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Three Year PhD Studentship in designing efficient, statistically advanced and robust software tools for outbreak analytics

Three Year PhD Studentship in tools for Modelling and Health economics
Fully funded PhD studentship with stipend available for entry in September 2021.
Based in Imperial College’s Department of Infectious Disease Epidemiology within the School of Public Health, the studentship is part of the National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Modelling and Health Economics ( The project will involve close collaboration with the Centre for Mathematical Modelling of Infectious Diseases (CMMID) at the London School of Hygiene and Tropical Medicine (LSHTM), and Public Health England (PHE).
The purpose of this studentship is to build upon developments initiated as part of the R Epidemics Consortium (RECON,, an initiative we created for designing efficient, statistically advanced and robust software tools for outbreak analytics. RECON tools have been widely adopted for informing the response to infectious disease outbreaks in real time, from automated data pipelines deployed for the Ebola outbreak in Eastern Democratic Republic of the Congo (DRC) to routine estimations of transmissibility of COVID-19 using EpiEstim (
One of the keys to informing operations in real time is to integrate various sources of information. Such integration requires sound statistical frameworks and well-designed software tools. The project supervisors have pioneered such applications, with a specific focus on outbreak reconstruction (“who infected whom?”) and the identification of clusters of related cases, by combining epidemiological, contact and genetic data. The PhD student will explore these methodological avenues further through a variety of exciting projects including:
• Extending outbreak reconstruction tools (combining epidemiological and genetic data) developed in the research team specifically for the real-time investigation of nosocomial outbreaks, e.g. to explore the role of health care workers in disease transmission
• Developing visualisation tools for patient movements and clinical timelines
• Applying these tools to nosocomial COVID-19 outbreaks and/or bacterial nosocomial outbreaks
• Integrating these tools as well as other clustering methods developed in the research team into existing genomics surveillance pipelines at Public Health England (PHE)
• Characterising user requirements (technical, cultural and training) to facilitate tools being used in practice
• Developing of modern training resources

The PhD student will be based in the Department of Infectious Disease Epidemiology at Imperial College London, which is host to several world-leading groups in infectious disease epidemiology and has a strong track record of applied collaborative work with national and international agencies in support of policy planning and response operations against emerging infectious disease threats.
The HPRU in Modelling and Health Economics combines the complementary strengths of the three largest and most diverse teams of infectious disease modellers in the UK, at Public Health England, London School of Hygiene and Tropical Medicine, and Imperial College. Its aim is to deliver a step change in research capacity available for health protection modelling. The PhD project is part of the ‘Capacity-building, dissemination, translation and tools’ theme, with interactions with related projects including and ‘Analysis, forecasting and response to outbreaks and acute health-system pressures’ and ‘Behavioural and economic drivers of disease transmission’
The PhD student will work closely with the Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, which since its foundation in 2007 has been an international resource and centre of excellence for research of the epidemiological analysis and modelling of novel infectious disease outbreaks. Imperial College London offers a range of training courses to PhD student that the successful candidate would have access to.
Applicants should have, a first or upper second-class degree and have, or expect to achieve, a Masters degree in relevant subject which includes all of those from the quantitative and life sciences – including biology, genetics, mathematics, physics, statistics, biostatistics, data science, statistical genetics/genomics, bioinformatics
Given the nature of the project, advanced programming skills are essential. Experience programming in R, writing R packages, and experience using version control system (such as git) are all highly desirable. Knowledge or interest of infectious disease epidemiology and/or genetic data analysis of pathogens is desirable as well.
One studentship providing a tax-free stipend to cover living expenses. The 2021 stipends will be not less than £17,285 in year 1, rising to £17,609 in year 2.
Tuition fees at the rate applicable to Home students are provided. Suitably qualified students non-eligible for home tuition fees are welcome to apply, but will be liable for paying the difference between the home and overseas fee rates. Eligibility criteria for home tuition are outlined here:

Application procedure
Applications should consist of 2 parts, combined in a single PDF document:
• A CV with the names, mailing addresses and email addresses of at least two academic referees
• A one page statement indicating why you want to join this PhD programme.
Please ensure that you include your own email address on your CV as this will be our main method of corresponding with you. Applications should be submitted via our application form only. Emailed applications not accepted.
Closing date for applications: 30 April 2021
Interviews will be held in May
Further Information
Informal enquiries can be directed to Dr Anne Cori:

PhD position
Imperial College London
United Kingdom
Closing date
April 30th, 2021
Posted on
April 9th, 2021 17:14
Last updated
April 9th, 2021 17:14