As mentioned on the main page, we have three main working streams:

• Pathogen evolution and immune evasion
  We investigate the evolution of gene families that enable pathogens to evade or manipulate the host immune system. This includes generating and annotating genomes across diverse pathogens, as well as modelling complex gene families such as var genes in malaria.
• Single-cell and spatial host–pathogen interactions
  We integrate single-cell transcriptomics and spatial omics data to study how pathogens interact with host cells, and how the immune system responds. A particular focus is on understanding variability in immune responses across individuals.
• Computational methods and tools
  We develop and apply computational approaches—including machine learning and modern AI methods—to support these research areas and to empower our collaborators.

Collaborations - Pathogen evolution and immune evasion

With my computational assembly tools, we describe novel malaria genomes to explore the speciation and understand the structure of variable gene families. I collaborate with Sylvain Gandon (Montpellier, France), Franck Prugnolle (Stellenbosch, South Africa), and Juliane Schaer (Berlin).

var genes, which encode the Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), particularly interest me. One aim is to explore the "var gene universe" structure, understand how diversity is maintained, and find patterns in polymorphic gene families. By assembling thousands of genes from clinical isolates, I hope to understand the recombination of them and use them to explore microevolution after drug and vaccine bottlenecks. I collaborate with several people in the field, including Dr Anna Bachman, Dr Antoine Claessens, Prof Alex Rowe and Prof Thomas Lavstsen.

We also have a strong collaboration with the Adams team at the University South Florida, exploring the opportunites of PiggyBac in Plasmodium. 

Collaborations - Single-cell and spatial host–pathogen interactions

We use single-cell approaches (transcriptomic and spatial) to explore further host-pathogen interactions and cell-cell interaction in diseases. Although I have an overarching theme to improve health in the Global South.  

To explore host-pathogen interactions I collaborate with Prof Matt Marti, Dr Chris Moxon, Prof James Brewer, Prof Francis Ndungu, Dr Lucas Amenga-Etego and Prof Gordon Awandare to generate samples and confirm findings. The aims are to understand niches of parasites, understand immunity and explore cell-cell interactions.

Further, I collaborate with many to apply tools and generate data to understand better data to generate novel tools. This list is not exhaustive and summarises more of the spirit.

• scRNA-Seq in Trypanosoma - Dr Manu De Rycker, Dr Emma Briggs, Prof Richard McCulloch and Martin Llewellyn
• scRNA-Seq in Malaria - Prof Andy Water, Prof Matt Marti, Lisa Ranford-Cartwright, Elena Gomez-Diaz and Prof John Adams

In Glasgows, we have also collaborations focussing more on immunology

• scRNA-Seq applied to immune cells - Prof Mariola Kurowska-Stolarska, Prof Julia Edgar and Dr Megan MacLeod
• Computational tools for clinical data (Immune mediated-inflammatory disease) - Prof Michael Barnes, Prof Iain McInnes and Prof Stefan Siebert.

Collaborations - Computational methods and tools

Please see the Computational Tools page for a list of tools. They cover following areas:

• Tools to visualise and analyse scRNA-Seq data through our Glasgow single-cell atlas. 
• Integrate multimodale dataset
• Tools to process scRNA-Seq and spatial data
• Host-parasite interactions