Category Archives: Public Health England

13Apr / 2021

New positions: Data Scientist in Public Health Epidemiology and Postdoc in Statistical Methods

I am looking to fill two positions at the Big Data Institute, Nuffield Department of Population Health, University of Oxford: a Data Scientist in Public Health Epidemiology and a Postdoctoral Researcher in Statistical Methods.

The Big Data Institute (BDI) is an interdisciplinary research centre that develops, evaluates and deploys efficient methods for acquiring and analysing biomedical data at scale and for exploiting the opportunities arising from such studies. The Nuffield Department of Population Health (NDPH), a key partner in the BDI, contains world-renowned population health research groups and is an excellent environment for multi-disciplinary teaching and research.  

The role of the Data Scientist in Public Health Epidemiology is to help pilot a project developing systems for continuous record linkage between a large Public Health England (PHE) data source and other population health records, with the aim of facilitating research into infectious diseases.

The post holder will manage and develop record linkage algorithms comparing records with relational databases containing health records via appropriate anonymization protocols, and manage and develop systems for identifying incoming records of interest, for near-real time updating of SQL databases, and for issuing email and SMS alerts in response to these events. The responsibilities will also include contributing to large-scale statistical studies using public health records to investigate disease epidemiology, and analysing and interpreting results, reviewing and refining working hypotheses, writing reports and presenting findings to colleagues.

To be considered, applicants will hold a degree in Computer Science, Data Science, Statistics, or another relevant subject with a strong quantitative component, or have equivalent experience. They will also need an understanding of relational database construction and SQL queries, experience coding in at least one common programming language (e.g. C#, Java, Python) and good interpersonal skills with the ability to work closely with others as part of a team, while taking personal responsibility for assigned tasks.

The role of the Postdoctoral Researcher in Statistical Methods is to develop statistical methods based on the harmonic mean p-value (HMP) approach. The HMP bridges classical and Bayesian approaches to model-averaged hypothesis testing, with applications to very large-scale data analysis problems in biomedical science.

The post holder will join a team with expertise in statistical inference, population genetics, genomics, evolution, epidemiology and infectious disease. The responsibilities will include developing statistical methods based on the HMP, undertaking research under the direction of the principal investigator, helping with supervision within the project as required, driving forward manuscripts for publication in collaboration with group members and disseminating results through other means such as academic conferences.

To be considered, applicants will hold, or be close to completion of, a PhD/DPhil involving statistical methods development and a track record of publication-quality methods development in statistical theory or methods development. The ability to work independently in pursuing the goals of an agreed research plan and excellent interpersonal skills and the ability to work closely with others as a team are also essential.

The closing date for both positions is noon on the 5th May 2021. Only applications received through the online system will be considered:

Posted by in Big Data Institute, data science, Harmonic mean p-value, Postdoc, Public Health England, Recruitment

Permalink

21Aug / 2020

The group’s research response to COVID-19

This is an update on the group's research response to the COVID-19 pandemic. As an infectious disease group we have been keen to contribute to the international research effort where we could be useful, while recognising the need to continue our research on other important infections where possible.

  • Bugbank. Thanks to a pre-existing collaboration between our group, Public Health England and UK Biobank, we were in a position to help rapidly facilitate COVID-19 research via SARS-CoV-2 PCR-based swab test results. Beginning mid-March, we worked to provide regular (usually weekly) updates of tests results, which were made available to all UK Biobank researchers beginning April 17th. This is one of several resources on COVID-19 linked to UK Biobank. Beginning in May we provided feeds to other cohorts: INTERVAL, COMPARE, Genes & Health and the NIHR BioResource. We provide updates on this work through the project website www.bugbank.uk. We have published a paper describing the dynamic data linkage in Microbial Genomics (press release). Key collaborators in this project are Jacob Armstrong (Big Data Institute) Naomi Allen (UK Biobank) and David Wyllie and Anne Marie O'Connell (Public Health England).


  • Epidemiological risk factors for COVID-19. Graduate student Nicolas Arning and I are developing an approach to quantify the effects of lifestyle and medical risk factors for COVID-19 in the UK Biobank that accounts for inherent uncertainty in which risk factors to consider. The new method employs the harmonic mean p-value, a model-averaging approach for big data that we published previously. We are in the process of evaluating the performance of the approach, comparing it to machine learning, and interpreting the results.

  • Antibody testing for the UK Government. Postdoc Justine Rudkin has been working in the lab with Derrick Crook, Sir John Bell and others to measure the efficacy of antibody tests for the UK Government. They have tested many hundreds of kits to establish the sensitivity and specificity of the tests to help evaluate the utility of a national testing programme. This work was crucial in demonstrating the limitations of early blood-spot based tests, and the credibility of subsequent generations of antibody tests. The work has been published in Wellcome Open Research.


Work on other infections that has continued during the lockdown. Postdoc Sarah Earle continues research into pathogen genetic risk factors for diseases including tuberculosis and meningococcal meningitis, while Steven Lin has continued to pursue work on hepatitis C virus genetics and epidemiology. Many of our close collaborators are infection doctors and they have of course been recalled to clinical duties. Laboratory work in the group has been severely disrupted, particularly several of Justine's Staphylococcus aureus projects. We are keen to pick up on those projects where we left off when the chance arrives.

Posted by in covid 19, COVID-19 Host Genetics Initiative, Epidemiology, GWAS, machine learning, microbial genomics, New England Journal of Medicine, Public Health England, statistics, UK Biobank, Wellcome Open Research

Permalink

21Aug / 2020

Presentation on identifying COVID-19 inpatients from Public Health England data

This is a presentation I gave at the COVID-19 Host Genetics Initiative meeting on 2nd July 2020 about using Public Health England's Second Generation Surveillance System to identify COVID-19 inpatients among SARS-CoV-2 positive individuals in England.

For further information, please see this bugbank blog post comparing inpatients identified using SGSS and Hospital Episode Statistics.

Posted by in covid 19, Presentations, Public Health England

Permalink

18May / 2018

Postdoc positions in Data Science and Molecular Microbiology

These positions are now closed
As part of the move to the Big Data Institute, two new postdoctoral positions funded by the Robertson Foundation are available in Data Science and Molecular Microbiology.

The BDI is a new interdisciplinary research centre aiming to develop, evaluate and deploy efficient methods for acquiring and analysing biomedical data at scale and for exploiting the opportunities arising from such studies. The BDI is a joint venture between the renowned Nuffield Department of Population Health (NDPH) and NDM.

The Data Scientist role, split between the BDI and London, will be part of a team developing systems for continuous record linkage between Public Health England and other population health records. The aims are to design record linkage algorithms, manage front ends for viewing the data source, and analyse and interpret results. We're looking for a graduate or equivalent experience in computer science, data science, statistics, or any other relevant subject with a strong quantitative component. Knowledge of databases like SQL and computer programming are needed.

The Molecular Microbiology role, based mainly at the John Radcliffe Hospital Microbiology Department, will be part of a team researching Staphylococcus aureus infection using RNA sequencing, genome wide association studies, and biochemical and immunological assays of bacterial behaviour. The aims include designing microbiological protocols, researching bacterial molecular genetics and data analysis. We're looking for a PhD or equivalent experience in a relevant subject such as microbiology, immunology, genetics or biochemistry. Experience designing protocols and basic microbiological and immunological skills are required.

The deadline for the posts is Noon on 6 June 2018. Both are one year positions. For more details or to apply click here for the Data Scientist role and here for the Molecular Microbiologist role.

Posted by in Big Data Institute, Nuffield Department of Medicine, Nuffield Department of Population Health, Postdoc, Public Health England, Recruitment, Staphylococcus aureus

Permalink