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 EMBL-UNESCO Residency in Infection Biology Research

EMBL-UNESCO Residency in Infection Biology Research

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.
read more
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.
read more
image from Peer Review of the pre-print 'Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2'

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

Introduction Constructing the null distribution Comparing observations to the null distributions How do new restriction site locations emerge naturally? Mutation analysis Conclusion This is a peer review of the pre-print “Endonuclease fingerprint indicates a synthetic origin of SARS-CoV2”, it is highly recommended that you go and read the pre-print in order to understand this review. Introduction The broad thread of the argument in the pre-print is that a synthetically engineered COVID-19 virus would be created using a process where ‘restriction’ enzymes cut the vaccine genome into roughly equal fragments so that they can be cloned in a bacterial system before being reassembled.
read more

More

Visualising microbial population structure with mandrake

All Blogs