Mr John Cole
- Research Scientist (Immunology & Infection)
0141 330 6267
I completed a B.Sci (Hons) in Molecular Genetics at University of Glasgow in 2009, modelling cultural and genetic coevolution for the project. I received a Research Assistant post under Dr Richard Wilson writing tools to detect mutability at the clinically important ADRB2 gene. In 2012 I completed an MRes in Bioinformatics at University of Glasgow, writing tools that detected over 200,000 new high frequency human STR alleles in the 1,000 genome project data. In 2013, I joined the Beatson Institute under Professor Peter Adams, working on the epigenetics of cancer, ageing and cellular senescence.
In 2016, I joined Professor Carl Goodyear's group in the Infection, Immunity and Inflammation (now School of Infection & Immunity), under the industry-academia collaboration The GLAZgo Discovery Centre, focussing on the omics of rheumatology and respiratory disease. In this time, I developed Searchlight - a tool for automating the data analysis step of bulk RNA-seq. I grew to appreciate that the wider Immunology groups needed additional bioinformatic support and started several initiatives - support drop-ins, training courses and introductory lectures. I also founded the Glasgow Bioinformatic Community - now the Glasgow Computational Biology Community. During the COVID-19 pandemic, I set up the Bioinformatic Support for Dry Masters Projects programme alongside Glasgow Polyomics, which has remained popular, and saved 100s of students from the tedium of a literature review.
The new Bioinformatics Facility - The Bioinformatic Core which I now manage, as a pay-for-use service - was launched in 2021. I provide bioinformatic support to the School on all levels, including omic data analysis, assistance with grant bids and manuscripts, and general advice in abundance. During this time, I have recognised the global demand for affordable, high quality bioinformatic training for PhD students and Post-Docs and have developed the Bioinformatics for Wet-Lab Biologists programme in response. This has been popular with over 200 attendees a year, from across Europe and Africa, and a median rating of 10/10 for content and delivery. We are now a formal training partner for the British Society of Immunology and its members.
My most recent work involves new methods for the analysis of Spatial Transcriptomics, combining image information with RNA-seq, as part of the Glasgow-Lilly collaboration. I am also developing new methods for assessing transcriptome aligners and the impact of misaligned reads on research.
- Level 4 bioinformatics and R for biologists (coordinator)
- Level 4: Personalised medicine and clinical trials (lecturer)
- Level 4: Genetics (lecturer)
- R and data analysis for bioinformatics (coordinator)
- Bioinformatics using R for biologists (coordinator)
- Introduction to omics for precision medicine (coordinator)
- Statistics and data analysis for bioinformatics (deputy coordinator)
Bioinformatics support for wet-lab masters summer projects (coordinator)
- RNA and Next Generation Sequencing (lecturer)
PhD student and Postdoc Training
I set up and run the Bioinformatics for Wet-Lab Biologists programme, which aims to equip wet-lab scientists who have no prior experience of omics or coding, with all the skills they need to perform their own analysis unaided. This is an entirely entry level and skills-based programme. Covering R and command line programming, omic tools and technologies, parsing, omic plots and data analysis (PCA, heatmaps, volcano plots, violin, fold vs fold, signature analysis, pathway analysis etc).
The full programme is split into four logical blocks, the first being essential, the others optional as required:
- Block 1 - Omic data analysis and visualisation using R (2 weeks)
- Block 2 - Complex experiments, signatures, and biomarkers (1 week)
- Block 3 - Command line omics (2 weeks)
- Block 4 - Single cell RNA-seq (1 week)
All blocks are run via zoom, five days a week, 9.30am to 12.30pm (allowing for regular wet-lab work in the afternoon) and run several times a year. They cost £125 per week for Glasgow members and £150 per week for external. For dates and to sign up please fill out this form (this form), or email John for further information.
Professional activities & recognition
- 2022 - present: Discover Immunology
Selected international presentations
- 2019: NGS & Single Cell Analysis Congress (London, UK)
- 2020: NGS & Single Cell Analysis Congress (London, UK)
- 2021: BSI Congress (Edinburgh, UK)
- 2022: BSI Summer School (Coventry, UK)
- 2022: BSI Congress (Liverpool, UK)