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Alistair Bailey
An engineer by training, I have since worked primarily as an informatician and research scientist. I currently work as a learning technologist supporting Librarians at the University of Southampton.
The topic of my research career has been the role of HLA antigen processing and presentation in disease recognition by T cells. In cancer this has focused on HLA-presented tumour antigens, and in infectious disease the focus has been HLA-presented viral and bacterial antigens. Exploiting these targets has the potential for enhancing personalised therapies, vaccine development and understanding allergy.
I have contributed to research into COVID19, skin sensitization to chemical allergens, asthma and contagious cancer in the Tasmanian Devil.
My core skills are processing and analysing data from whole exome sequencing, RNAseq, scRNAseq and proteomics assays. My workflow combines command line tools with micromamba, the R programming language and git version control.
Proteomics data I have curated, deposited and I am the data controller for is deposited at the PRoteomics IDEntifications Archive. Whole Exome and RNAseq data I have curated, deposited and I am the data controller for is deposited at the European Genome-phenome Archive.
I am a Data and Software Carpentry instructor and I have also created and delivered my own workshops to teach foundational R coding and data science skills to bioscientists and web design to librarians.
Education
Carpentries Instructor
Worldwide
The Carpentries
2017
- I trained as a Carpentries instructor as part of their volunteer led mission to increase global capacity in essential data and computational skills for conducting efficient, open, and reproducible research.
Machine Learning
Stanford University
Coursera
2016
- 10 week online introduction to machine learning.
Data Science Specialization
John Hopkins University
Coursera
2015
- 12 month online set of courses on data science using R, git and command line tools.
PhD, Immunology
Cancer Sciences, University of Southampton
Southampton, UK
2013 - 2008
- Thesis: Relating the structure, function and dynamics of the MHC Class I antigen presenting molecule.
BEng, Civil Engineering
University of Southampton
Southampton, UK
2008 - 2005
- First Class Honours in Civil Engineering.
Engineering, Science & Mathematics Foundation Year
University of Southampton
Southampton, UK
2005 - 2004
- Maths and physics foundation year preparation for undergraduate study.
BTEC ND Audio-Visual Production
Bournemouth & Poole College of Art & Design
Bournemouth, UK
1994 - 1992
- Foundation course in film, photography, TV and radio production.
Research Experience
Research Fellow
School of Biological Sciences, University of Southampton
Southampton, UK
2023
- scRNAseq analysis of T-cell response to neutrophil exposure. Bioinformatician maternity leave cover for Medical Research Council funded project.
Research Fellow
Centre for Proteomic Research/Cancer Sciences,
University of Southampton
Southampton, UK
2023 - 2018
- Cancer Research UK Accelerator: this project aims to identify potential treatment targets for hard to treat cancers using multi-omics methods. In this project our focus was on oesophageal, lung and neuroendocrine cancers.
As an informatician I processed, analysed and managed data from whole exome sequencing, RNAseq, scRNAseq and proteomics.
For sequencing fastq data, my workflow comprised of a mixture of command line tools using bash scripts and R/RStudio. I followed the Broad Institute Best Practices for genomic data analysis and Cornell Bioinformatics Core. For proteomics data, my worklfow used Peaks Studio, and post-process in R and RStudio.
Scripts and processed data were managed using git version control. Raw data was deposited along with processed outputs in PRoteomics IDEntifications Archive and the European Phenome-Genome Archive.
We also developed our method to identify treatment targets for infectious diseases from influenza and bacterial proteins. In 2020 I also worked to develop a COVID19 test using proteomics methods.
Research Fellow
Centre for Proteomic Research/Cancer Sciences,
University of Southampton
Southampton, UK
2018 - 2015
- Developed peptidomics methodology at the UoS for research into the role of MHC molecules in skin sensitisation to chemical allergy.
Research Fellow
Cancer Sciences, University of Southampton
Southampton, UK
2015 - 2013
- MRC Centenary Fellow
Teaching Experience
I enjoy teaching foundational coding and data science skills to researchers and developing evidence-based best practices. I am especially interested in helping novices and making coding more accessible to all.
Webpage Design
University of Southampton
Southampton, UK
2024
- I created a webpage design workshop and materials for Librarians at the University of Southampton
BIOL 2013: Introduction to bioinformatics
University of Southampton
Southampton, UK
2022 - 2021
- I taught the undegraduate introduction to bioinformatics module on variant discovery using the University Galaxy Server.
Coding Together
University of Southampton
Southampton, UK
2020 - 2019
- I created and taught an eight week series of collaborative workshops to teach foundational R coding and data science skills based on Carpentries materials.
Academic Support Tutor
IntoUniversity Millbrook
Southampton, UK
2019 - 2018
- IntoUniversity supports young people from disadvantaged backgrounds to attain either a university place or another chosen aspiration. I volunteered as an academic support tutor for secondary school learners.
Software Carpentry
Umeå University
Umeå, Sweden
2018
- Taught R for Reproducible Research and assisted in Command Line Basics.
British Society for Proteomics 2018 Data Science Workshop
University of Bradford
Bradford, UK
2018
- I created and taught a proteomics data science workshop including introduction to R, Volcano plots, heatmaps and peptide logos.
Data Carpentry
University of Southampton
Southampton, UK
2017
- Taught R for Reproducible Research and assisted in Command Line Basics and git.
Data Carpentry
University of Southampton
Southampton, UK
2017
- Taught R for Reproducible Research and assisted in introduction to SQL.
Software Carpentry
University of Southampton
Southampton, UK
2017
- Assisted with python and git for reproducible research.
Research Data
Immunopeptidomic analysis of influenza A virus infected human tissues identifies internal proteins as a rich source of HLA ligands, Publicly released
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- Proteomics data: PRIDE Project PXD022884
Identification of neoantigens in esophageal adenocarcinoma, Publicly released
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- Proteomics data: PRIDE Project ID PXD031108
- WES & RNAseq data EGA Study ID EGAS00001005957
Characterization of the Class I MHC Peptidome Resulting From DNCB Exposure of HaCaT Cells, Publicly released
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- Proteomics data: PRIDE Project PXD021373
Neoantigen identification in pancreatic neuroendocrine tumours, Unreleased pending publication
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- Proteomics data: PRIDE Project ID PXD037449
- WES & RNAseq data EGA Study ID EGAS00001006722
Immunopeptidomics guided identification of neoantigens in non-small cell lung cancer, Unreleased pending publication
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- Proteomics data: PRIDE Project ID PXD028990
- WES & RNAseq data EGA Study ID EGAS00001005499
Immunopeptidomics of a brain tumour cell line to identify HLA presented Zika, Unreleased pending publication
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- Proteomics data: PRIDE Project ID PXD037627
Non-small cell lung cancer global proteomics, Unreleased pending publication
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- Proteomics data: PRIDE Project ID PXD054390
Oesophageal adenocarcinoma global proteomes, Unreleased pending publication
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- Proteomics data: PRIDE Project ID PXD054428
Industry Experience
I have worked in a variety of roles ranging from engineering to research scientist. I like collaborative environments where I can learn from my peers.
Internship
Microsoft Research
Cambridge, UK
2012
- Helped develop computational model of MHC I peptide selection.
Freelance Satellite Communications Engineer
Globecast
London, UK
2012 - 2004
- I continued to work as an engineer in broadcast TV from 2004 and 2012 on major events such as the Olympics and Football World Cup.
Satellite Communications Engineer
Globecast
London, UK
2004 - 2000
- Full time engineer working in global broadcast TV primarily on sports, news and live entertainment events.
Film and television post-production engineer
Telecine
London, UK
2000 - 1995
- I trained as an engineer to operate various TV & film post-production equipment.
Publications
Proteogenomics guided identification of functional neoantigens in non-small cell lung cancer
bioRxiv
N/A
2024
- Ben Nicholas, Alistair Bailey, Katy J McCann, Oliver Wood, Eve Currall, Peter Johnson, Tim Elliott, Christian Ottensmeier, Paul Skipp
Operation Moonshot: rapid translation of a SARS-CoV-2 targeted peptide immunoaffinity liquid chromatography-tandem mass spectrometry test from research into routine clinical use
Clinical Chemistry and Laboratory Medicine
N/A
2022
- Jenny Hällqvist, Benjamin I. Nicholas, Alistair Bailey et al.
Identification of neoantigens in esophageal adenocarcinoma
Immunology
N/A
2022
- 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
Analysis of cell‐specific peripheral blood biomarkers in severe allergic asthma identifies innate immune dysfunction
Clinical & Experimental Allergy
N/A
2022
- Ben Nicholas, Jane Guo, Hyun‐Hee Lee, Alistair Bailey, Rene de Waal Malefyt, Milenko Cicmil, Ratko Djukanovic
Immunopeptidomic analysis of influenza A virus infected human tissues identifies internal proteins as a rich source of HLA ligands
PLoS Pathogens
N/A
2022
- Ben Nicholas, Alistair Bailey, Karl J. Staples, Tom Wilkinson, Tim Elliott, Paul Skipp.
The differentiation state of the Schwann cell progenitor drives phenotypic variation between two contagious cancers
PLOS Pathogens
N/A
2021
- Rachel S. Owen, Sri H. Ramarathinam, Alistair Bailey, Annalisa Gastaldello, Kathryn Hussey, Paul J. Skipp, Anthony W. Purcell, Hannah V. Siddle
Characterization of the Class I MHC Peptidome Resulting From DNCB Exposure of HaCaT Cells
Toxicological Sciences
N/A
2021
- Alistair Bailey, Ben Nicholas, Rachel Darley, Erika Parkinson, Ying Teo, Maja Aleksic, Gavin Maxwell, Tim Elliott, Michael Ardern-Jones, Paul Skipp.
The immunopeptidomes of two transmissible cancers and their host have a common, dominant peptide motif
Immunology
N/A
2021
- Annalisa Gastaldello, Sri H. Ramarathinam, Alistair Bailey, Rachel Owen, Steven Turner, N. Kontouli, Tim Elliott, Paul Skipp, Anthony W. Purcell, Hannah V. Siddle.
Dynamically Driven Allostery in MHC Proteins: Peptide-Dependent Tuning of Class I MHC Global Flexibility
Frontiers in Immunology
N/A
2019
- Cory M. Ayres, Esam T. Abualrous, Alistair Bailey, Christian Abraham, Lance M. Hellman, Steven A. Corcelli, Frank Noé, Tim Elliott, Brian M. Baker.
Direct evidence for conformational dynamics in major histocompatibility complex class I molecules
JBC
N/A
2017
- Andy van Hateren, Malcolm Anderson, Alistair Bailey, Jörn M. Werner, Paul Skipp, Tim Elliott.
Recent advances in Major Histocompatibility Complex class I antigen presentation: Plastic MHC molecules and TAPBPR mediated quality control
F1000 Research
N/A
2017
- Andy van Hateren, Alistair Bailey, Tim Elliott.
Selector function of MHC I molecules is determined by protein plasticity
Scientific Reports
N/A
2015
- Alistair Bailey, Neil Dalchau, Rachel Carter, Stephen Emmott, Andrew Phillips, Jörn M. Werner, Tim Elliott
Two Polymorphisms Facilitate Differences in Plasticity between Two Chicken Major Histocompatibility Complex Class I Proteins
PLoS One
N/A
2014
- Alistair Bailey, Andy van Hateren, Tim Elliott, Jörn M. Werner.
A Mechanistic Basis for the Co-evolution of Chicken Tapasin and Major Histocompatibility Complex Class I Proteins
JBC
N/A
2013
- Andy van Hateren, Rachel Carter, Alistair Bailey, Nasia Kontouli, Anthony P. Williams, Jim Kaufman, Tim Elliott.
The cell biology of major histocompatibility complex class I assembly: towards a molecular understanding
Tissue Antigens
N/A
2010
- A. Van Hateren, E. James, A. Bailey, A. Phillips, N. Dalchau, T. Elliott