South African National Bioinformatics Institute (SANBI): Recent submissions
Now showing items 41-60 of 84
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Development of Open source Laboratory Information Management System (LIMS) For Human Biobanking
(University of the Western Cape, 2018)Biobanks are collections of biological samples and associated data for future use. The day to day activities in a biobank laboratory is underpinned by a laboratory information management system (LIMS). For example, the ... -
Identification of coding variants associated with familial systemic lupus erythematosus through whole exome sequencing
(University of the Western Cape, 2016)Systemic lupus erythematosus (SLE) is a chronic inflammatory autoimmune disease characterized by the production of a wide range of autoantibodies directed against selfantigens. SLE can influence almost any organ system and ... -
Identification and ranking of pervasive secondary structures in positive sense single-stranded ribonucleic acid viral genomes
(University of the Western Cape, 2018)The plasticity of single-stranded viral genomes permits the formation of secondary structures through complementary base-pairing of their component nucleotides. Such structures have been shown to regulate a number of ... -
Computational prediction of host-pathogen protein-protein interactions
(University of the Western Cape, 2017)Supervised machine learning approaches have been applied successfully to the prediction of protein-protein interactions (PPIs) within a single organism, i.e., intra-species predictions. However, because of the absence of ... -
SNP based literature and data retrieval
(University of the Western Cape, 2016)Reference single nucleotide polymorphism (refSNP) identifiers are used to earmark SNPs in the human genome. These identifiers are often found in variant call format (VCF) files. RefSNPs can be useful to include as terms ... -
“An investigation into the MicroRNA-gene interactions involved in the pathogenesis of systemic lupus erythematosus”
(University of the Western Cape, 2015)Systemic lupus erythematosus is a chronic, inflammatory disease characterised by the production of autoantibodies which target particularly the nuclear components of multiple cell types throughout the body. MicroRNA’s have ... -
Computational strategies to identify, prioritize and design potential antimalarial agents from natural products
(University of the Western Cape, 2015)Introduction: There is an exigent need to develop novel antimalarial drugs in view of the mounting disease burden and emergent resistance to the presently used drugs against the malarial parasites. A large amount of natural ... -
Integrating regulatory and methylome data for the discovery of clear cell Renal Cell Carcinoma (ccRCC) variants
(University of the Western Cape, 2015)Kidney cancers, of which clear cell renal cell carcinoma comprises an estimated 70%, have been placed amongst the top ten most common cancers in both males and females. With a mortality rate that exceeds 40%, kidney cancer ... -
Computational genomics approaches for kidney diseases in Africa
(University of the Western Cape, 2015)End stage renal disease (ESRD), a more severe form of kidney disease, is considered to be a complex trait that may involve multiple processes which work together on a background of a significant genetic susceptibility. ... -
The phylogeography, epidemiology and determinants of Maize streak virus dispersal across Africa and the adjacent Indian Ocean Islands
(University of the Western Cape, 2015)Maize streak disease (MSD), caused by variants of the Maize streak virus (MSV) A strain, is the world's third and Africa’s most important maize foliar disease. Outbreaks of the disease occur frequently and in an erratic ... -
Computational analysis of multilevel omics data for the elucidation of molecular mechanisms of cancer
(University of the Western Cape, 2015)Cancer is a group of diseases that arises from irreversible genomic and epigenomic alterations that result in unrestrained proliferation of abnormal cells. Detailed understanding of the molecular mechanisms underlying a ... -
Computational characterisation of DNA methylomes in mycobacterium tuberculosis Beijing hyper- and hypo-virulent strains
(University of the Western Cape, 2014)Mycobacterium tuberculosis, the causative agent of tuberculosis, is estimated to infect approximately one-third of the world’s population and is responsible for around 2 million deaths per year. The disease is endemic in ... -
Normalization and statistical methods for crossplatform expression array analysis
(University of the Western Cape, 2012)A large volume of gene expression data exists in public repositories like the NCBI’s Gene Expression Omnibus (GEO) and the EBI’s ArrayExpress and a significant opportunity to re-use data in various combinations for novel ... -
The identification of biologically important secondary structures in disease-causing RNA viruses.
(University of the Western Cape, 2012)Viral genomes consist of either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). The viral RNA molecules are responsible for two functions, firstly, their sequences contain the genetic code, which encodes the viral ... -
The identification of biologically important secondary structures in disease-causing RNA viruses
(University of the Western Cape, 2012)Viral genomes consist of either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). The viral RNA molecules are responsible for two functions, firstly, their sequences contain the genetic code, which encodes the viral ... -
A computational characterisation of the relationship between genome structure and disease genes
(University of the Western Cape, 2012)This is a pilot study to investigate the relationship between disease gene status and the structure of the human genome with specific reference to regions of recombination. It compares certain characteristics of a control ... -
Modulation of soybean and maize antioxidant activities by Caffeic acid and nitric oxide under salt stress
(University of the Western Cape, 2012)This study explores the roles of exogenously applied nitric oxide, exogenously applied caffeic acid and salt stress on the antioxidant system in cereal (exemplified by maize) and legume (using soybean as an example) plants ... -
Evolution of HIV-1 subtype C gp120 envelope sequences in the female genital tract and blood plasma during acute and chronic infection
(University of the Western Cape, 2014)Heterosexual transmission of HIV-1 via the female genital tract is the leading route of HIV infection in sub-Saharan Africa. Viruses then traffic between the cervical compartment and blood ensuring pervasive infection. ... -
Genome-wide annotation of chemosensory and glutamate-gated receptors, and related genes in Glossina morsitans morsitans tsetse fly
(University of the Western Cape, 2014)Tsetse flies are the sole vectors of trypanosomes that cause nagana and sleeping sickness in animals and humans respectively in tropical Africa. Tsetse are unique: both sexes adults are exclusive blood-feeders, females are ... -
The molecular evolution and epidemiology of Rubella virus
(University of the Western Cape, 2014)Despite widespread rubella virus (RV) vaccination programs, annually RV still causes severe congenital defects in an estimated 100,000 children globally. A concerted attempt to eradicate RV is currently underway and ...