Scientific Writing

BioSAVE: Display of scored annotation within a sequence context  (709 Kb PDF)

Publication in BMC Bioinformatics 9:157

MRC Laboratory of Molecular Biology, 2007

Having graduated from my BA MSci, I continued working alongside Dres. Adryan and Teichmann, but now focusing on bioinformatics. The result was BioSAVE, a piece of software for visualisation of annotations of protein or DNA sequences. The novel feature of BioSAVE is its ability to dynamically show and hide sequence annotations based on arbitary scoring systems (e.g. BLAST E-values, evolutionary conservation, hydrophobicity, polarity, etc).

Determination of transcription factor expression patterns in Drosophila melanogaster tracheogenesis

Master’s project (85%, highest in year)

MRC Laboratory of Molecular Biology, 2006-07

Returning to the LMB, I undertook my master's project under the supervision of Dr. Boris Adryan in Dr. Sarah Teichmann's group. The project involved a systematic exploration of transcription factor expression in the Drosophila melanogaster tracheal system using in situ hybridisation. The goal of this was to verify results obtained by the BDGP and to infer “functional regulatory modules” of genes. The project scored 85%, ranking first in the 2007 biochemistry cohort.

Structural and functional characterisation of the RhlB helicase interaction with E. coli RNase E

Third-year undergraduate project

University of Cambridge, Department of Biochemistry, 2006

My third-year undergraduate project was in Dr. Ben Luisi’s group with supervision from Salima Nurmohamed. During the project, I developed a reliable purification protocol for the RhlB helicase (a component of the E. coli RNA degradosome) and then moved on to homology modelling using four other DEAD-box proteins as the basis for the model. Following this, limited proteolysis and DMS cross-linking mobility shift assays were performed on the purified protein to begin verifying the model.

RNA-based life forms  (140 Kb PDF)

Trinity College Science Essay Prize Winner, 2005

This 4,000 word essay on the RNA world hypothesis won £300 and first place in the Trinity College Science Essay Prize in 2005.

Perpetuation rather than repair of a DNA lesion  (3.9 Mb PDF)

Trinity College Summer Studentship

MRC Laboratory of Molecular Biology, 2005

A 3 month project working in Prof. Michael Neuberger’s group under the supervision of Dr. Javier Di Noia. The work used a mammalian 2-hybrid system to investigate the hypothetical interaction between the proliferating cell nuclear antigen (PCNA) and the uracil DNA glycosylase (UNG). Such an interaction might explain how phase IB somatic hypermutation could occur prior to cell replication and hence before the apyrimidinic endonuclease initiates polymerase-mediated repair of the UNG-induced lesion.