Alistair Bailey

Alistair Bailey

Research Fellow in Immunoproteomics

University of Southampton

Biography

I am a research scientist at the University of Southampton. An engineer by training, I now work primarily as an informatician. My research subject is antigen processing and presentation by major histocompatibility molecules.

My principal project aims to improve immunotherapy treatment for cancer patients. Other projects include research into influenza, COVID19, skin sensitization to chemical allergens, asthma and contagious cancer in the Tasmanian Devil. I am also a Data and Software Carpentry instructor.

Interests

  • Antigen processing and presentation
  • Omics (WES, RNAseq, scRNAseq, Proteomics)
  • Informatics
  • Cancer immunotherapy
  • Data science in R

Education

  • PhD in Immunology, 2013

    University of Southampton

  • BEng in Civil Engineering, 2008

    University of Southampton

  • BTEC ND in Audio-Visual Production, 1994

    Bournemouth & Poole College of Art & Design

Publications

Identification of neoantigens in esophageal adenocarcinoma

Esophageal adenocarcinoma (EAC) has a relatively poor long-term survival and limited treatment options. Promising targets for …
Ben Nicholas, Alistair Bailey, Katy J. McCann, Oliver Wood, Robert C. Walker, Robert Parker, Nicola Ternette, Tim Elliott, Tim J. Underwood, Peter Johnson, Paul Skipp
PDF DOI

Analysis of cell-specific peripheral blood biomarkers in severe allergic asthma identifies innate immune dysfunction

Our study sought cell type-specific gene signatures of severe allergic asthma in peripheral blood. We identified changes in monocytes …
Ben Nicholas, Jane Guo, Hyun-Hee Lee, Alistair Bailey, Rene de Waal Malefyt, Milenko Cicmil, Ratko Djukanovic
PDF DOI

Immunopeptidomic analysis of influenza A virus infected human tissues identifies internal proteins as a rich source of HLA ligands

CD8+ and CD4+ T cells provide cell-mediated cross-protection against multiple influenza strains by recognising epitopes bound as …
Ben Nicholas, Alistair Bailey, Karl J. Staples, Tom Wilkinson, Tim Elliott, Paul Skipp
PDF DOI

The differentiation state of the Schwann cell progenitor drives phenotypic variation between two contagious cancers

Contagious cancers are a rare pathogenic phenomenon in which cancer cells gain the ability to spread between genetically distinct …
Rachel Owen, Sri Ramarathinam, Alistair Bailey, Annalisa Gastaldello, Kathryn Hussey, Paul J.Skipp, Anthony W. Purcell, Hannah V. Siddle
PDF DOI

Characterization of the Class I MHC Peptidome Resulting From DNCB Exposure of HaCaT Cells

Skin sensitization following the covalent modification of proteins by low molecular weight chemicals (haptenation) is mediated by …
Alistair Bailey, Ben Nicholas, Rachel Darley, Erika Parkinson, Ying Teo, Maja Aleksic, Gavin Maxwell, Tim Elliott, Michael Ardern-Jones, Paul Skipp
PDF DOI
See all publications

Projects

*
All MHC I antigen processing Proteomics R

Coding togetheR

Materials for Coding togetheR. A series of collaborative workshops to teach foundational R coding and data science skills at the University of Southampton 2019-2020.
Coding togetheR

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
Creating and using a colour palette and colour gradients for plotting

Umeå Software Carpentry Workshop

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

British Society for Proteomics 2018 Data Science Workshop

Materials for proteomics data science workshop including introduction to R, Volcano plots, heatmaps and peptide logos
British Society for Proteomics 2018 Data Science Workshop

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.
Machine Learning for MHC I peptide classification

MHC dynamics dashboard

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

R heatmap tutorial using d3heatmap

A short tutorial for producing heatmaps in R using some sample data.
R heatmap tutorial using d3heatmap

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.
Selector function of MHC I molecules is determined by protein plasticity

Biochem Calculator

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

Contact