Christopher Quince is a recent appointment to the Earlham and Quadram Institutes from the University of Warwick. Having started his career as a PhD student in Theoretical Physics, where he studied ecosystem models at the University of Manchester, Chris Quince quickly sought to move away from purely theoretical work. Following time in Arizona and Toronto, he took up a fellowship to model microbial communities at the University of Glasgow. Intrigued by the potential of next generation sequencing to profile microbiomes, Quince taught himself bioinformatics and demonstrated that sequencing noise was creating huge amounts of diversity in apparently simple microbial communities. He then developed some of the first tools for removing noise from amplicon sequences, enabling far more accurate estimates of diversity in microbial communities ranging from deep sea vents to the human gut. He then went on to pioneer novel methods for the analysis of microbiomes including some of the first probabilistic models for community structure, used to define clusters or enterotypes in the human gut and detect whether communities were consistent with neutral assembly. He then switched focus to metagenome data, developing one of the first algorithms CONCOCT, to bin metagenome assembled genomes (MAGs) from metagenome assemblies using coverage and composition. His most recent research has focussed on resolving strains within MAGs from time series culminating in algorithms that resolve strains directly on short read assembly graphs. He has used these metagenome techniques and analysis methods, in conjunction with his wide network of collaborators, to address urgent clinical questions, such as trialling new treatments for paediatric Crohn’s disease and understanding what drives antimicrobial resistance (AMR) in the gut microbiome.
Group members:
Dr Gaetan Benoit
Dr Rob James
Dr Sebastien Raguideau
Role in Respharm:
They will be responsible for the UK side of the bioinformatics. Dr Seb Raguideau will run custom pipelines on the metagenome samples. Annotating AMR, constructing MAGs and calculating diversity. This will be coordinated by Dr Christopher Quince. They will also assist in visualisation and statistical analysis of the AMR profiles across samples linking with the site metadata.
