (H3Africa) program, has developed node-assessment exercises to gauge the ability of its participating research and service groups to analyze typical genome-wide datasets being generated by H3Africa research groups. We describe a fram...
The diverse, rapidly developing discipline of bioinformatics has become an integral component of all areas of biomedical research in recent years. The ability to manage, analyse and interpret large complex datasets hinges on having access to skilled researchers who have received adequate training in specialised technical areas. Currently in Africa,...
Background:
Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Afric...
FOXP2 is a member of the P subfamily of FOX transcription factors, the DNA binding domain of which is the winged helix forkhead domain. In this work we show that the FOXP2 forkhead domain is able to bind to various DNA sequences, including a novel sequence identified in this work, with different affinities and rates as detected using surface plasmo...
Fig. 1. The evolutionary history of several species of Oscheius was centred on the analysis of 18S rDNA ITS region inferred by using the Maximum Likelihood method based on the Tamura-Nei model. The bootstrap consensus tree inferred from 1000 replications and tree is drawn to scale, with branch lengths measured in the number of substitutions per sit...
Presented at the ECCB2016, den Haag, NL, Sept 2016
Africa is not unique in its need for basic bioinformatics training for individuals from a molecular biology background. However, unique logistical challenges in Africa, most notably access to bioinformatics expertise and internet stability, must be addressed in order to meet this need on the conti...
The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants and microbiota occurs in Africa, yet genomic research outp...
Background
Population differentiation is the result of demographic and evolutionary forces. Whole genome datasets from the 1000 Genomes Project (October 2012) provide an unbiased view of genetic variation across populations from Europe, Asia, Africa and the Americas. Common population-specific SNPs (MAF > 0.05) reflect a deep history and may have i...
Keratolytic winter erythema (KWE), also known as Oudtshoorn skin disease, is characterised by a cyclical disruption of normal epidermal keratinisation affecting primarily the palmoplantar skin with peeling of the palms and soles, which is worse in the winter. It is a rare monogenic, autosomal dominant condition of unknown cause. However, due to a f...
Keratolytic winter erythema (KWE) or Oudtshoorn skin disease is a rare autosomal dominant monogenic disorder of epidermal keratinisation characterized clinically by cyclical peeling of the palms and soles. Due to a founder effect many KWE families have been identified in South Africa and the gene has been localized to 8p23.1-22, but the causal gene...
Pseudoxanthoma elasticum (PXE) is an autosomal recessive metabolic disorder with ectopic mineralization in the skin, eyes and cardiovascular system. PXE is caused by mutations in ABCC6.
To examine 54 unrelated South African PXE patients for ABCC6 PXE causing mutations.
Patients were screened for mutations in ABCC6 using two strategies. The first in...
