A5017042855- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Rare Diseases
- Biomedical and Engineering Education
- Genomics and Phylogenetic Studies
- Genetic Associations and Epidemiology
- vaccines and immunoinformatics approaches
- Biotechnology and Related Fields
- Biomedical Text Mining and Ontologies
- Research Data Management Practices
- Genomic variations and chromosomal abnormalities
- Scientific Computing and Data Management
- Hemoglobinopathies and Related Disorders
- Pharmacogenetics and Drug Metabolism
- SARS-CoV-2 and COVID-19 Research
- Cancer Genomics and Diagnostics
- Immunotherapy and Immune Responses
- Epigenetics and DNA Methylation
- Cell Image Analysis Techniques
- Insect symbiosis and bacterial influences
- Phytoplasmas and Hemiptera pathogens
- Ichthyology and Marine Biology
- Bacteriophages and microbial interactions
- Trypanosoma species research and implications
- Global Health and Surgery
- Innovation and Socioeconomic Development
University of Cape Town
2015-2024
Wellcome Centre for Infectious Diseases Research in Africa
2020-2022
Wellcome Trust
2021
University of the Western Cape
2007-2014
Zagazig University
2014
Center for Genomic Science
2014
Rhodes University
2014
The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage lobe-finned fish thought to have become extinct 70 million years ago. modern looks remarkably similar many its ancient relatives, and evolutionary proximity our own ancestors provides glimpse the that first walked on land. Here we report genome sequence African coelacanth, Latimeria chalumnae. Through phylogenomic analysis, conclude lungfish, not is closest relative tetrapods. Coelacanth protein-coding...
Cancer/Testis (CT) genes, normally expressed in germ line cells but also activated a wide range of cancer types, often encode antigens that are immunogenic patients, and present potential for use as biomarkers targets immunotherapy. Using multiple silico gene expression analysis technologies, including twice the number sequence tags used previous studies, we have performed comprehensive genome-wide survey set 153 previously described CT genes normal libraries. We find although they generally...
The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping sequencing improved data analysis capabilities. Some the greatest genetic diversity among humans, animals, plants, microbiota occurs Africa, yet genomic outputs from continent are limited. Human Heredity Health Africa (H3Africa) initiative was established drive development for human health through recognition critical role bioinformatics...
Africa is not unique in its need for basic bioinformatics training individuals from a diverse range of academic backgrounds. However, particular logistical challenges Africa, most notably access to expertise and internet stability, must be addressed order meet this on the continent. H3ABioNet (www.h3abionet.org), Pan African Bioinformatics Network H3Africa, has therefore developed an innovative, free-of-charge "Introduction Bioinformatics" course, taking these into account as part...
The discipline of bioinformatics has developed rapidly since the complete sequencing first genomes in 1990s. development many high-throughput techniques during last decades ensured that grown into a overlaps with, and is required for, modern practice virtually every field life sciences. This placed scientific premium on availability skilled bioinformaticians, qualification extremely scarce African continent. reasons for this are numerous, although absence bioinformatician at academic...
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 gauge ability of its participating research service groups analyze typical genome-wide datasets being generated by H3Africa groups. We describe a framework for assessment computational genomics analysis skills, includes standard operating procedures, training test datasets, process administering exercise. present...
Cancer/testis (CT) genes are normally expressed only in germ cells, but can be activated the cancer state. This unusual property, together with finding that many CT proteins elicit an antigenic response patients, has established a role for this class of as targets immunotherapy regimes. Many families have been identified human genome, their biological function most part remains unclear. While it shown some under diversifying selection, question not addressed before whole.To shed more light...
The Pan-African bioinformatics network, H3ABioNet, comprises 27 research institutions in 17 African countries. H3ABioNet is part of the Human Health and Heredity Africa program (H3Africa), an African-led consortium funded by US National Institutes UK Wellcome Trust, aimed at using genomics to study improve health Africans. A key role support H3Africa projects building infrastructure such as portable reproducible workflows for use on heterogeneous computing environments. Processing analysis...
Scientific research plays a key role in the advancement of human knowledge and pursuit solutions to important societal challenges. Typically, occurs within specific institutions where data are generated subsequently analyzed. Although collaborative science bringing together multiple is now common, such collaborations analytical processing often performed by individual researchers team, with only limited internal oversight critical analysis workflow prior publication. Here, we show how...
Abstract There is growing evidence that comprehensive and harmonized metadata are fundamental for effective public data reusability. However, it often challenging to extract accurate from repositories. Of particular concern the metagenomic related African individuals, which omit important information about features of these populations. As part a collaborative consortium, H3ABioNet, we created web portal, namely Human Microbiome Portal (AHMP), exclusively dedicated human microbiome samples....
ABSTRACT G‐protein coupled chemosensory receptors (GPCR‐CRs) aid in the perception of odors and tastes vertebrates. So far, six GPCR‐CR families have been identified that are conserved most vertebrate species. Phylogenetic analyses indicate differing evolutionary dynamics between teleost fish tetrapods. The coelacanth Latimeria chalumnae belongs to lobe‐finned fishes, which represent a phylogenetic link these two groups. We searched genome L. for GPCR‐CRs found taste more similar those...
Introduction: Investigating variation in genes involved the absorption, distribution, metabolism, and excretion (ADME) of drugs are key to characterizing pharmacogenomic (PGx) relationships. ADME gene is relatively well characterized European Asian populations, but data from African populations under-studied—which has implications for drug safety effective use Africa. Results: We identified significant using 458 high-coverage whole genome sequences, 412 which novel, previously available...
Abstract Sickle cell disease (SCD) is one of the most common monogenic diseases in humans with multiple phenotypic expressions that can manifest as both acute and chronic complications. Although described more than a century ago, challenges comprehensive management collaborative research on this are compounded by complex molecular clinical phenotypes SCD, environmental psychosocial factors, limited therapeutic options ambiguous terminology. This terminology has hampered integration...
With more microbiome studies being conducted by African-based research groups, there is an increasing demand for knowledge and skills in the design analysis of data. However, high-quality bioinformatics courses are often impeded differences computational environments, complicated software stacks, numerous dependencies, versions tools along with a lack local infrastructure expertise. To address this, H3ABioNet developed 16S rRNA Microbiome Intermediate Bioinformatics Training course,...
Sickle cell disease (SCD) is a debilitating single gene disorder caused by point mutation that results in physical deformation (i.e. sickling) of erythrocytes at reduced oxygen tensions. Up to 75% SCD newborns world-wide occurs sub-Saharan Africa, where neonatal and childhood mortality from sickle related complications high. While research across the globe tackling on multiple fronts, advances have yet significantly impact health quality life patients, due lack coordination these disparate...
Genome-wide association studies (GWAS) are a powerful method to detect associations between variants and phenotypes. A GWAS requires several complex computations with large data sets, many steps may need be repeated varying parameters. Manual running of these analyses can tedious, error-prone hard reproduce.The H3AGWAS workflow from the Pan-African Bioinformatics Network for H3Africa is powerful, scalable portable implementing pre-association analysis, implementation various testing methods...
The diverse, rapidly developing discipline of bioinformatics has become an integral component all areas biomedical research in recent years. ability to manage, analyse and interpret large complex datasets hinges on having access skilled researchers who have received adequate training specialised technical areas. Currently Africa, individuals with these skills are sparsely scattered across the continent there is urgent need develop sustainable programs improve capacity. As part Human Heredity...
Bioinformatics training programs have been developed independently around the world based on perceived needs of local and global academic communities. The field bioinformatics is complicated by need to train audiences from diverse backgrounds in a variety topics various levels competencies. While there several attempts develop standardised approaches provide globally, challenges encountered resource limited settings hinder adaptation these approaches. H3ABioNet, Pan-African Network with 27...