Research Articles (SANBI)
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Covid-19 among adults living with HIV: Correlates of mortality among public sector healthcare users in Western Cape, South Africa
(Wiley, 2023)Introduction: While a large proportion of people with HIV (PWH) have experienced SARS-CoV-2 infections, there is uncertainty about the role of HIV disease severity on COVID-19 outcomes, especially in lower-income settings. ... -
Record linkage for routinely collected health data in an African health information exchange
(Swansea University, 2023)The Patient Master Index (PMI) plays an important role in management of patient information and epidemiological research, and the availability of unique patient identifiers improves the accuracy when linking patient ... -
Application of an in silico approach identifies a genetic locus within ITGB2, and its interactions with HSPG2 and FGF9, to be associated with anterior cruciate ligament rupture risk
(Taylor and Francis Group, 2023)We developed a Biomedical Knowledge Graph model that is phenotype and biological functionaware through integrating knowledge from multiple domains in a Neo4j, graph database. All known human genes were assessed through ... -
Predicting amplification of mycn using cpg methylation biomarkers in neuroblastoma
(Future Science Group, 2021)Neuroblastoma is the most common extracranial solid tumor in childhood. Amplification of MYCN in neuroblastoma is a predictor of poor prognosis. Materials and methods: DNA methylation data from the TARGET data matrix were ... -
Exploring new genetic variants within col5a1 intron 4‐exon 5 region and tgf‐β family with risk of anterior cruciate ligament ruptures
(Wiley, 2020)Variants within genes encoding structural and regulatory elements of ligaments have been associated with musculoskeletal soft tissue injury risk. The role of intron 4‐exon 5 variants within the α1 chain of type V collagen ... -
Computational characterization of iron metabolism in the tsetse disease vector, glossina morsitans: Ire stem-loops
(BMC, 2016)Iron metabolism and regulation is an indispensable part of species survival, most importantly for blood feeding insects. Iron regulatory proteins are central regulators of iron homeostasis, whose binding to iron response ... -
Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City – from Alpha to Omicron
(Public Library of Science, 2023)Since the latter part of 2020, SARS-CoV-2 evolution has been characterised by the emergence of viral variants associated with distinct biological characteristics. While the main research focus has centred on the ability ... -
RAMICS: Trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA
(Oxford University Press, 2014)The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly ... -
FRAGS: Estimation of coding sequence substitution rates from fragmentary data
(BMC, 2004)Rates of substitution in protein-coding sequences can provide important insights into evolutionary processes that are of biomedical and theoretical interest. Increased availability of coding sequence data has enabled ... -
The contribution of exon-skipping events on chromosome 22 to protein coding diversity
(Cold Spring Harbor Laboratory Press, 2001)Completion of the human genome sequence provides evidence for a gene count with lower bound 30,000–40,000. Significant protein complexity may derive in part from multiple transcript isoforms. Recent EST based studies have ... -
Transforming RNA-Seq gene expression to track cancer progression in the multi-stage early to advanced-stage cancer development
(Public Library of Science, 2023)Cancer progression can be tracked by gene expression changes that occur throughout early-stage to advanced-stage cancer development. The accumulated genetic changes can be detected when gene expression levels in advanced-stage ... -
Changes in subcutaneous adipose tissue microRNA expression in response to exercise training in African women with obesity
(Nature Research, 2022)The mechanisms that underlie exercise-induced adaptations in adipose tissue have not been elucidated, yet, accumulating studies suggest an important role for microRNAs (miRNAs). This study aimed to investigate miRNA ... -
Role of Indigenous and local knowledge in seasonal forecasts and climate adaptation: A case study of smallholder farmers in Chiredzi, Zimbabwe
(Elsevier, 2023)Accessible, reliable and diverse sources of climate information are needed to inform climate change adaptation at all levels of society, particularly for vulnerable sectors such as smallholder farming. Globally, many ... -
Using multiplex amplicon pcr technology to efficiently and timely generate rift valley fever virus sequence data for genomic surveillance
(MDPI, 2023)Rift Valley fever (RVF) is a febrile vector-borne disease endemic in Africa and continues to spread in new territories. It is a climate-sensitive disease mostly triggered by abnormal rainfall patterns. The disease is ... -
Application of anin silicoapproach identifies a genetic locus withinITGB2,and itsinteractions withHSPG2 and FGF9,to be associated with anterior cruciateligament rupture risk
(Taylor and Francis Group, 2023)We developed a Biomedical Knowledge Graph model that is phenotype and biological function-aware through integrating knowledge from multiple domains in a Neo4j, graph database. Allknown human genes were assessed through the ... -
Investigation of distinct gene expression profile patterns that can improve the classification of intermediate-risk prognosis in AML patients
(Frontiers In Genetics, 2023)Acute myeloid leukemia (AML) is a heterogeneous type of blood cancer that generally affects the elderly. AML patients are categorized with favorable-, intermediate-, and adverse risks based on an individual’s genomic ... -
Proteomics analysis of the p.G849D variant in neurexin 2 alpha may reveal insight into Parkinson’s disease pathobiology
(Frontiers, 2022)Parkinson’s disease (PD), the fastest-growing neurological disorder globally, has a complex etiology. A previous study by our group identified the p.G849D variant in neurexin 2 (NRXN2), encoding the synaptic protein, ... -
SysBiolPGWAS: Simplifying post-GWAS analysis through the use of computational technologies and integration of diverse omics datasets
(Oxford University Press, 2023)Post-genome-wide association studies (pGWAS) analysis is designed to decipher the functional consequences of significant single-nucleotide polymorphisms (SNPs) in the era of GWAS. This can be translated into research ... -
SysBiolPGWAS: simplifying post-GWAS analysis through the use of computational technologies and integration of diverse omics datasets
(Bioinformatics, 2022)Motivation: Post-genome-wide association studies (pGWAS) analysis is designed to decipher the functional consequences of significant single-nucleotide polymorphisms (SNPs) in the era of GWAS. This can be translated into ... -
Investigation of distinct gene expression profile patterns that can improve the classification of intermediate-risk prognosis in AML patients
(Frontiers Media, 2023)Acute myeloid leukemia (AML) is a heterogeneous type of blood cancer that generally affects the elderly. AML patients are categorized with favorable-, intermediate-, and adverse-risks based on an individual’s genomic ...
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