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Software for detection and monitoring of biological threats from metagenomics data

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  • Full or part time
    Prof Denis Shields
  • Application Deadline
    No more applications being accepted
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

Principal UCD Supervisor: Denis Shields (School of Medicine).
UCD Co-supervisor: Professor Seamus Fanning;

JRC Ispra Supervisor: Dr. Alex Patak.
JRC Ispra Co-supervisor: Mauro Petrillo

This 4 year PhD project will develop pathogen screening software and methodologies in metagenomic datasets. It is a collaboration between University College Dublin, which brings expertise in bioinformatics and pathogen screening in food safety, and the Joint Research Centre, whose main base is at Ispra Italy, which carries out research underpinning policy development for the European Commission. The student will develop the tools required to automatically screen metagenomic datasets for pathogens on submission to centralised repositories which record the geographic origins of the samples , including the European Bioionformatics Institute (EBI), an international leader in the storage and provision of nucleotide data, with which we will collaborate on this project. The ultimate goal is to inform policy on the feasibility of continuous active screening of metagenomes for pathogenic biological threat risk assessment. Such policy assessments will be relevant to the areas of food safety, defence, and disease epidemiology. This project will suit a student with a strong proven aptitude for bioinformatic research (programming and data analysis) and with interests in policy development, microbiology and disease risks. The student will split their time between UCD and JRC. UCD is close to Dublin’s city centre, while the JRC main base at Ispra is near the Maggiore Lake, an area of natural beauty on the south of the Italian alps.
Informal enquiries: [Email Address Removed]


In the near future, technical support for the application of WGS for food pathogen detection will be needed. At the same time, defence programmes (in the context of CBRN-E, Chemical, Biological, Radiological, Nuclear, and Explosive materials) are of increasing importance for the European Commission. These two priorities could be addressed together in a proposal to use NGS and sequence data for the detection and monitoring of biological threats. The European Nucleotide Archive (ENA) maintained by the European Bioinformatics Institute (EBI) is an international leader in the storage of nucleotide data, including metagenomics experiments and their associated metadata (e.g. the geographic origin of the sample). Importantly, it is possible to develop and deploy custom applications on top of this resource, mining and processing the stored data. As part of joint ongoing actions against biothreats across the EU and in the context of a collaborative agreement, currently a proposal for a joint JRC-EBI collaboration is under discussion, aimed at developing a passive software-based monitoring system, screening for the presence of bio-threat agents (e.g. anthrax, botulism, cholera, etc.) in the samples whose metagenomics sequences are stored at the ENA. The project is also of interest to the EU Centres of Excellence on Chemical, Biological, Radiological and Nuclear Risk Mitigation (EU CBRN CoE). The PhD student will have the opportunity to interact with the scientific leading entities of these initiatives and to actively contribute to the success of such an action.

The project work programme:
The student will:
(i) review literature for existing methodologies;
(ii) explore appropriate statistical criteria for distinguishing the optimal pipelines for detection and monitoring
(iii) establish a pilot study to detect bio-threats of interest, identifying the key biomarkers to be used in the scans;
(iv) having defined this reference set, a pipeline will be developed with a view to being suitable for scanning metagenomics datasets on upload at ENA, thus monitoring risks as datasets are made available.

Funding Notes

Funding is provided from both UCD and JRC during the PhD project.

Eligibility: requirement for strong proven aptitude for bioinformatic research (programming and data analysis)

Related Subjects

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