Research Associate in Outbreak Response analytics and System Design

Imperial College London - Department of Infectious Disease Epidemiology, School of Public Health Faculty of Medicine

Campus: St Mary’s Campus, Paddington

Applications are invited for the post of Research Associate in Outbreak Response analytics and System Design to join the Department of Infectious Disease Epidemiology in the School of Public Health at Imperial College London.

The post-holder will be part of the National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Modelling Methodology, based in the Department of Infectious Disease Epidemiology, 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.

Epidemic investigation increasingly relies on the analysis of various types of data, such as dates of symptom onset, geographic locations, contact data and pathogen genome sequences. Besides the methodological challenges posed by such analyses, their integration  into a coherent, robust data analysis pipeline remains testing, especially in the context of epidemic emergency and low resource settings. To address these challenges, the R Epidemics Consortium (RECON, has been formed as an initiative for creating efficient, statistically advanced and robust software tools for outbreak response.

The purpose of this post is to build upon these developments and translate them into flexible and robust data analysis pipelines adapted to different contexts, ranging from the integration of evidence synthesis methods for genomic pathogen surveillance, to easily deployable systems for short term incidence forecasting and situation report automation. The postholder will be able to work on a variety of exciting projects, including:

  • Integrating clustering methods developed in the research team into existing genomics surveillance pipelines at Public Health England (PHE)
  • Templated graphical user interfaces for RECON packages
  • Reproducible data cleaning/curation
  • Automated situation report systems using literate programming
  • Deployable analysis systems, using self-contained R environments and container technology
  • Interfacing mobile-based data collection with analytics pipelines
  • Secured data analysis
  • Modern training resources: technical blogs (blogdown), interactive tutorials (learnr), cheatsheets, and podcasts.

Applicants should have a PhD in any of the following disciplines: biostatistics, data science, statistical genetics/genomics, bioinformatics and experience in high-profile R package development.

This post is full time and fixed term until 31 March 2019 and will be based at the St Mary’s Campus, Paddington. Imperial College is supportive of flexible working. The College is happy to discuss the possibility of implementing such arrangements for this post, with suitably qualified people, subject to operational requirements.

Should you have any queries please contact: Dr Thibaut Jombart

Closing date: 4 April 2018 (Midnight BST)

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Committed to equality and valuing diversity, we are also an Athena SWAN Silver Award winner, a Stonewall Diversity Champion, a Disability Confident Employer and are working in partnership with GIRES to promote respect for trans people.

The College is a proud signatory to the San-Francisco Declaration on Research Assessment (DORA), which means that in hiring and promotion decisions, we evaluate applicants on the quality of their work, not the journal impact factor where it is published. For more information, see

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