SOUTH AFRICAN NATIONAL BIOI s Junaid Gamieldien
Director: Prof Alan Christoffels
Dr Junaid Gamieldien leads the Knowledge Integration and Biomarker Discovery group in SANBI. His team is part of a number of very large-scale next-generation sequencing projects, including two collaborations targeting the discovery of disease variants. This involves sequencing an entire exome, which are made up of the genome’s exons, ie the coding portions of the genes. The first is a SANBI project on multiple sclerosis, the second a partnership with Stellenbosch University on Parkinson’s disease. In another project, a collaboration with Stellenbosch and drug company Novartis, the group is conducting a transcriptomics study – ie focusing on RNA – on a drug known as D-cycloserine, used as an antibiotic in TB infections. Other studies look to identify biomarkers and drug targets in cancer, as well as novel drug leads against coronaviruses.
Faculty: 5 Chairs: SARChI Chair in Bioinformatics and Health Genomics Awards, honours & other highlights: Renewal of SARChI chair; secured funding from National Institutes of Health (US) on three grants for Human Heredity and Health in Africa (H3Africa) Initiative; DST research award to Simon Travers; developed cloud environment for biomedical research; awarded MRC flagship project with three-year funding for tuberculosis research.
32
Collaborations: Stellenbosch University; Scripps Institute, US; Rutgers Cell and DNA Repository, US; Novartis, Switzerland; University of Cape Town; Wits; international centre for insect physiology and entymology, Kenya; University of Cambridge, UK; Research interests: Communicable diseases, including HIV, tuberculosis, malaria; non-communicable diseases, including breast cancer and Parkinson’s disease; agriculture Master’s students: 3 PhD students: 22 Postdoctoral fellows: 10
Alan Christoffels
Prof Alan Christoffels and his team are trying to understand host-pathogen interactions, in so doing shedding light on the mechanisms that underlie infectious diseases. To this end they are harnessing computational tools that are based on both DNA similarity – producing lists of genes, for example, that are similar in sequence to a target gene – and on machine-learning methods, where such programs ‘learn’ to detect patterns in data. Christoffels is applying such models to immune-response mechanisms in tuberculosis, malaria and fungal pathogens. Underlying these projects is the development of tools to make sense of large volumes of sequencing data. Recently, his lab partnered with Tygerberg Hospital in Cape Town to develop a biobank – for storing biosamples that can be used in research – under the umbrella of the Human Heredity and Health in Africa (H3Africa) project of the National Institutes of Health in the US. Among other highlights, his team has modeled nine potential drug targets for drug-resistant TB and these will be validated as part of an MRC flagship project.