Miguel Lacerda

Biography

I am a former graduate student from the University of Cape Town, having obtained my bachelors degree in Business Science in December 2005 and my masters degree in Statistical Sciences in June 2008. Both degrees were awarded with distinction. I lectured on a contract basis in the Department of Statistical Sciences for two years while completing my masters, before moving to the National University of Ireland, Galway to pursue my doctorate in Bioinformatics under the supervision of Prof Cathal Seoighe. My PhD thesis investigated how HIV evolves in order to avoid the host’s immune response and introduces novel statistical methods for identifying regions of the viral genome that are relevant for vaccine design. I assumed a permanent position of lecturer in the Department of Statistical Sciences at UCT in September 2009.

Research Interest

I am primarily interested in statistical problems in bioinformatics, with a focus on computational molecular evolution, phylogenetics and population genetics. I am particularly interested in how host-pathogen interactions shape the evolution of the Human Immunodeficiency Virus (HIV), allowing the virus to escape the immune response and drug therapy. My recent work involved the development of phylogenetic models that allow the stochastic process of molecular evolution to depend on environmental variables, such as genetic markers of the host's immune system in the case of viral evolution. Under the supervision of Prof Cathal Seoighe at the National University of Ireland, Galway, I have developed a phylogenetic hidden Markov model (phylo-HMM) to identify regions of the HIV genome (called epitopes) that illicit an adaptive immune response and which may be relevant for vaccine design. I was also involved in a large project in which we extended this model to detect regions of the HIV envelope glycoprotein that are targeted by broadly neutralising serum antibodies.