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. We currently have two main lines of research: understanding the mechanisms of pathogen evolution, and developing methods and resources that lower the barrier to entry for infectious disease genomics and modelling.

We use the following methods to address these questions:

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.

Databases and training course materials can be found under resources.

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 ggCaller installation

ggCaller installation

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image from Multiple horses for multiple courses

Multiple horses for multiple courses

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image from Graph-based gene prediction with ggCaller

Graph-based gene prediction with ggCaller

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Review: Wellcome Ideathon 2023

EMBL-UNESCO Residency in Infection Biology Research

Mutation Spectra in Streptococcus pneumoniae

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

All Blogs