bacpop (bacterial population genomics & modelling)

We are the Pathogen Informatics and Modelling group at EMBL-EBI (also known as the Lees Group).

We aim to develop innovative, ethical and sharable approaches which help realise the power of sequencing to control pathogen threats. We are interested in both producing methods, and generating biological insights by applying these methods to data from a range of sources.

Our current main areas of work are:

For more information about these areas, see our research.

Find out more

To learn who we are and who we work with, see about us. Current vacancies are listed under working with us.

For more about our tools and methods, we have collated information on the software page, and you can also see our code on github.

We also have a youtube channel where we post some of our talks.

Guides and blog posts

We publish sample workflows and recommendations for common population genomics workflows in our guides.

Other posts, such as paper summaries, reviews and short how-to guides can be found on our blog.

Recent Blogs

image from Review: Wellcome Ideathon 2023

Review: Wellcome Ideathon 2023

The format Our Project (Student Team) Our Experience We attended the Wellcome Data Science Ideathon as semi-finalists in July 2023, which saw the Wellcome Trust invite around 100 researchers across 25 teams to compete to answer some of the biggest public health challenges we face today. The format The Ideathon was similar to a Hackathon; groups were tasked with answering specific questions in one of three themes - Infectious Disease, Climate & Health, and Mental Health.
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image from EMBL-UNESCO Residency in Infection Biology Research

EMBL-UNESCO Residency in Infection Biology Research

This application is now closed EMBL and UNESCO have recently announced a visitor programme as part of its infection biology scheme, in which we are participating (along with many other EMBL groups, see the link at the end for a full list). Our group is participating in the scheme, and we’d be love to hear from interested candidates who would like to work with us. We have particular expertise in analysing genomic data from bacterial pathogens, developing and using new bioinformatic tools to do so, as well as developing mathematical models for pathogen transmission and evolution.
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image from Mutation Spectra in Streptococcus pneumoniae

Mutation Spectra in Streptococcus pneumoniae

An Introduction to Mutation Spectra Mutational Spectra in Pneumococcal Epidemiology Conclusion An Introduction to Mutation Spectra It is intutitive that an organism’s ecological, phenotypic, or epidemiological context exposes it to distinct mutagens, and might thus produce specific signatures and patterns of mutation – that organism’s mutational spectrum. This idea is well-established in oncology. Cancer epidemiolgy studies have shown that a handful of genes, most prominently the human p53 gene, show patterns of mutation specific to the corresponding cancer types.
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More

Peer Review of the pre-print 'Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2'

Visualising microbial population structure with mandrake

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