- Joint Faculty, Wellcome Trust Sanger Institute
- Director, Cenre for Genomic Pathogen Surveillance, Wellcome Genome Campus.
- Honorary Scientist - University of Cambridge NHS Trust
Our focus is on applied genomic epidemiology and the use and development of translational bioinformatic web/mobile applications for public health, evolutionary and population biology of micro-organisms using Whole Genome Sequencing (WGS).
RESEARCH GROUP MEMBERS - Imperial College
Corin Yeats - Lead Computational Biologist (Wellcome funded)
Mirko Menegazzo - Lead EpiCollect Developer (EU funded)
Derek Huntley - Software Developer (Wellcome funded)
RESEARCH GROUP MEMBERS - Sanger Institute
Corinna Glasner - Post-doctoral Fellow
Silvia Argimon - Genomic Epidemiologist
Stephen Reece - Project Manager
David Garcia - Java Developer
EpiCollect (www.epicollect.net) is a generic mobile data gathering tool providing a web application for the generation of forms and freely hosted project websites (using Google's AppEngine) for many kinds of mobile data collection projects.
Data can be collected using multiple mobile phones running either the Android Operating system or the iPhone (using the EpiCollect mobile app) and all data can be synchronised from the phones and viewed centrally (using Google Maps) via the Project website or directly on the phones.
We have produced EpiCollect to be as simple and generic as possible to allow groups / individuals / orgainsations to get up and running with data gathering as quickly and easily as possible. Projects people have set up range from simple surveys of wildlife and plants, through archaelogical dig sites and street art locations to the use by international organisations such as the Food and Agriculture Organisation of the United Nations (FAO) , or for the tracking of animal and human pathogens in Africa ,for Widespread vaccination campaigns (eg Rabies in India ) and for tracking EBOLA in Liberia.
We are part of the EU funded Citizen Cyberlab project aimed at building digital tools and online collaborative platforms for Citizen Science and education, and striving to enhance the opportunities for learning and creativity available to Citizens world wide.
The Consortium Team consists of seven partners: the European Organization for Nuclear Research (CERN), the United Nations Institute for Training and Research (UNITAR/UNOSAT), University College London (UCL), Université de Genève (UNIGE), Université Paris Descartes (UPD), The Mobile Collective (TMC) and Imperial College London
The BURST algorithm, developed by Ed Feil, has been developed into a JAVA WebStart application (Derek Huntley) and built and integrated with mlst datasets into the website.
The BURST algorithm first identifies mutually exclusive groups of related genotypes in the population (typically a multilocus sequence typing [MLST] database), and attempts to identify the founding genotype (sequence type or ST) of each group. The algorithm then predicts the descent from the predicted founding genotype to the other genotypes in the group, displaying the output as a radial diagram, centred on the predicted founding genotype. The procedure was developed for use with the data produced by MLST (STs and their allelic profiles) but can be used with some other molecular typing methods that define isolates as strings of integers.
In collaboration with James Abbott at the Bioinformatics Support Service, Imperial College London
WebACT provides a database of sequence comparisons between all publicly available prokaryotic genome sequences, allowing the on-line visualisation of comparisons between up to five genomic sequences, using the Artemis Comparison Tool (ACT) developed by the Sanger Institute.
Sequence comparisons can also be generated 'on the fly' for up to five user-entered sequences, by either uploading sequences, or querying public databases using sequence identifiers (GenBank or RefSeq).
Neisseria gonorrhoeae multi-antigen Sequence typing.
The two-locus NG-MAST procedure has been developed for the characterisation of isolates of N. gonorrhoeae, the causative bacterium of gonorrhoea. See Martin et al.(2004)
Reference 1 | Reference 2
Spatialepidemiology.net provides a map-based interface for the display and analysis of infectious disease epidemiological data, including molecular data, utilising Google Maps and Google Earth. MLST databases have been made available to view geographically.
I have also been working in collaboration with Stephen Bentley at the Sanger Institute and Prof. Peter Reeves of the University of Sydney on the genetic analysis of the capsular biosynthetic loci (cps) from 90 serotypes of Streptococcus pneumoniae.
Reference1 | Reference 2 | Reference 3
et al., 2016, Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe, Mbio, Vol:7, ISSN:2150-7511
Argimon S, Aanensen DM, 2016, Species Mash-up, Nature Reviews Microbiology, Vol:14, ISSN:1740-1526, Pages:730-730
et al., 2016, Microreact: visualizing and sharing data for genomic epidemiology and phylogeography., Microb Genom, Vol:2, ISSN:2057-5858
et al., 2016, Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection, Scientific Reports, Vol:6, ISSN:2045-2322
et al., 2016, Genomic Analysis and Comparison of Two Gonorrhea Outbreaks, Mbio, Vol:7, ISSN:2150-7511