Leads the Centre, bringing together a unique blend of expertise in data modelling, software development, epidemiology, bioinformatics and machine learning, genomic technology, Good Financial Grant Practice (GFGP), training and capacity building.
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For endemic pathogens (and outbreak scenarios), epidemiological data combined with genomics can inform control strategies and interventions on a local, national and international scale. Data generation, integration, analytical flow and interpretation in real-time is challenging, but crucial for decision making and action. Within the Centre we focus on data flow and the use of genome sequencing for surveillance of microbial pathogens through a combination of web application and software engineering, methods development and large-scale structured pathogen sequencing surveys - to deliver actionable information. Working with major public health agencies such as the US CDC, the European CDC, Public Health England, Wales, Scotland and the WHO, our systems are utilised globally to interpret and aid decision making for infection control.
Based across Oxford University’s Big Data Institute and the Wellcome Genome Campus, the Centre also hosts an NIHR-funded Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance (AMR), working with partners leading National AMR strategies in The Philippines, Colombia, Nigeria and India to implement genomic surveillance and linking to routine phenotypic and epidemiological data for priority pathogens.
Our major software applications include:
Epicollect5 – A mobile data gathering platform used globally and by major health agencies, citizen scientists, ecologists, epidemiologists, business analytics, schools and colleges. Currently contains 14,000 projects and > 28 million data points.
Microreact - Open data visualisation and sharing for genomic epidemiology. Used by major agencies such as CDC, ECDC and PHE for routine investigation of public health incidents.
Pathogenwatch - A global platform for genomic surveillance of microbial pathogens (including all major WHO Priority bacterial pathogens) Rapid prediction of resistant genotypes, and clustering giving epidemiological context.
Data-flo - An easy to use, open source web application that builds data transformation data flows by combining ready-to-use data adaptors
For a list of key publications, please refer to our "Resources" section