Publications

Major histocompatibility complex class I molecules (MHC I) help protect jawed vertebrates by binding and presenting immunogenic …

We have known since the late 1980s that the function of classical major histocompatibility complex (MHC) class I molecules is to bind …

The selection of peptides for presentation at the surface of most nucleated cells by major histocompatibility complex class I molecules …

Major histocompatibility complex class I molecules (MHC I) present peptides to cytotoxic T-cells at the surface of almost all nucleated …

MHC class I molecules display peptides at the cell surface to cytotoxic T cells. The co-factor tapasin functions to ensure that MHC I …

Major histocompatibility complex class I (MHC I) proteins protect the host from intracellular pathogens and cellular abnormalities …

Projects

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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

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