Undergraduate NERC-REP student Summer 2107
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Over the summer period of 2017 I worked in Milardlab focusing on temperate phages capable of infecting the Vibrio genus. The research was targeted at isolating a range of marine Vibrio isolates from UK coastal waters, genome sequencing selected isolates, and then into the crux of my project – using statistical computing to develop a classification system for Vibrio prophages based on genetic content. Bioinformatic analysis was performed in R using dimensionality reduction techniques to explore data extracted from sequenced genomes, with data cleaned and sorted prior to input using Perl. Given the scale of the data set, I was using iterative algorithms to predict prophages in new isolates, label genes, and create the necessary files for analysis. For example, by using the recently developed pVOG set of hidden Markov models the presence of pVOGs in bacteriophages was extracted. Much of the quantitative analysis consisted of hierarchal clustering, then going on to visualisation of the data and exploring characteristics by cluster.
Currently I am an undergraduate mathematician at the University of Warwick with great interest in exploratory data analysis, bioinformatics, statistical computing and inference, machine learning, and big data. Over the next few years, I plan to continue researching these areas. I also have an interest in statistical astrophysics, where I am a fellow of the Royal Astronomical Society.