Statistical Genetics and Epidemiology

The group carries out a broad range of computational biology research including Genetics, Genomics and Epidemiology. The research is both theoretical and applied, generating both new methods and genetic and epidemiological insights as well as computational tools and software. In Statistical Genetics we work to identify how mutations drive variability among people in health and disease risk, to understand the history of our and other species, and to understand the forces that have shaped evolution across the tree of life, whilst in Epidemiology we work to gain  robust insights into the transmission and control of outbreaks, epidemics and pandemics of infectious diseases including COVID-19, Ebola, H1N1 influenza, MERS, rabies, dengue and Zika.

Within the University of Oxford, we have close links to the Wellcome Centre for Human Genetics, the Pandemic Sciences Institute and the Big Data Institute. Members of the group have played central roles in some of the most important international collaborative projects in human genetics such as the HapMap Project, the Wellcome Trust Case-Control Consortium, the 1000 Genomes Project, the People of the British Isles Project, the Haplotype Reference Consortium, UK Biobank and the 100,000 Genomes Project. Others have worked collaboratively with the World Health Organization.

Join us for doctoral study

Our research group is truly collaborative. Most epidemiology students are jointly supervised by someone based elsewhere (including other University of Oxford departments such as Biology, the Nuffield Department of Medicine and the Mathematical Institute) or other organizations (including the World Health Organization, the Zoological Society London, the UKHSA, the University of Liverpool and Liverpool School of Hygiene and Tropical Medicine). We currently have around 20 research students. 

Take a look at our research, and if you're interested, get in contact. 

Working in a group with such a wide range of interconnected research, from examining the social implications of public health policy to proving mathematical properties of epidemiological models, provides a great opportunity for learning and collaboration.

Matthew Penn, DPhil Student

Dr Matthew Raybould

Postdoctoral Researcher


 

About Me

I’m currently a postdoctoral researcher in immunoinformatics working with Professor Charlotte Deane in the Oxford Protein Informatics Group.

Background

2021-Present: Postdoctoral Researcher in Immunoinformatics, Oxford Protein Informatics Group
2020-2021: Postdoctoral Research Assistant in Immunoinformatics, Oxford Protein Informatics Group
2016-2020: DPhil in Immunoinformatics, Oxford Protein Informatics Group (New College)
2012-2016: MChem in Chemistry (University of Oxford, Merton College)

Research Interests

Analysing datasets of B-cell/antibody/T-cell sequences and structures to better characterise the adaptive immune system, improving our understanding of pathogen responses, immunosenesence, immunodeficiency, autoimmunity, allergy, and cancer. I’m particularly motivated to translate the lessons we learn to the design of novel diagnostics and therapeutics that improve patient outcomes.

Publications

Contact Details

Email: matthew.raybould@stats.ox.ac.uk

Office: 2.04

Professor Tom Rainforth

Associate Professor of Statistical Machine Learning

Biographical sketch

I am an Associate Professor of Statistical Machine Learning, leader of the RainML Research Lab (rainml.uk), Tutorial Fellow at Mansfield College, and Principal Investigator of the ERC Starting Grant Data-Driven Algorithms for Data Acquisition (Mar 2024 - Feb 2029, funded by the UKRI Horizon Guarantee Scheme).  Though I only started my current Associate Professor role in September 2024, I have been a member of the Department since 2017, first as a postdoc working with Yee Whye Teh (Sep 2017 - Aug 2019), then as an associate member as part of a Junior Research Fellow in Computer Science at Christ Church College (Sep 2019 - Dec 2019), then as a Florence Nightingale Bicentennial Fellow and Tutor in Statistics and Probability (Jan 2020 - Feb 2024), and finally a Senior Research Fellow supported by my own ERC grant (Mar 2024 - Aug 2024). I originally studied Mechanical Engineering (MEng) at the University of Cambridge, while I did my D.Phil in Oxford under the supervision of Frank Wood and Michael Osborne, focusing mostly on probabilistic programming and Monte Carlo methods.  I also had a stint working in the Ferrari Formula 1 team in between the two.

Personal website: https://www.robots.ox.ac.uk/~twgr/

Research Interests

My research covers a wide range of topics in and around statistical machine learning and experimental design, with areas of particular interest including: 

  • Bayesian experimental design
  • Probabilistic and data-efficient approaches to machine learning
  • Active learning
  • Deep learning, with a particular focus on probabilistic approaches, deep representation learning, and deep generative models
  • Probabilistic programming
  • Approximate inference and Monte Carlo methods

Please see my Google Scholar page for an up-to-date list of publications.

Publications

Contact Details

Email: rainforth@stats.ox.ac.uk

Office: 1.21

Pronouns: He/Him

Graduate Students

Alex Forster
Angus Phillips
Freddie Bickford Smith
Guneet Singh Dhillon
Andrew Campbell
Desi Ivanova
Jannik Kossen
Kianoosh Ashouritaklimi

Ning Miao

Marcel Hedman
Tim Reichelt
Mrinank Sharma
Yuyang Shi
Shahine Bouabid
Jin Xu

Dr Konstantin Shestopaloff

Senior Postdoctoral Researcher

About Me

I received my PhD in Biostatistics from the University of Toronto, Canada in 2017, specializing in methods for analysis of microbiome and ecological community data. Subsequently, I worked as a biostatistician in arthritis research, conducting analyses of metabolomic and miRNA signature data, and in population health, where I estimated temporal effects of polygenic risk scores in obesity. Currently I'm the Analytics Lead for the IL-17 project group within the Oxford-Novartis collaboration.

Research Interests

My research focus is on methods development with applications to clinical and biomedical data, particularly methods for addressing sparsity. Some of my previous work includes inference methods for rare species in microbiome data and total species estimators. My current work is using random effect splines for modelling and prediction in longitudinal data.

Contact Details

Email: konstantin.shestopaloff@ndm.ox.ac.uk

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