Building pan-African Bioinformatics Capacity
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal
Member Node
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal
Member Node
KRISP at UKZN challenges the status quo to create a scientific environment in (South) Africa that delivers high level science, creates innovations and reverses the brain drain. We are based at Nelson Mandela School of Medicine at UKZN, which was the first Medical School of South Africa for non-white students, which was rewarded by Mandela as the first democratic president of South Africa with his name. URL: http://www.krisp.org.za
Prof. Tulio de Oliveira - Director KRISP, Professor UKZN
Prof. Tulio de Oliveira is a bioinformatician that has been working with HIV research since 1997. He has received his PhD at the Nelson R Mandela School of Medicine, UKZN, South Africa. He was a Marie Curie research fellow at the University of Oxford, U.K. from 2004 to 2007 and a Royal Society Newton Fellow at the Sanger Institute from 2015 to 2018. He is current the director of KRISP, Professor at UKZN and Affiliate Professor at the Department of Global Health at University of Washington. He has over 140 publications and an H-score of 40.
BioinformaticsGenomicsEvolutionary Biology Translational MedicineVirology
Mr Vagner Fonseca - PhD Student
PhD student in Virology at the Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, South Africa. My research interests are the ongoing development of the NGS assembly, phylogenetic analsysis and in the built of a more stable JAVA environment to pre-process host and pathogen sequence data for MicroGWAS, ViroGWAS and GWAS. Vagner is active in Information Technology sector since 2004 with: Systems Analysis and Development, Project Management and IT Infrastructure Projects. Experienced in large projects and high complexity, covering the following areas of activity: Analysis and systems development (Web/Desktop/Mobile), Analysis and Development for Databases (Administration, Modeling, Data Migration, Tuning SQL, Optimization, Functions, Triggers and Stored Procedures), Development team manager, identification of functional prerequisites (APF, RUP, UML), Systems Auditing, Software Quality, Agile Methods, Configuration and Windows/Linux Servers Maintenance, Configuration Management and Continuous Integration Servers
BioinformaticsComputer ScienceComputational BiologyData Security Data ManagementGWAS StudyData Architecture, Analysis and Design Data MiningData Quality ManagementMicrobiology
Mr. Emmanuel James San - PhD Student
San Emmanuel James is a doctoral candidate at the University of Kwazulu Natal and research associate at the Kwazulu Natal Research and Innovation Sequencing Platform (KRISP) He is currently pursuing his PhD in Medical Virology and majoring in Bioinformatics. He is a programmer and research data analyst. His research interests areas of Microbiome, Transcriptomics, Short gun Metagenomics and Microbial GWAS analyses. Additionaly, he is interested in in-silico gene editing which he believes has the potential to enhance human life. San is passionate about the development of optimised,efficient and user friendly bioinformatics software and analysis pipelines. He is currently developing a web based microbial GWAS analysis pipeline and analysing gut and female tract microbiome (FMT) datasets. He is experienced in Java, PHP, R, Python and Linux Shell (back end), MySQL and PostgreSQL (DBMSs) and JavaScript, HTML, CSS3 (front end). In the H3ABionet community, he also contributes to the Machine Learning and Pipelines and Workflow work packages. He is also a certified Carpentries instructor who has organised and facilitated various data and software carpentry workshops.
BioinformaticsMathematicsMedical InformaticsMetagenomicsWorkflows Data VisualizationGWAS StudyData GovernanceComputer Science GenomicsMachine LearningMicrobiologyTranscriptomics Virology 
Dr. Werner Smidt - PostDoc
Werner Smidt is a bioinformatician that spends his time in both Pretoria and Durban. He is currently employed by KRISP. His focus areas are phylogenetics and epigenetics with special focus on graph theory based methods to solve biological problems, especially those relating to the immune system and HIV. He has recently developed an interest in the application of modern Bayesian methods focusing on variational inference to ascertain uncertainty in parameter estimation of complex data sets. He has advanced knowledge of the Python and R scripting languages and bioinformatic packages interfacing with them.
BioinformaticsGenomicsChIP-SeqMetagenomicsWhole Genome Sequencing WorkflowsData VisualizationData MiningEpigeneticsEpigenomics Functional GenomicsGene ExpressionGenetic VariationGenotype and Phenotype ImmunologyMachine LearningMedical InformaticsPhylogeny RNA-Seq Sequence analysisSequence AssemblyTranscriptomics
