James Boot, PhD

Bioinformatician at Queen Mary University of London, experienced in a wide variety of data analysis pipelines.

Research Expertise

Hepatology

About

PhD graduate from Queen Mary University of London, my research was undertaken in Professor Silvia Marino’s brain tumour research group. Specifically, I was part of a team researching Glioblastoma Multiforme, the most prevalent and deadly adult brain tumour. Throughout my PhD I developed my wet lab skills and learnt to code for the purpose of analysing high throughput sequencing data such as RNAseq and DNA methylation array data. Since finishing my PhD I have worked as a Bioinformatician in the Genome Centre at the Blizard Institute, QMUL, where I have built up a experience in a very wide variety of Bioinformatics pipelines and analyses for a variety of datasets.

Publications

Global hypo-methylation in a proportion of glioblastoma enriched for an astrocytic signature is associated with increased invasion and altered immune landscape

eLife / Nov 22, 2022

Boot, J., Rosser, G., Kancheva, D., Vinel, C., Lim, Y. M., Pomella, N., Zhang, X., Guglielmi, L., Sheer, D., Barnes, M., Brandner, S., Nelander, S., Movahedi, K., & Marino, S. (2022). Global hypo-methylation in a proportion of glioblastoma enriched for an astrocytic signature is associated with increased invasion and altered immune landscape. ELife, 11. CLOCKSS. https://doi.org/10.7554/elife.77335

Comparative epigenetic analysis of tumour initiating cells and syngeneic EPSC-derived neural stem cells in glioblastoma

Nature Communications / Oct 21, 2021

Vinel, C., Rosser, G., Guglielmi, L., Constantinou, M., Pomella, N., Zhang, X., Boot, J. R., Jones, T. A., Millner, T. O., Dumas, A. A., Rakyan, V., Rees, J., Thompson, J. L., Vuononvirta, J., Nadkarni, S., El Assan, T., Aley, N., Lin, Y.-Y., Liu, P., … Marino, S. (2021). Comparative epigenetic analysis of tumour initiating cells and syngeneic EPSC-derived neural stem cells in glioblastoma. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-26297-6

Toll-like receptor 5 signalling mediates pro-inflammatory and fibrogenic responses in non-alcoholic steatohepatitis (NASH)

Journal of Hepatology / Jun 01, 2023

Li, W., Garrido, P., Mir, I. G., Waller, K., Jong, A. V., Brindley, J. H., Khan, W., Hood, G., Boot, J., Mein, C., Devalia, K., Loy, J., & Alazawi, W. (2023). Toll-like receptor 5 signalling mediates pro-inflammatory and fibrogenic responses in non-alcoholic steatohepatitis (NASH). Journal of Hepatology, 78, S740. https://doi.org/10.1016/s0168-8278(23)02141-4

Education

University of Bath

BSc Biochemistry / August, 2016

Bath

Queen Mary University of London

Ph.D., Oncology and Cancer Biology / January, 2021

London

Experience

MedImmune

Industrial Placement Student / June, 2014 — June, 2015

Commencing July 2014, as part of my degree I undertook a year in industry, carrying out my own research project within the Oncology department of MedImmune. The project was focussed on assay development and utilising innovative 3D culture techniques.

PhoreMost

Intern Associate Scientist / July, 2015 — September, 2015

Ten weeks’ work experience at a new start-up company, based in Cambridge. I helped set up processes and systems in a new laboratory, the company moved into, this included health and safety procedures. I also helped purchase consumables and large equipment. Finally, I carried out wet lab work, mainly involving cloning, transformations, restriction digests and gel electrophoresis.

Queen Mary University of London

Bioinformatician / May, 2021 — Present

Bioinformatician in the Genome Centre core facility at Queen Mary, based at the Blizard Institute. I perform and support analyses of genomics data for clients, ranging from bulk RNAseq, scRNAseq, ATACseq, methylation, WGS, long read sequencing and more! Working across a variety of projects and modalities.

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