Browsing Research Articles (SANBI) by Title
Now showing items 58-77 of 132
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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 ... -
Functional and structural analysis of predicted proteins obtained from homo sapiens' minisatellite 33.15-tagged transcript pAKT-45 variants
(Hindawi, 2020)The spermatozoa are transcriptionally dormant entities which have been recognized to be an archive of mRNA, coding for a variety of functionally crucial cellular proteins. This significant repository of mRNA is predicted ... -
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 ... -
Genome sequence of the tsetse fly (glossina morsitans): vector of African trypanosomiasis
(American Association for the Advancement of Science, 2014)Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between ... -
Genome sequencing of a severe acute respiratory syndrome Coronavirus 2 isolate obtained from a South African patient with Coronavirus disease 2019
(American Society for Microbiology, 2020)As a contribution to the global efforts to track and trace the ongoing coronavirus pandemic, here we present the sequence, phylogenetic analysis, and modeling of nonsynonymous mutations for a severe acute respiratory ... -
Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map
(BioMed Central, 2010)Determining the position and order of contigs and scaffolds from a genome assembly within an organism’s genome remains a technical challenge in a majority of sequencing projects. In order to exploit contemporary technologies ... -
Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale
(Nature Publishing Group, 2018)Disease emergence events regularly result from human activities such as agriculture, which frequently brings large populations of genetically uniform hosts into contact with potential pathogens. Although viruses cause ... -
A glance at quality score: implication for de novo transcriptome reconstruction of Illumina reads
(Frontiers, 2014)Downstream analyses of short-reads from next-generation sequencing platforms are often preceded by a pre-processing step that removes uncalled and wrongly called bases. Standard approaches rely on their associated base ... -
Gonad differentiation in zebrafish is regulated by the canonical Wnt signalling pathway
(Society for the Study of Reproduction, 2014)Zebrafish males undergo a ‘‘juvenile ovary-to-testis’’ gonadal transformation process. Several genes, including nuclear receptor subfamily 5, group A (nr5a) and anti-Mu¨ llerian hormone (amh), and pathways such as Tp53-mediated ... -
Hackathons as a means of accelerating scientific discoveries and knowledge transfer
(Cold Spring Harbor Laboratory Press, 2018)Scientific research plays a key role in the advancement of human knowledge and pursuit of solutions to important societal challenges. Typically, research occurs within specific institutions where data are generated and ... -
HIV-1 diversity and the implementation of integrase strand-transfer inhibitors as part of combination antiretroviral therapy
(SAMA, 2020): The integrase (IN) strand-transfer inhibitor (InSTI) dolutegravir (DTG) is now recommended by the World Health Organization as part of salvage and/or first-line combination antiretroviral therapy (cART).[1] DTG has a ... -
Human African trypanosomiasis research gets booost: unravelling the tsetse Genome
(PLOS, 2014)Human African trypanosomiasis (HAT), also known as sleeping sickness, is a neglected disease that impacts 70 million people distributed over 1.55 million km2 in sub-Saharan Africa. Trypanosoma brucei gambiense accounts for ... -
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 ... -
Human Leukocyte Antigen-A, B, C, DRB1, and DQB1 Allele and Haplotype Frequencies in a subset of 237 donors in the South African Bone Marrow Registry
(Hindawi, 2018)Human leukocyte antigen- (HLA-) A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 allele and haplotype frequencies were studied in a subset of 237 volunteer bone marrow donors registered at the South African Bone Marrow Registry ... -
Identification of novel prognostic markers of survival time in high-risk neuroblastoma using gene expression profiles
(Impact Journals, 2020)Neuroblastoma is the most common extracranial solid tumor in childhood. Patients in high-risk group often have poor outcomes with low survival rates despite several treatment options. This study aimed to identify a genetic ... -
Impact of subtype C-specific amino acid variants on HIV-1 Tat-TAR interaction: insights from molecular modelling and dynamics
(BMC, 2024)HIV-1 produces Tat, a crucial protein for transcription, viral replication, and CNS neurotoxicity. Tat interacts with TAR, enhancing HIV reverse transcription. Subtype C Tat variants (C31S, R57S, Q63E) are associated with ... -
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 ... -
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 ... -
Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms
(BioMed Central, 2015)Background: De novo transcriptome assembly of short transcribed fragments (transfrags) produced from sequencing-by-synthesis technologies often results in redundant datasets with differing levels of unassembled, partially ... -
The Influence of N-Linked Glycans on the MolecularDynamics of the HIV-1 gp120 V3 Loop
(PLoS ONE, 2013)N-linked glycans attached to specific amino acids of the gp120 envelope trimer of a HIV virion can modulate the binding affinity of gp120 to CD4, influence coreceptor tropism, and play an important role in neutralising ...