- Historical perspective on the development of the theory of evolution. Mechanisms of molecular evolution and speciation.
- Traits, phylogenies, evolutionary models and divergence times.
- Complexity of the space of phylogenetic models, heuristics to map it. Tree building with distance matrix methods. Parsimony approaches.
- Tree building with maximum likelihood approaches. Bayesian viewpoint. Branch support measures.
|Session||Lecture Recordings||Lecture Slides||Practical Assignment|
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Jean-Baka Domelevo Entfellner
Affiliation: University of the Western Cape
My formal education took place in France, mainly in Mathematics, Physics and Computer Science at undergrad level. After completing a BSc and a MSc in Computer Science (Ecole Normale Supérieure de Cachan and University of Rennes, France), my PhD in bioinformatics (University of Montpellier, France, PhD supervisor: O. Gascuel) was about the combination of longitudinal and phylogenetic models to identify remote homologous proteins. I successfully completed that PhD in 2011. Since 2012, I am a postdoctoral fellow at the South African National Bioinformatics Institute (SANBI) with the H3ABioNet project (part of the H3Africa initiative) and since 2016, I am also Senior Lecturer in Computer Science at the University of the Western Cape (Cape Town, South Africa).
Affiliation: Ugandan Virus Research Institute
I am a Senior Research Officer (SRO) at the Uganda Virus Research Institute (UVRI), with a molecular genetic training background. My research encompasses investigations on disease vectors and pathogens with a focus on the genetics of malaria transmitting mosquitoes and HIV drug resistance. I am currently involved in research exploring controlling malaria vectors using engineered endonucleases, and the design of more sensitive assays for detection of HIV-drug resistance minority variants. I also contribute to Bioinformatics capacity development at the institute where various analysis pipelines, e.g. for NGS-based metagenomics and variant calling, are being developed to enhance pathogen detection for research purposes or disease outbreak investigations. The Uganda Virus Research Institute is a reference centre for various viral infections and is involved in investigations on communicable and also non-communicable diseases to generate information that will help initiate new or to improve on existing control and prevention strategies.