Projects
- Analysing the sudden unexpected death of an infant through molecular autopsy and co-segregation analysis
Project title
Analysing the sudden unexpected death of an infant through molecular autopsy and co-segregation analysisPeople involved
Principal investigator: Dr Laura Heathfield
Coinvestigators: Dr Shameemah Abrahams
Support request by: Sune Mostert... - Assessing the efficacy and safety of new antibiotic regimens against serious bacterial infections
Project title
Assessing the efficacy and safety of new antibiotic regimens against serious bacterial infections caused by carbapenem-resistant Enterobacterales and/or Pseudomonas aeruginosa (CREP)People involved
Support requested by: Fadheela Patel... - Clinical and molecular epidemiology of carbapenemase-producing Enterobacterales in hospitalized patients
Project title
Clinical and molecular epidemiology of carbapenemase-producing Enterobacterales in hospitalized patients in the Cape Town Metropole, South AfricaPeople involved
Principal investigator : Dr Clinton Moodley & Dr. Shantelle Claassen-Weitz ... - COVID-19 arrays
Project title
Longitudinal analysis of antibody titres in a convalescent COVID-19 health care worker cohort.People involved
Principal investigator: Prof Jonathan Blackburn
Co-investigators: Prof Burgers; Prof Ntusi
Support request made by: Michelle Mullins... - Genetics factors associated with resistance to Mtb infection in healthcare workers
Project title
Genetics factors associated with resistance to Mycobacterium tuberculosis (Mtb) infection in healthcare workersPeople involved
Principal investigators: Muki Shey
Co-investigators: Prof. Graeme Meintjes, Dr Charlotte Schutz
Bioinformatics support team: Gerrit Botha and Ephifania Geza... - HIV latency transcriptomics of resting CD4+ T cells
Project title
HIV latency transcriptomics of resting CD4+ T cellsPeople involved
Principal investigator : Walter Nevondo
Bioinformatics support team: Katie LennardShort description of project
Despite anti-retroviral therapy HIV persists in a latent form of replication‐competent genome in anatomical and cellular reservoirs. This study has the following specific questions:... - Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN)
Project title
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN)People involved
Principal investigator: Relebohile Matobole (PhD candidate)
Supervisors: Prof Khumalo and Prof Bayat
Bioinformatics support team: Gerrit Botha, Jon Ambler (RNA-seq), Katie Lennard (RNA-seq Nextflow pipeline), Matthys Potgieter (Proteomics).... - IMPI-3: Bulk RNA-Seq analysis
People involved:
Principal Investigator: Mpiko Ntsekhe, Robert Wilkinson
Bioinformatics Support Team: Kuhle Mcinga, Ephie Geza, Mohammed Farahat
Support Requested: Rob RousseauShort description of the project:
This clinical trial is a unique opportunity to comprehensively measure and compare Mycobacterium tuberculosis (Mtb) responding immune responses(including conventional & unconventional T cell response as well as innate response) in blood and at the site of the Pericardial Fluid (PCF).... - Investigating the prevalence of Helicobacter Pylori in South Africa
Project title
Investigating the prevalence of Helicobacter Pylori in South AfricaPeople involved
Support requested by: Dr Francis Innocent Ekparolaguaziba
Principal investigator: Prof Mashiko Setshedi
Coinvestigators: Prof Adrian Brian
Bioinformatics support team: Ephifania Geza and Katie Lennard... - Investigating the role of the vaginal microbiome in genital inflammation
Project title
Investigating the role of the vaginal microbiome in genital inflammationPeople involved
Principal investigator: Pro Jo-Ann Passmore & Dr. Ramla Tanko
Bioinformatics support team: Ephifania GezaShort description of project
By identifying microbial compositions and interactions linked to inflammatory processes, this study explores how the vaginal microbiome influences genital inflammation.... - Lactobacillus iners MAGs: Genital inflammation in adolescent women
Project title
Lactobacillus iners MAGs: Genital inflammation in adolescent womenPeople involved
Support requested by: Adijat Jimoh
Principal investigator: Dr. Anna-Ursula Happel, Prof. Heather Jaspan
Bioinformatics support team: Ephie Geza, Gerrit Botha... - Metagenomic sequencing of CSF samples
Project title
Metagenomic sequencing of CSF samples.People involved
Principal investigators: Nicola Mulder
Co-investigators: Adrian Brink and Diana Hardie
Support request made by: Gert Marais
Bioinformatics support team: Ephifania Geza and Gerrit Botha ... - MetaNovo: Metaproteomics database generation
Project title
MetaNovo: Metaproteomics database generationPeople involved
Principal investigator: Prof Nicola Mulder
Phd student: Matthys PotgieterShort description of project
A pipeline to generate protein sequence databases from MGF mass spectrometry data and a UniProt release, using de novo sequencing and probabilistic ranking. ... - Metaproteome functional and taxonomic profiling
Project title
Top-level project for metaproteome related work, including pipelines and bionformatics support.People involved
Principle investigator: Prof. Nicola Mulder, Prof. Jonathan Blackburn
Imane Allali
Matthys PotgieterShort description of project...
- Infant stool metaproteome analysis
Project title
Characterizing the effects of HIV exposure on the infant stool microbiome.People involved
Principle investigator: Jonathan Blackburn
Primary author: Suereta Fortuin
Bioinformatics support team: Imane Allali, Matthys PotgieterShort description of project...
- Microbiota profiling of cows milk with and without traditional fermentation
Project title
Microbiota profiling of cows milk with and without traditional fermentationPeople involved
Principal investigator : Prof Mike Levin
Support request made by: Pieter de Waal
Bioinformatics support team: Katie LennardShort description of project...
- MTB CRISPRi-seq
Project title
Functional anti-tubercular screening of M. tuberculosis and M. smegmatis by CRISPRi-seqPeople involved
Principal investigator : Prof Valerie Mizrahi
Co-investigator: Mandy Mason
Collaborator: Dr Luiz Carvalho (Francis Crick Institute)... - Multi-omics analysis of 2 differentially virulent strains of Mycobacterium tuberculosis Beijing.
Project title
Multi-omics analysis of 2 differentially virulent strains of Mycobacterium tuberculosis Beijing.People involved
Principle Investigators: Prof. Nicola Mulder, Prof. Jonathan Blackburn
Jon Ambler
Matthys Potgieter
Suereta Fortuin
...- A proteogenomic analysis of 2 differentially virulent strains of Mycobacterium tuberculosis
Project title
Proteogenomic analysis of 2 differentially virulent strains of Mycobacterium tuberculosisPeople involved
Principle Investigators: Prof. Nicola Mulder, Prof. Jonathan Blackburn
Matthys Potgieter
Suereta Fortuin
Jon AmblerShort description of project...
- Pathogen outbreak study - Pseudomonas single isolate WGS
Project title
Pathogen outbreak study - Pseudomonas single isolate WGSPeople involved
Principal investigator : Prof Mark Nicol
Bioinformatics support team: Katie LennardShort description of project
This study was prompted by an unusual outbreak of wild type Pseudomonas that coincided with the Cape Town drought. Preliminary molecular analysis suggests clonality, the interest is therefore to try an establish how this outbreak came about and whether the drought is in some way responsible. Pseudomonas are waterborne opportunistic pathogens that can form biofilms in plumbing pipes. One hypothesis is therefore that the drought, with decreased water pressure allowed increased biofilm formation and subsequently increased concentrations in drinking water. The data will include WGS of blood culture isolates and water samples from before, during, and after the outbreak (96 samples).... - RNA seq analysis and downstream analysis--Effects of HIV and ageing on adipose tissue biology
Project title
Effects of HIV and ageing on adipose tissue biologyPeople involved
Principal investigator : Dr. Amy Mendham
Bioinformatics support team : Katie Lennard and Ephifania GezaShort description of project
We propose three time points across a woman’s life course where alterations in fat distribution are evident and may be further exacerbated in people living with HIV. These alterations relate to the influence of hormonal regulation on adipose tissue redistribution from the gynoid to android region, which can have profound effects on subcutaneous adipose tissue biology and subsequent metabolic health. The data will include samples collected at three time points before, during and after menopause (500 human samples). The bioinformatics analysis involve the RNA preprocessing, analysis and downstream analysis.... - RNAseq analysis of Folliculitis keloidalis nuchae
Project title
RNAseq analysis of Folliculitis keloidalis nuchae (FKN)People involved
Principal investigator : Dr Afolake Arowolo
Bioinformatics support team: Katie LennardShort description of project
Folliculitis keloidalis nuchae (FKN)... - RNAseq blood profiling of liver fibrosis during schistosomiasis
Project title
An atlas of blood regulators of liver fibrosis during schistosomiasisPeople involved
Principal investigator : Dr Justin Nono
Student: Severin Kamdem
Bioinformatics support team: Katie LennardShort description of project
Schistosomiasis is the most debilitating human helminthiasis. Whereas the acute phase of the disease can afflict individuals at first exposure, chronic schistosomiasis is a more frequent and severe form of the disease in endemic areas which affects individuals that have repeatedly been exposed to schistosomes. In such endemic areas, constant re-infection and the ensuing poorly symptomatic course of the disease at early stages undermine the benefits of available control strategy of which chemotherapy with praziquantel is the core component. Moreover, tissue fibroproliferative pathology consequent to chronic schistosomiasis which is not fully reversed by praziquantel treatment leaves most exposed individuals with a long-lasting-to-persistent impairment of the affected organ function. The development of alternative therapeutic measures that would integrate the control of fibroproliferative pathology upon infection with schistosomes is therefore desperately needed as this would provide more efficient means to achieve the elimination of the disease burden. For this, a fine knowledge of the molecular bases of tissue pathology during schistosomiasis is therefore crucial....- schistosomiasis metagenomics profiling
Project title
An atlas of blood regulators of liver fibrosis during schistosomiasisPeople involved
Principal investigator : Dr Justin Nono
Student: Severin Kamdem
Bioinformatics support team: Katie LennardShort description of project
Metagenomics data was acquired for the same sample set as we have RNAseq and metabolomics data available. This is a subproject of Project 'RNAseq blood profiling of liver fibrosis during schistosomiasis'...
- Serratia & GBS single isolate seq
Project title
Serratia and Group B Streptococcus characterisationPeople involved
Principal investigator : Dr Clinton Moodley
Students: Kimona Rampersadh (PhD) Dr. Amanda Overmeyer (MMed)
Bioinformatics support team: Katie LennardShort description of project...
- Setting up a portable metagenome assembly pipeline for CBIO
Project title
Setting up a portable metagenome assembly pipeline for CBIOPeople involved
Principal investigator : Prof Nicola Mulder
Bioinformatics support team: Katie Lennard, Gerrit BothaShort description of project
The plan is to setup a metagenome assembly pipeline pipeline. Taking raw metagenome sequence data, QC, assemble metagenomes, detect environmental composition, diversity and function. ... - Setting up a portable RNA-Seq pipeline for CBIO
Project title
Setting up a portable RNA-Seq pipeline for CBIOPeople involved
Principal investigator: Prof Nicola Mulder
Bioinformatics support team: Katie Lennard, Gerrit BothaShort description of project
The plan is to setup a pipeline that does differential gene expression analysis on human RNA-Seq data. Once we have something running we can start focusing on setting up pipelines for other types of RNA-Seq projects (if needed).... - Single isolate pathogen sequencing
Project title
S. pneumonia resistance gene analysisPeople involved
Principal investigator: Dr Clinton Moodley
Co-investigators: Kimona Rampersadh (PhD); Dr. Amanda Overmeyer (MMed)
Bioinformatics support team: Katie LennardShort description of project...
- TB Biomarkers Analysis (Lipidomics)
Project title
TB Biomarkers Analysis (Lipidomics)People involved
Principal investigator: Prof Jonathon Blackburn
Bioinformatics support team: Katie LennardShort description of project
TB biomarkers study consisting of 26 urine samples with the following groups: active TB (N=16), latent TB (N=10)...- TB Biomarkers Analysis (Lipidomics) Zandile
Project title
TB Biomarkers Analysis (Lipidomics)People involved
Principal investigator: Prof Jonathon Blackburn
Bioinformatics support team: Katie LennardShort description of project
TB biomarkers study consisting of 45 urine samples with the following groups: active TB (N=15), latent TB (N=15), no TB (N=15)...
- Testing Redmine project features
Project title
Testing Redmine project featuresPeople involved
Principal investigator : Prof Nicola Mulder
Bioinformatics support team: Gerrit BothaShort description of project
This is just a project where I will be testing all functionalities of a Redmine project. Gant charts, file upload, ticketing emails, permissions e.g....- Test sub-project
Project title
Testing Redmine project features - sub-projectPeople involved
Principal investigator : Prof Nicola Mulder
Bioinformatics support team: Gerrit BothaShort description of project
This is just a project where I will be testing all functionalities of a Redmine project. Gant charts, file upload, ticketing emails, permissions e.g....
- The effect of tadpole-tail blastema extract on rhabdomyosarcoma
Project title
The effect of tadpole-tail blastema extract on rhabdomyosarcomaPeople involved
Principal investigator : Prof Sharon Prince
Support request made by: Ms Jenna Bleloch, Professor Vincent Harrison
Bioinformatics support team: Katie Lennard... - The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infection
Project title
The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infectionPeople involved
Principal investigator: Dr Nyaradzo Chigorimbo-Tsikiwa
Coinvestigators:
Support request by: Dr. Nyaradzo Chigorimbo-Tsikiwa
Bioinformatics support team: Ephifania Geza and Gerrit Botha... - Transcriptomic analysis of CNS TB
Project title
Transcriptomic analysis of CNS TBPeople involved
Principal investigator : Prof Muazzam Jacobs
Co-investigator: Nai-Jen Hsu
Collaborator: Natalie Nieuwenhuizen (Max Planck Institute for Infection Biology)
Bioinformatics support team: Katie Lennard... - Transcriptomic profiling of HIV exposure in infant Treg cells
Project title
Transcriptomic profiling of HIV exposure in infant Treg cellsPeople involved
Investigator: Sonwabile Dzanibe
Principal investigator : Prof Clive Gray
Bioinformatics support team: Katie LennardShort description of project
The goal of the work is to determine transcriptomic differences in sorted Treg cells between infants who are HIV-exposed uninfected and HIV-unexposed uninfected.... - Vaginal 16S foetal alcohol spectrum disorder
Project title
Vaginal 16S full length reconstruction in women who give birth to foetal alcohol spectrum disorder babiesPeople involved
Principal investigator : Prof Sian Hemmings (smjh@sun.ac.za)
Support request made by: Ms Lauren Martin (MSc student, lcmartin@sun.ac.za)... - Variant calling using whole exome sequencing (WES) data.
Project title
Variant calling using whole exome sequencing (WES) data.People involved
Principle Investigator: Prof. Gasnat Shaboodien
Co-investigator: Polycarp Ndibangwi
Bioinformatics support team: Gerrit Botha, Thandeka Mavundla, Ephiefania Geza... - Variant calling: detecting SNPs in WGS data relative to H37Rv
Project title
Variant calling: detecting SNPs in WGS data relative to H37RvPeople involved
Principal investigator: A/Prof Anna Coussens
Coinvestigators: Prof Robert Wilkinson and Dr Anastasia Koch
Support request by: Mthawelanga Ndengane
Bioinformatics support team: Ephifania Geza and Gerrit Botha... - Whole genome sequencing of blowflies (Diptera: Calliphoridae)
Project title
Whole genome sequencing of blowflies (Diptera: Calliphoridae)People involved
UCT Principal investigator: A/Prof Laura Heathfield
Co-investigators: Dr Marise Heyns, Kyle Kulenkampff
Support requested by: Kyle Kulenkampff
Bioinformatics support team: Ephifania Geza and Gerrit Botha...
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