Research

Research at SANBI has set well recognised milestones in the field of computational biology. Our tools and techniques have not only been developed but also implemented across heterogenous domains of advanced research. Local and international efforts have driven our discoveries. Until recently, the core of SANBI’s research has focused upon gene expression biology.

Methods developed and applied at SANBI revolve around a greater understanding of the underlying causes of diseases. We approach the problem by comparison of genes, genomes and transcriptomes. We use computational gene expression biology to create novel biological insights and to provide biomarkers for experimental validation. We perform analysis of human genome variation, transcriptional diversity on both the expression and splicing level and the unravelling of transcriptional regulatory networks.

Cancer research

SANBI is involved in cancer research from many perspectives. We assess variation of gene expression, regulation of gene expression and biomarker development. The understanding of variable gene expression during etiology and progression of cancers allows us to help pin-point culprit genes. Variation in expression patterns of marker genes are compared with normal expression states, yielding further leads to key players in cancer development. The identification of such diagnostic markers is of utmost importance to identify the collection of biomarkers, facilitating the early detection, diagnosis and eventually a cure of cancer subtypes.

Cancer research is being conducted in tight collaborations with local and international groups such as the Ludwig Institute for Cancer Research and the RIKEN institute, focussing on the development of systems to identify new candidates for therapeutics. Areas of research include analysis of gene structure, the alteration of genes as a result of selection during the process of cancer, changes in transcriptional regulation and expression profiling of cancerous tissues.

Pathogen and Vector research

SANBI has a well established research programme in pathogen genomics, creating novel discoveries and providing greater understanding of the processes and consequences of host pathogen interactions.

The institute is playing a leadership role in HIV research as part of the Collaborative Aids Programme of Research in South Africa (CAPRISA), funded by the U.S. National Institutes of Health. As part of its commitment to Caprisa SANBI is engaged in research into the evolution of HIV sequences. Much of this research is carried out in collaboration with researchers at UKZN, UCT and NICD.
We are the African site for translational bioinformatics and annotation of the Glossina morsitans genome, currently being sequenced at the RIKEN institute, Japan, and Sanger centre, UK. Together with other collaborators in the International Glossina Genome Initiative (IGGI) we are seeking means to rapidly translate genome sequence into a more effective means to control the spread of the insect vector for sleeping sickness.

Multifactorial disease research

Disease gene detection requires a thorough understanding of the human transcriptome and the complete integration of available data sources. Many factors are involved in the etiology of complex diseases. The imbalance at molecular, immunological and environmental levels affects the disease states and contribute to person to person variability in disease symptoms.

Work entails the mapping and analysis of gene expression states, transcript and genome diversity and the modelling of transcriptional regulation. Areas of research have included an analysis of diabetes related genes in collaboration with Professor Mark McCarthy at Oxford University and currently, an analysis of macrophage inflammation response pathways as part of the Genome Network Project (Japan).

Other active projects include the analysis of mouse macrophage reaction during Leishmania infection (Alia Benkhala, Tunisia) and the analysis and annotation of the Vibrio cholera genome

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Papers

2012 Peter van Heusden, Long Yi and Alan Christoffels. An OpenNebula-based cloud computing environment for bioinformatics. SATNAC 2012 Proceedings Fisher R, van Zyl GU, Travers SA, Kosakovsky Pond SL, Engelbrech S, Murrell B, Scheffler K, Smith D. Deep sequencing reveals minor protease resistance mutations in patients failing a protease inhibitor regimen. J Virol. 2012 Jun;86(11):6231-7. …

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Theses

2010 2009 Adele Kruger – PhD Thesis, September 2009: Development and Implementation of Ontology-Based Systems for Mammalian Gene Expression Profiling Feziwe Mpondo – MSc Thesis, September 2009: A Comparative Genomics Approach Towards Classifying Immunity-related Proteins in the Tsetse Fly Kavisha Ramdayal – MSc Thesis, September 2009: Incidence and Regulatory Implications of Single Nucleotide Polymorphisms among …

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