Publications

. Direct evidence for conformational dynamics in major histocompatibility complex class I molecules. J Biol Chem, (292), pp. 20255-20269, https://doi.org/10.1074/jbc.M117.809624, 2017.

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. Selector function of MHC I molecules is determined by protein plasticity. Sci Rep, (5), pp. 14928, https://doi.org/10.1038/srep14928, 2015.

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. A mechanistic basis for the co-evolution of chicken tapasin and major histocompatibility complex class I (MHC I) proteins. J Biol Chem, (288), pp. 32797-808, https://doi.org/10.1074/jbc.M113.474031, 2013.

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. The cell biology of major histocompatibility complex class I assembly: towards a molecular understanding. Tissue Antigens, (76), pp. 259-275, https://doi.org/10.1111/j.1399-0039.2010.01550.x, 2010.

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Posts

This post was motivated in part by Maëlle Salmon’s post about blogging and secondly from discussion with Laura Graham about my long term mission is to convince the University of Southampton (here in the UK) of the need to provide some minimum data science training and support. The aim is to try to define the problem(s) a bit better and also a bit of a cry for help. I appreciate that none of this may be novel, but I needed to get it written down and out of my head.

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Projects

Creating and using a colour palette and colour gradients for plotting

A tutorial is to demonstrate one way to create a colour palette and corresponding gradients in R

Umeå Software Carpentry Workshop

Slides from Software Carpentry Workshop, 9th and 10th October 2018 in Umeå Sweden

British Society for Proteomics 2018 : Data Science Workshop

Materials for proteomics data science workshop including introduction to R, Volcano plots, heatmaps and peptide logos

How to build this website

A guide to building this website using blogdown.

Machine Learning for MHC I peptide classification

A toy model that attempts to classify peptides from my some of my experiments according to one of five MHC class I allotypes present in the cells I use.

MHC dynamics dashboard

A dashboard to display the results of the MHC I HDX project

R heatmap tutorial using d3heatmap

A short tutorial for producing heatmaps in R using some sample data.

Selector function of MHC I molecules is determined by protein plasticity

This project sought to explain the mechanism of peptide selection by two functionally distinct MHC I allotypes using a combination of molecular dynamics and mathematical modelling of biochemical experiments.

Biochem Calculator

A Shiny app I made for calculating the amount to weigh out or dilute for making solutions

Contact

  • ab604[at]soton.ac.uk
  • Building 85, Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK