Welcome and 2016 recap

Welcome. I’ve created this site as a place to host my work and draw together my various research activities into one up-to-date online hub.  I thought it’d be a nice to kick-off with a summary of what I got up to in the last calendar year.

In the new year I started in my current research assistant position at the University of Glasgow, working with Louise Matthews and my PhD supervisor Richard Reeve. I have joined a large NSF and BBSRC funded project investigating the mechanisms underpinning the maintenance and dissemination of antimicrobial resistance (AMR) in the Greater Serengeti Ecosystem, Tanzania. My role has primarily involved the development of Bayesian models to infer genotypes underlying observed multi-drug resistant phenotypes. We hope inferences from these models will help us to shed light on the cross-species dynamics of AMR among traditional agro-pastoralist farming communities in Northern Tanzania.

In Spring, I submitted the final version of my PhD thesis, titled Quantifying the genetic basis of antigenic variation among human influenza A viruses. This followed a viva full of interesting discussion that had taken place in December 2015. Examined by Sam Lycett (The Roslin Institute, University of Edinburgh) and Olwyn Byron (University of Glasgow), the questions and conversation ranged from protein-folding and structural biophysics to the population dynamics of influenza viruses at a global scale.


Antigenic impacts of substitutions predicted from models and observed experimentally.

In April, we also published the first flu paper based on my PhD work in PLoS Pathogens. In it, we identify the substitutions responsible for the antigenic evolution of A(H1N1) viruses over a period of more than ten years up until it’s replacement in the human population by the swine-origin A(H1N1) strain that caused the 2009 ‘swine-flu’ pandemic. We tested the predicted effect sizes of these substitutions by generating some of them in the lab using reverse genetics. To demonstrate the importance of these substitutions in the antigenic evolution of the virus, we identified their position in the phylogeny, relative to vaccine changes, and used antigenic maps.


During my PhD, I enjoyed a short lab stint here at the impressive home of the National Institute for Medical Research in Mill Hill.

The data on which the A(H1N1) paper was based was generated over a number of years by the Worldwide Influenza Centre (WIC) at the National Institute for Medical Research. My PhD was co-supervised by WIC director John McCauley and conversations with John, his predecessor Alan Hay, and deputy director Rod Daniels during  visits to Mill Hill always provided invaluable insights into the evolution of seasonal influenza. We have now published a curated A(H1N1) dataset consisting of over 48,000 measures of antigenic similarity online.


Attendees of the UK-Malaysia Vaccinology Worskhop, August ’16.

In August I was delighted to be funded by RCUK to attend the UK-Malaysia Vaccinology Workshop, hosted by the Institute of Bioscience at the Universiti Putra Malaysia. The workshop organised by UPM and The Pirbright Institute brought together researchers based at UK and Malaysian institutes from a range of disciplines to discuss emerging and next generation vaccine technologies against veterinary viruses. I presented some of the work from my PhD relating to human seasonal influenza and some results from a more recent collaboration with Pirbright on translating methods from my PhD to the analysis of avian influenza A(H9N2).

As the year drew to an end I traveled down to Liverpool to attended the Annual meeting of the British Ecological Society. This was my first time at an ecology conference, my largest conference to date, and also my first time presenting my work on AMR in Northern Tanzania to a wider audience.


Presenting a hypothesis of AMR spread at BES.

It was great to see many familiar faces there and I enjoyed the dose of festive spirit thrown in on the final day with plenty of people sporting Christmas jumpers and mulled wine served. Favourite talks included Grant Hopcraft presenting on using wildebeest tail hair to derive longitudinal data from cross-sectional sampling and Rosie Woodroffe on the opportunities for spread of bTB between badgers and cattle.