Magister Scientiae - MSc (Bioinformatics)
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Item Computational verification of published human mutations(University of the Western Cape, 2008) Kamanu, Frederick Kinyua; Lehväslaiho, Heikki; Bajic, Vladimir; Faculty of ScienceThe completion of the Human Genome Project, a remarkable feat by any measure, has provided over three billion bases of reference nucleotides for comparative studies. The next, and perhaps more challenging step is to analyse sequence variation and relate this information to important phenotypes. Most human sequence variations are characterized by structural complexity and, are hence, associated with abnormal functional dynamics. This thesis covers the assembly of a computational platform for verifying these variations, based on accurate, published, experimental data.Item A deep learning approach to predicting potential virus species crossover using convolutional neural networks and viral protein sequence patterns(University of the Western Cape, 2022) Serage, Rudolph; Anderson, DominiqueMedical science has made substantial progress toward diagnosing, understanding the pathogenesis, and treating various causative agents of infectious disease; however, novel microbial pathogens continue to emerge, and existing pathogens continue to evolve alternative means to thrive in ever-changing environments. Various infectious disease etiological agents originate from animal reservoirs, and many have, over time, acquired the ability to cross the species barrier and alter their host range. The emergence and re-emergence of zoonotic pathogens is reported to be a consequence of changes in several factors, including ecological, behavioural, and socioeconomic variables which are arguably impossible to control. Computational methods with the capacity to evaluate large datasets, are considered invaluable tools for predicting and tracking disease outbreaks and are especially powerful when combined with machine learning techniques.Item Development and implementation of ontology-based systems for mammalian gene expression profiling(University of the Western Cape, 2009) Kruger, Adele; Hide, WinstonThe use of ontologies in the mapping of gene expression events provides an effective and comparable method to determine the expression profile of an entire genome across a large collection of experiments derived from different expression sources. In this dissertation I describe the development of the developmental human and mouse e voe ontologies and demonstrate the ontologies by identifying genes showing a bias for developmental brain expression in human and mouse, identifying transcription factor complexes, and exploring the mouse orthologs of human cancer/testis genes.Item The development of a single nucleotide polymorphism database for forensic identification of specified physical traits(University of the Western Cape, 2009) Naidu, Alecia Geraldine; Bajic, Vladimir; NULL; Faculty of ScienceMany Single Nucleotide Polymorphisms (SNPs) found in coding or regulatory regions within the human genome lead to phenotypic differences that make prediction of physical appearance, based on genetic analysis, potentially useful in forensic investigations. Complex traits such as pigmentation can be predicted from the genome sequence, provided that genes with strong effects on the trait exist and are known. Phenotypic traits may also be associated with variations in gene expression due to the presence of SNPs in promoter regions. In this project, the identification of genes associated with these physical traits of potential forensic relevance have been collated from the literature using a text mining platform and hand curation. The SNPs associated with these genes have been acquired from public SNP repositories such as the International HapMap project, dbSNP and Ensembl. Characterization of different population groups based on the SNPs has been performed and the results and data stored in a MySQL database. This database contains SNP genotyping data with respect to physical phenotypic differences of forensic interest. The potential forensicrelevance of the SNP information contained in this database has been verified through in silico SNP analysis aimed at establishing possible relationships between SNP occurrence and phenotype. The software used for this analysis is MATCH™. Data management and access has been enhanced by the use of a functional web-based front-end which enables the users to extract and display SNP information without running complex Structured Query Language (SQL) statements from the command line. This Forensic SNP Phenotype resource can be accessed at http://forensic.sanbi.ac.za/alecia_forensics/Index.htmlItem An investigation into the genetic basis of autosomal recessive Osteogenesis imperfecta (OI) III in a South African family of mixed ancestry(University of the Western Cape, 2022) Fernol, Susan Alicia; Christoffels, AlanOsteogenesis Imperfecta (OI) is a rare skeletal dysplasia that is primarily characterized by bone fragility, recurrent fractures, and bone deformities. Over the years there has been an increase in the number of genes associated with OI. Currently there are twenty causative genes involved in OI spread across an autosomal dominant form, autosomal recessive form, and an X-linked form. Among the different types of OI, the progressively deforming OI, has more than one causative OI gene associated with it, and both AD and AR mode of inheritance. A severe autosomal recessive form of OI type III has been studied in SA for more than 40 years.Item Reconstruction of gene regulatory networks of inflammation-associated genes in different clinical stages of diffuse large B-cell lymphoma(University of the Western Cape, 2022) Mfuphi, Nomlindelo Witness; Bendou, HocineDiffuse large B-cell lymphoma (DLBCL) is a heterogeneous malignancy that is driven by complex gene regulatory networks (GRNs). Numerous genes exert distinct effects on the progression and therapeutic outcome of DLBCL. Previous studies have associated DLBCL with inflammation but the GRNs involved in this mechanism have not yet been explored. The objectives of this current study are to reconstruct inflammation-associated networks and to understand the effects of inflammation on the pathogenesis and progression of DLBCL in different clinical stages.Item SNP based literature and data retrieval(University of the Western Cape, 2016) Veldsman, Werner Pieter; Christoffels, AlanReference 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 submitted to search engines when sourcing biomedical literature. In this thesis, the development of a bioinformatics software package is motivated, planned and implemented as a web application (http://sniphunter.sanbi.ac.za) with an application programming interface (API). The purpose is to allow scientists searching for relevant literature to query a database using refSNP identifiers and potential keywords assigned to scientific literature by the authors. Multiple queries can be simultaneously launched using either the web interface or the API. In addition, a VCF file parser was developed and packaged with the application to allow users to upload, extract and write information from VCF files to a file format that can be interpreted by the novel search engine created during this project. The parsing feature is seamlessly integrated with the web application's user interface, meaning there is no expectation on the user to learn a scripting language. This multi-faceted software system, called SNiPhunter, envisions saving researchers time during life sciences literature procurement, by suggesting articles based on the amount of times a reference SNP identifier has been mentioned in an article. This will allow the user to make a quantitative estimate as to the relevance of an article. A second novel feature is the inclusion of the email address of a correspondence author in the results returned to the user, which promotes communication between scientists. Moreover, links to external functional information are provided to allow researchers to examine annotations associated with their reference SNP identifier of interest. Standard information such as digital object identifiers and publishing dates, that are typically provided by other search engines, are also included in the results returned to the user.