BA Biological Sciences at University of Oxford
2011 - 2014 (First Class)
MPhil Computational Biology at University of Cambridge
DPhil Systems Biology at University of Oxford
2013-2014 - Six months of lab work and data analysis on an independent project entitled “Epigenetic effects of developmental plasticity in response to temperature.” A
method known as MSAP (methylation-sensitive amplified fragment length polymorphism) was used to determine whether low incubation temperature causes differential methylation in response to temperature in the common wall lizard (Podarcis muralis). The work required a range of laboratory skills (dissection, DNA extraction, selective PCR, electrophoresis) as well as statistical programming in R. Contributed to a 2016 paper in the Journal of Experimental Zoology Part A
2013 - Six weeks in a group of three students on a research project in bioinformatics: “eQTL effects on coexpression network structure”. Programming in R and Python was used to produce simulated networks of correlated gene expression as well as networks based on real data from the Arabidopsis thaliana MAGIC population. The effect of the presence of eQTL on network structure was investigated (and found to be minimal), and various methods of network clustering were compared. Evidence was found to support the hypothesis that genes with functional similarity exhibit correlated expression levels - for example a tightly interconnected subnetwork consisting of both transposable elements and genes involved in transposable element silencing was discovered.
2016 - Three months on a dissertation project: “Genetic analysis of a transmissible cancer in Tasmanian devils (Sarcophilus harrisii).” DFTD1 is a clonally transmitted cancer cell line that gives rise to a fatal facial tumour in Tasmanian devils. R as well as command line programs were used to explore the phylogeny and evolution of DFTD1 by investigating copy number variations (CNVs) and single nucleotide variations (SNVs) in 150 tumour samples sequenced at very low coverage (1x). Clustering of CNVs and SNVs uncovered several instances of previously unknown structure in the DFTD1 phylogenetic tree, and the CNVs and SNVs themselves may provide the basis for future investigation into DFTD1 pathogenicity. 14,000 word report produced.