Building pan-African Bioinformatics Capacity
Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, JohannesburgMember Node
Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg
Member Node
The University of the Witwatersrand (Wits) is a leading African research-intenstive university situated in Johannesburg South Africa. Established as an independent university in 1922, Wits currently has 38000 students and over 1000 permanent, academic staff members. The Sydney Brenner Institute for Molecular Bioscience is one of the University's 21st Century Research Institutes. The SBIMB is based in the Faculty of Health Sciences and has strong links with the Faculties of Science and Engineering & the Built Environment. The SBIMB has strength in genetics of monogenic and complex diseases, cancer genomics, populations genetics and bioinformatics, and excellent collaborations with Wits groups in public health and others. The SBIMB is host to the H3A AWI-Gen Collaborative Centre investigating genetic and environmental factors in cardio-metabolic disorders. The Wits node of H3ABioNet has links with another H3A Project, Deciphering Developmental Disorders in Africa (DDD-Africa).
Prof. Scott Hazelhurst - Professor and Node PI
Scott Hazelhurst is Professor of Bioinformatics in the School of Electrical and Information Engineering at the University of the Witwatersrand, Johannesburg and an associate member of the Sydney Brenner Institute for Molecular Bioscience. He is PI of the Wits node of H3ABioNet and a collaborator on the H3A AWI-Gen project, which is a multi-site project investigating the genetic and environemental factors in cardio-metabolic disorders. His current research interests include genome-wide association studies, population genetics in Africa, the microbiome and designing portable and reproducible workflows. He has been involved in several H3A projects including being a member of the team that designed the H3A Genotyping Array and the H3A BioNet Workflows project. He is PI of an H3A Collaboration investigating the impact of variations in African genomes on the ADME genes, which have significant pharmacological impact. Originally a computer scientist, he has been working in bioinformatics for over 15 years. He completed his BScHons and MSc degrees at Wits and his PhD at the University of British Columbia. http://dept.ee.wits.ac.za/~scott
BioinformaticsComputer ScienceComputational BiologyGWAS StudyMetagenomics Population GenomicsWorkflows
Dr. Shaun Aron - Lecturer and Bioinformatics Consultant
Shaun Aron is currently a bioinformatics consultant and lecturer at the Sydney Brenner Institute for Molecular Bioscience (SBIMB) at the University of the Witwatersrand in Johannesburg, South Africa. After pursuing an undergraduate degree in Genetics and Microbiology followed by an Honours degree in Human Genetics, he handed over the pipettes to the experts and entered the then still developing field of bioinformatics pursing an MSc degree. Currently he is a member of the H3Africa Pan African Bioinformatics Network (H3ABioNet), which is a network consisting of 28 research institutes in 18 countries, tasked with developing and supporting informatics and genomics research in Africa. His research interests include GWAS of complex diseases in African populations, exploring population diversity, structure and admixture in Africa and bioinformatics education and training.
BioinformaticsComparative GenomicsEvolutionary BiologyPharmacogenomics GenomicsPopulation GenomicsWorkflowsFunctional GenomicsGWAS Study Genetic VariationGenotype and PhenotypeMolecular BiologyPopulation Genetics RNA-SeqSequence AnalysisSequence AssemblyWhole Genome Sequencing 
Dr Jean-Tristan Brandeburg - Researcher PostDoc
Jean-Tristan Brandenburg, Post doc in Sydney Brenner institute for molecular bioscience with Michele Ramsay. Inside institute, We are working inside h3africa - AWI-Gen, to analyse epidemiological, genetics data and the link with GWA studies. My project is based on Chronic Kidney disease for epidemiological and GWAS, also we work to develop h3abionet pipeline for GWAS studies.
BioinformaticsExome SequencingEvolutionary BiologyGenetic Variation GenomicsPopulation GenomicsWorkflowsGenotype and Phenotype GWAS StudyHuman GeneticsRare DiseasesWhole Genome Sequencing Population Genetics
Dr Ananyo Choudhury - Senior Scientist
Ananyo Choudhury obtained his Masters in Zoology from the University of Kalyani, India and a Ph.D. in Bioinformatics from the University of Calcutta, India. He moved to South Africa in 2010 to join the Sydney Brenner Institute for Molecular Bioscience at the Wits University as a Postdoctoral Fellow. He is presently employed at SBIMB as a Senior Scientist and co-leading the AWI-Gen genome-wide association study as well AWI-Gen population structure study analyst teams. He has contributed to many of the major genomic studies conducted in Africa, including the African Genome Variation Project, the H3Africa genotyping array design, the H3Africa Whole Genome Study and the Southern African Human Genome Program. His key interests are population genomics, genomics of complex traits and developing computational resources for genomic analysis.
BioinformaticsGenetic VariationGenomicsPopulation Genomics Genotype and PhenotypeGWAS StudyPopulation Genetics
Mr Jorge Da Rocha - PhD Student
Jorge da Rocha is a PhD candidate at the Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand. He is investigating genomic variants of potential pharmacogenomic impact via genomic and protein based analyses. His MSc (SBIMB, Wits) work consisted of variant analysis relevant to cancer pharmacogenomics in Africa. He completed his BSc(Hons) (Molecular and Cell Biology, Wits) majoring in Biochemistry and Bioinformatics. He enjoys working in bioinformatics and takes active roles in teaching and sharing what he has learned. He is also engaged in multiple community outreach programs which help teach school learners more about genomics.
BioinformaticsPersonalized MedicineGenomicsProtein Structure Analysis Genetic VariationPharmacogenomics 
Mr Phelelani Mpangase - Bioinformatics Consultant
Phelelani Mpangase obtained his BSc degree in Biochemistry and Genetics at the University of Kwa-Zulu Natal in 2008. In 2009, he completed his BSc Honours degree in Biochemistry, also at the University of Kwa-Zulu Natal. He then pursued an MSc degree in Bioinformatics at the University of Pretoria, where he worked on a project aimed designing a web resource for integrating protein annotations for the identification of potential drug targets in malaria. In 2013, Phelelani joined the Sydney Brenner Institute for Molecular Bioscience (SBIMB) at University of the Witwatersrand as a Bioinformaticist. He has since provided Bioinformatics support, not only to the students, but to other researchers in the University community that require Bioinformatics assistance. He has worked on projects involving protein structure and function, next generation sequencing (NGS) data analysis, pipeline/workflow design, metagenomics and transcriptomics. He is also involved in teaching introductory Bioinformatics courses. Apart from being a Bioinformaticist, he is also in the 3rd year of his PhD in Bioinformatics. His PhD project is mainly focused at analysing transcriptomic data from black South African patients with the systemic sclerosis (SSc) disease and designing reproducible pipelines using Nextflow for analysing transcriptomic data and metagenomics. His main research interests are protein bioinformatics, drug target discovery, data-mining/database design, NGS, pipeline/workflow design, metagenomics and transcriptomics. His passion lies in programming and designing resources that help biologists analyse their biological data.
BioinformaticsComparative GenomicsGenomicsData MiningSequence Assembly Genetic VariationFunctional GenomicsGene ExpressionHuman GeneticsWorkflows MetagenomicsTranscriptomicsRNA-SeqSequence Analysis 
Mr Jonathan Padavatan - Senior Research Computing Specialist
Jonathan Padavatan is the Senior Research Computing Specialist at the eResearch office, Wits University. He is also a Wits graduate, with an Honours degree in Physics. He previously worked as a software engineer at iThemba Labs for Accelerator-based Sciences, and in science communication and outreach at the Wits Planetarium. His technical interests include fault tolerance and monitoring, and file management systems in cluster computing.
Data GovernanceData Architecture, Analysis and DesignData Integration and Warehousing Software Engineering 
Dr. Dhriti Sengupta - Postdoctoral Fellow
Dhriti Sengupta is a postdoctoral fellow at the Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand. She received her PhD in Bioinformatics from University of Calcutta, India in 2013. Her PhD research involved application of systems approaches to study protein architecture and gene-regulatory network. Her present research interests include studying population structure, inferring demographic history and analyzing signatures of selection from genomic data. She has also started working on genome wide association studies in African populations.
BioinformaticsGWAS StudyGenomicsPopulation GeneticsPopulation Genomics
Mrs Azra Siddiqui - PhD Student
Azra Siddiqui is a doctoral candidate at Witwatersrand University. Her work focuses on how good and possible is to replace traditional reference genome with the genome graphs. In her research she is introducing genome graph to ADME genes to know how the drugs react to African population. Azra is also working in Business intelligence Department . Her work mainly targets on creating , designing and analysing different types of business report to help executives to make better decisions. She has published couple of papers on computer architecture in Indian journals.
Computer ScienceData Architecture, Analysis and DesignPopulation Genetics Population Genomics 
Mr David Twesigomwe – PhD Student and Node Ambassador
David Twesigomwe is a PhD student of Human Genetics at the Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand. David’s research is focused on studying variation in highly polymorphic pharmacogenes (such as CYP2D6, CYP2B6, and CYP2A6) in African populations. Prior to joining the SBIMB, David did a one-and-a-half year Bioinformatics internship at the Uganda Virus Research Institute (UVRI), which was supported by H3ABioNet as well as the Makerere University/UVRI Centre of Excellence for Infection and Immunity (MUII-Plus). David enjoys taking part in peer mentorship and organising or assisting in Bioinformatics training activities.
Mr Henry Wandera - Software Developer
Henry Wandera is a software developer at Sydney Brenner Institute for Molecular Bioscience. His interests contribute to the development of data analytics tools and use of data science approaches for strategic and operational decisions. He is part of team that is redeveloping Genesis: PCA and Admixture plot viewer, and also performs AWI-Gen data quality control processes. He likes deadlines because of the whooshing sound they make as they fly by.
Dr. Houcemeddine Othman - Post-Doctoral Fellow
My name is Houcemeddine Othman. I work at the Sydney Brenner Institute for Molecular Bioscience at Wits University as a postdoctoral fellow. Before my current position, I have been a member of several research projects applying biomolecular simulation, molecular modeling, and docking to understand the structure-activity relationship of anti-cancer peptides. In my current position, we are implementing structural bioinformatics methods within high throughput genome annotation pipelines to predict the impact of mutations. We use these approaches to characterize the pharmacogenomic landscape of African populations and to predict the effect of genetic variability on drug response which might improve the clinical guidance for drug indication in precision medicine. Other interests that have been part of my regular research or my toy projects include data science (although I hate this buzz word), database development, promoting open access practices in research, supporting bioinformatics education in LMIC, blogging, history, and music.
Computational BiologyComputational ChemistryData Submission, Annotation and Curation Molecular BiologyPersonalised MedicinePharmacogenomicsProtein Structure Analysis ProteinsProtein Structure AnalysisSequence AnalysisSequence Assembly Structure PredictionWhole Genome SequencingsBioinformaticsGenomics Structural AnalysisBiomedical ScienceDrug DiscoveryMachine Learning Gene and Protein Families 
Dr. Ovokeraye Hilda Oduaran - Post-Doctoral Fellow
Ovokeraye Oduaran is a postdoctoral fellow at the Sydney Brenner Institute for Molecular Bioscience (SBIMB) at the University of the Witwatersrand in Johannesburg, South Africa. Her research broadly focuses on the role of the gut microbiome in cardiometabolic diseases on the African continent. She believes that in-depth knowledge of the microbiome will greatly inform our current understanding of disease etiology.
BioinformaticsHuman GeneticsMicrobial Ecology 
