South African National Bioinformatics Institute (SANBI): Recent submissions
Now showing items 21-40 of 132
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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 ... -
Semantic interrogation of a multi knowledge domain ontological model of tendinopathy identifies four strong candidate risk genes
(Nature Research, 2016)Tendinopathy is a multifactorial syndrome characterised by tendon pain and thickening, and impaired performance during activity. Candidate gene association studies have identified genetic factors that contribute to ... -
Modelling human protein interaction networks as metric spaces has potential in disease research and drug target discovery
(BMC, 2014)We have recently shown by formally modelling human protein interaction networks (PINs) as metric spaces and classified proteins into zones based on their distance from the topological centre that hub proteins are primarily ... -
Prioritization of anti-malarial hits from nature: Chemo-informatic profiling of natural products with in vitro antiplasmodial activities and currently registered anti-malarial drugs
(BMC, 2016)A large number of natural products have shown in vitro antiplasmodial activities. Early identification and prioritization of these natural products with potential for novel mechanism of action, desirable pharmacokinetics ... -
Understanding biobanking : An assessment of the public engagement speaking book intervention Biobanking and Me
(South African Medical Association, 2019)Meaningful engagement with donors of biological samples intended for human-sample biobanking increases knowledge, and allows donors to make informed decisions. Informed donors provide a platform for public awareness, ... -
Human coronavirus OC43 3CL protease and the potential of ML188 as a broad-spectrum lead compound: Homology modelling and molecular dynamic studies
(Springer Nature, 2015)The coronavirus 3 chymotrypsin-like protease (3CLpro) is a validated target in the design of potential anticoronavirus inhibitors. The high degree of homology within the protease’s active site and substrate conservation supports ... -
Galaxy training: A powerful framework for teaching!
(NLM (Medline), 2023)There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational ... -
The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance
(American Association for the Advancement of Science, 2022)Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the ... -
Increasing African genomic data generation and sharing to resolve rare and undiagnosed diseases in Africa: A call‑to‑action by the H3Africa rare diseases working group
(BMC, 2022)The rich and diverse genomics of African populations is significantly underrepresented in reference and in diseaseassociated databases. This renders interpreting the Next Generation Sequencing (NGS) data and reaching a ... -
Selection analysis identifies clusters of unusual mutational changes in omicron lineage ba.1 that likely impact spike function
(Oxford University Press, 2022)Among the 30 nonsynonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the ... -
A view on genomic medicine activities in Africa: Implications for policy
(Frontiers Media, 2022)Genomics policy development involves assessing a wide range of issues extending from specimen collection and data sharing to whether and howto utilize advanced technologies in clinical practice and public health initiatives. ... -
Repurposing based identification of novel inhibitors against mmps5-mmpl5 efflux pump of Mycobacterium smegmatis: A combined in silico and in vitro study
(MDPI, 2022)In the current era of a pandemic, infections of COVID-19 and Tuberculosis (TB) enhance the detrimental effects of both diseases in suffering individuals. The resistance mechanisms evolving in Mycobacterium tuberculosis ... -
The combat-tb workbench: Making powerful Mycobacterium tuberculosis bioinformatics accessible
(American Society for Microbiology, 2022)Whole-genome sequencing (WGS) is a powerful method for detecting drug resistance, genetic diversity, and transmission dynamics of Mycobacterium tuberculosis. Implementation of WGS in public health microbiology laboratories ... -
In silico repurposing of a Novobiocin derivative for activity against latency associated Mycobacterium tuberculosis drug target nicotinate-nucleotide adenylyl transferase (Rv2421c)
(Public Library of Science, 2021)Nicotinamide-nucleotide adenylyl transferase (Rv2421c) was selected as a potential drug target, because it has been shown, in vitro, to be essential for Mycobacterium tuberculosis growth. It is conserved between mycobacterium ... -
Current Status of Next-Generation Sequencing Approaches for Candidate Gene Discovery in Familial Parkinson´s Disease
(Frontiers in Genetics, 2022)Parkinson’s disease is a neurodegenerative disorder with a heterogeneous genetic etiology. The advent of next-generation sequencing (NGS) technologies has aided novel gene discovery in several complex diseases, including ... -
Computational approaches for the design of novel anticancer compounds based on pyrazolo[3,4-d]pyrimidine derivatives as trap1 inhibitor
(Switzerland: MDPI AG, 2021)In the present in-silico study, various computational techniques were applied to determine potent compounds against TRAP1 kinase. The pharmacophore hypothesis DHHRR_1 consists of important features required for activity. ... -
Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City
(Public Library of Science, 2021)During the first phase of the COVID-19 epidemic, New York City rapidly became the epicenter of the pandemic in the United States. While molecular phylogenetic analyses have previously highlighted multiple introductions and ... -
A novel nano therapeutic using convalescent plasma derived exosomal (CPExo) for Covid-19: A combined hyperactive immune modulation and diagnostics
(Elsevier, 2021)Extracellular vesicles like exosomes are important therapeutic tactics for treating COVID -19. By utilizing convalescent plasma derived exosomes (CPExo) from COVID-19 recovered persistence could accelerate the treatment ...