Dr David Aanensen

 

Lecturer in Bioinformatics

My focus is on the use and development of web technology to address the global genetic epidemiology, population and evolutionary biology of micro-organisms, mainly  utilising Multilocus Sequence Typing (MLST) http://www.mlst.net

MLST is a nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms via the internet and MLST was developed in the laboratories of Martin Maiden, Dominique Caugant, Ian Feavers, Mark Achtman and Prof Brian Spratt.

 

Associated Developments - 

 

http://www.epicollect.net

EpiCollect is a generic mobile data gathering tool. EpiCollect.net provides 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 tracking of animal and human pathogens in Africa. 

PLoS publication | BBC News  | BBC World Podcast  

 

http://eburst.mlst.net/

 

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.

Reference 1 | Reference 2

 

http://www.webact.org

 

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).

 All pre-computed and user-generated comparisons can be viewed on-line using a webstart version of ACT or can be downloaded.

Reference 1 | Reference 2

 

http://www.ng-mast.net/

 

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

 

http://www.spatialepidemiology.net/

 

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.

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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