About Me

I am a research data scientist with the research engineering group at the Alan Turing Institute.

I previously completed a PhD in bioinformatics at QMUL looking at developing stratified medicine models for patients with rheumatoid arthritis. To achieve this, I combined data from multiple biological sources including the genome, transcriptome, and proteome to try and identify drivers of disease.

In particular I focus on creating computational tools to analyse big biological data online interactively using Shiny, R, and Plotly.

Software Packages

  • volcano3D

    An R package to plot interactive three-way differential expression analysis

  • glmmSeq

    Gene-level general linear mixed model

Research Websites

CV

Work Experience

  • Research Data Scientist, the Alan Turing Institute
    November 2022 - Current • London, United Kingdom
    Performing research software engineering and data science across a wide range of areas.

  • Bioinformatician, William Harvey Research Institute, Queen Mary University of London
    July 2022 - October 2022 • London, United Kingdom
    Delivery of computational biology research in collaboration with the Centre for Experimental Medicine & Rheumatology (EMR) and the Centre for Translational Bioinformatics (C4TB).

  • PhD Candidate, William Harvey Research Institute, Queen Mary University of London
    January 2018 - May 2022 • London, United Kingdom
    Developing models for multi-omic data integration in autoimmune diseases as a collaboration between the Centre for Experimental Medicine & Rheumatology (EMR) and the Centre for Translational Bioinformatics (CTB). Primarily analysing data from rheumatoid arthritis cohorts.

  • Enrichment Placement, Alan Turing Institute
    September 2019 - September 2020 • London, United Kingdom
    Collaborating with, and learning from, researchers at the Alan Turing Institute as part of an Enrichment placement.

  • Junior Bioinformatician, William Harvey Research Institute, Queen Mary University of London
    December 2016 - December 2017 • London, United Kingdom
    Performed transcriptomic analysis of rheumatoid arthritis data collaborating with clinicians and computational biologists. Developed a Shiny R website to visualise big data clearly and intuitively.

  • Piazzi Smyth Scholarship, Royal Society of Edinburgh
    July 2014 • The University of St. Andrews
    Modeled the 3D morphology of galaxies in Python from their 2D structure to determine a correlation between shape and kinematics. It was found that galaxies with high bulge to disk ratios tend to be fast rotators and form spiral arms.

  • Institute for Astronomy Research Intern, The University of Edinburgh
    July 2013 • Royal Observatory, Edinburgh
    Investigated the formation and evolution of fragments within protostellar discs. This analysis found that there is a threshold mass required for protostellar fragments to form planets or brown dwarfs without disintegrating.

Education

  • PhD, Bioinformatics, Queen Mary University London
    January 2018 - May 2022 • London, United Kingdom
    Thesis title: A Multi-Omic Approach to Stratified Medicine in Rheumatoid Arthritis

  • Master of Physics, Astrophysics, The University of Edinburgh
    September 2010 - May 2015 • Grade: First Class Honours
    Dissertation title: Effective Field Theory of Dark Energy and Modified Gravity

  • Master of Biomedical Engineering, University of Strathclyde
    September 2015 - May 2016 • Grade: Distinction
    Thesis title: Transcutaneous Spinal Stimulation and the Effect on Muscle Power Output in Healthy Subjects

Publication Highlights

  • Rituximab versus tocilizumab in rheumatoid arthritis: synovial biopsy-based biomarker analysis of the phase 4 R4RA randomized trial
    Nature medicine 28NA1256-1268, 2022.
    Rivellese, Felice; Surace, Anna EA; Goldmann, Katriona; Sciacca, Elisabetta; Çubuk, Cankut; Giorli, Giovanni; John, Christopher R; Nerviani, Alessandra; Fossati-Jimack, Liliane; Thorborn, Georgina; … Lewis, Myles J; Pitzalis, Costantino.
    DOI: 10.1038/s41591-022-01789-0

  • Molecular portraits of early rheumatoid arthritis identify clinical and treatment response phenotypes
    Cell reports 28: 9 2455-2470. e5, 2019
    Lewis, Myles J; Barnes, Michael R; Blighe, Kevin; Goldmann, Katriona; Rana, Sharmila; Hackney, Jason A; Ramamoorthi, Nandhini; John, Christopher R; Watson, David S; Kummerfeld, Sarah K; … Pitzalis, Costantino.
    DOI: 10.1016/j.celrep.2019.07.091