John Lees
@johnlees.bacpop.org
Pathogen informatics and modelling http://bacpop.org
(Research group leader at EMBL-EBI - http://ebi.ac.uk/research/lees/)
(Research group leader at EMBL-EBI - http://ebi.ac.uk/research/lees/)
Reposted by John Lees
🎉 New year, NEW PREPRINT!
Bacteria exhibit astonishing genetic diversity, but where do new genes come from?
My best friend Arya Kaul (/labmate in the @baym lab) investigates how advantageous deletions can spawn new genes - "deletion-born fusions." 🧵:
Bacteria exhibit astonishing genetic diversity, but where do new genes come from?
My best friend Arya Kaul (/labmate in the @baym lab) investigates how advantageous deletions can spawn new genes - "deletion-born fusions." 🧵:
Novel genes arise from genomic deletions across the bacterial tree of life https://www.biorxiv.org/content/10.64898/2026.01.05.697752v1
January 6, 2026 at 4:09 PM
🎉 New year, NEW PREPRINT!
Bacteria exhibit astonishing genetic diversity, but where do new genes come from?
My best friend Arya Kaul (/labmate in the @baym lab) investigates how advantageous deletions can spawn new genes - "deletion-born fusions." 🧵:
Bacteria exhibit astonishing genetic diversity, but where do new genes come from?
My best friend Arya Kaul (/labmate in the @baym lab) investigates how advantageous deletions can spawn new genes - "deletion-born fusions." 🧵:
Our new preprint which reimplements "the NFDS model" (of Corander et al) to forecast populations after vaccination as a compartmental model, and uses new bioinformatic tools to create and process the pangenome data
We look at which surveillance strategies are best to correctly forecast changes
We look at which surveillance strategies are best to correctly forecast changes
Very happy to share our preprint on a mathematical model for Streptococcus pneumoniae population dynamics after vaccine introductions. It's a reusable model that describes vaccine replacement dynamics and can help to determine strategies for genomic surveillance: doi.org/10.64898/2025.12.18.695090
A reusable model of pangenome selection informs optimal surveillance strategies over vaccine introductions
The human pathogen Streptococcus pneumoniae is a major cause of disease, including pneumonia and meningitis. The introduction of Pneumococcal Conjugate Vaccines (PCVs) initially reduced the burden of ...
doi.org
January 6, 2026 at 3:49 PM
Our new preprint which reimplements "the NFDS model" (of Corander et al) to forecast populations after vaccination as a compartmental model, and uses new bioinformatic tools to create and process the pangenome data
We look at which surveillance strategies are best to correctly forecast changes
We look at which surveillance strategies are best to correctly forecast changes
RIP automated downloads of PDFs from biorxiv it seems, I suppose we have AI to thank for that
January 5, 2026 at 5:05 PM
RIP automated downloads of PDFs from biorxiv it seems, I suppose we have AI to thank for that
Some blogging from over the holiday, something for everyone I'm sure:
Cooking johnlees.me/posts/xmas-d...
Video games johnlees.me/posts/review...
DIY johnlees.me/posts/towel-...
(back to preprints tomorrow)
Cooking johnlees.me/posts/xmas-d...
Video games johnlees.me/posts/review...
DIY johnlees.me/posts/towel-...
(back to preprints tomorrow)
Christmas dinner
Mostly for personal reference for next year, here were my xmas dinner notes. I forgot about stuffing, and didn’t make yorkshire puddings properly because our main oven is broken (we have a convection ...
johnlees.me
January 5, 2026 at 1:49 PM
Some blogging from over the holiday, something for everyone I'm sure:
Cooking johnlees.me/posts/xmas-d...
Video games johnlees.me/posts/review...
DIY johnlees.me/posts/towel-...
(back to preprints tomorrow)
Cooking johnlees.me/posts/xmas-d...
Video games johnlees.me/posts/review...
DIY johnlees.me/posts/towel-...
(back to preprints tomorrow)
We're organising a microbes & deep learning session at SMBE next year -- looking forward to seeing your abstracts!
Organisers
- @bacpop.org | @embl.org
- @aweimann.bsky.social | University of Cambridge
Invited Speaker
- @audeber.bsky.social | Institut Pasteur
- @bacpop.org | @embl.org
- @aweimann.bsky.social | University of Cambridge
Invited Speaker
- @audeber.bsky.social | Institut Pasteur
December 15, 2025 at 11:26 AM
We're organising a microbes & deep learning session at SMBE next year -- looking forward to seeing your abstracts!
Nice to see some of our tools getting used in public health
(in this case PopPIPE, which is downstream subclustering/transmission tool to be run on PopPUNK data)
(in this case PopPIPE, which is downstream subclustering/transmission tool to be run on PopPUNK data)
Antimicrobial resistance is putting public health under pressure.
Find out how PopPIPE, a bioinformatics tool developed at EMBL-EBI, is helping Public Health Scotland track outbreaks, reveal transmission links, and respond faster.
www.ebi.ac.uk/about/news/r...
#WAAW2025 #ActOnAMR
🧬💻
Find out how PopPIPE, a bioinformatics tool developed at EMBL-EBI, is helping Public Health Scotland track outbreaks, reveal transmission links, and respond faster.
www.ebi.ac.uk/about/news/r...
#WAAW2025 #ActOnAMR
🧬💻
Case study: EMBL-EBI tool enables genomic outbreak surveillance for NHS Scotland
A new genomic analysis tool developed at EMBL-EBI, is helping NHS Scotland tackle antimicrobial resistance and improve outbreak response.
www.ebi.ac.uk
November 25, 2025 at 9:10 AM
Nice to see some of our tools getting used in public health
(in this case PopPIPE, which is downstream subclustering/transmission tool to be run on PopPUNK data)
(in this case PopPIPE, which is downstream subclustering/transmission tool to be run on PopPUNK data)
Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
Antimicrobial resistance (AMR) is a growing health threat, making infections harder to treat and complicating routine medical care.
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
A new gateway to global antimicrobial resistance data
New online portal connects bacterial genomes with experimental resistance data to support antimicrobial resistance research.
www.ebi.ac.uk
November 19, 2025 at 12:27 PM
Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
Reposted by John Lees
A PhD project on historical genomics in the declining red squirrel in Britain is available in my group, through the @aries-dtp.bsky.social. Use historical genomes to track the effects of decline and genetic rescue in this charismatic species. aries-dtp.ac.uk/studentships...
Historical genomics of the declining red squirrel in Britain | Aries
Dr Anders Bergström, School of Biological Sciences, University of East Anglia Professor Cock van Oosterhout, School of Environmental Sciences, University of East Anglia Dr Selina Brace…
aries-dtp.ac.uk
November 17, 2025 at 1:12 PM
A PhD project on historical genomics in the declining red squirrel in Britain is available in my group, through the @aries-dtp.bsky.social. Use historical genomes to track the effects of decline and genetic rescue in this charismatic species. aries-dtp.ac.uk/studentships...
Congratulations to Zam!
Honoured and quite blown-over to receive this award. I have been, and continue to be, very lucky - first with great mentors, and then really prodigious students, postdocs and collaborators. Working with them has been a joy.
Congratulations to @zaminiqbal.bsky.social from @milnerevolution.bsky.social on being awarded the 2026 Mary Lyon Medal!
November 14, 2025 at 2:26 PM
Congratulations to Zam!
Reposted by John Lees
Just a quick plug: I've made a few updates to ExpEvoAnalyzer (variant functional annotation in experimental evolution studies) to use bwa as well as ska2, and to use existing or de novo annotations. It just might help streamline your pesky bioinformatics analysis! github.com/samhorsfield...
GitHub - samhorsfield96/ExpEvoAnalyzer: A workflow to analyse experimental evolution data.
A workflow to analyse experimental evolution data. - samhorsfield96/ExpEvoAnalyzer
github.com
November 7, 2025 at 3:07 PM
Just a quick plug: I've made a few updates to ExpEvoAnalyzer (variant functional annotation in experimental evolution studies) to use bwa as well as ska2, and to use existing or de novo annotations. It just might help streamline your pesky bioinformatics analysis! github.com/samhorsfield...
Reposted by John Lees
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Reposted by John Lees
Going through @samuelhorsfield.bsky.social presentation on pangenome graphs in comparative genomics, courtesy of @training.ebi.embl.org.
Fascinating tidbit on history of alignment based sequence graph - it goes all the way back to 1989 (Hein), era of Apple IIs and IBM PS/2s. Great talk!
💻🧬🦠🧫
Fascinating tidbit on history of alignment based sequence graph - it goes all the way back to 1989 (Hein), era of Apple IIs and IBM PS/2s. Great talk!
💻🧬🦠🧫
November 5, 2025 at 3:19 PM
Going through @samuelhorsfield.bsky.social presentation on pangenome graphs in comparative genomics, courtesy of @training.ebi.embl.org.
Fascinating tidbit on history of alignment based sequence graph - it goes all the way back to 1989 (Hein), era of Apple IIs and IBM PS/2s. Great talk!
💻🧬🦠🧫
Fascinating tidbit on history of alignment based sequence graph - it goes all the way back to 1989 (Hein), era of Apple IIs and IBM PS/2s. Great talk!
💻🧬🦠🧫
Reposted by John Lees
Bonjour! Masters students in France 🇫🇷, we’ve got an internship for you, in collaboration with the French Embassy in London.
Aimed at students of computer science, statistics or bioinformatics.
Deadline: 7 December 2025
Find out more and apply:
www.ebi.ac.uk/about/jobs/i...
Aimed at students of computer science, statistics or bioinformatics.
Deadline: 7 December 2025
Find out more and apply:
www.ebi.ac.uk/about/jobs/i...
November 3, 2025 at 11:00 AM
Bonjour! Masters students in France 🇫🇷, we’ve got an internship for you, in collaboration with the French Embassy in London.
Aimed at students of computer science, statistics or bioinformatics.
Deadline: 7 December 2025
Find out more and apply:
www.ebi.ac.uk/about/jobs/i...
Aimed at students of computer science, statistics or bioinformatics.
Deadline: 7 December 2025
Find out more and apply:
www.ebi.ac.uk/about/jobs/i...
Reposted by John Lees
🧬Join us for the next TARGetAMR webinar!
💊Dangerous Miracle: A Brief History of Antibiotics
🗓️Wednesday 19 November🕐 1–2pm 💻 Online
🎙️With Liam Shaw, Computational Biologist at University of Bristol
🔗Register now! www.targetamr.org.uk/hdrevents/ta...
💊Dangerous Miracle: A Brief History of Antibiotics
🗓️Wednesday 19 November🕐 1–2pm 💻 Online
🎙️With Liam Shaw, Computational Biologist at University of Bristol
🔗Register now! www.targetamr.org.uk/hdrevents/ta...
November 3, 2025 at 11:04 AM
🧬Join us for the next TARGetAMR webinar!
💊Dangerous Miracle: A Brief History of Antibiotics
🗓️Wednesday 19 November🕐 1–2pm 💻 Online
🎙️With Liam Shaw, Computational Biologist at University of Bristol
🔗Register now! www.targetamr.org.uk/hdrevents/ta...
💊Dangerous Miracle: A Brief History of Antibiotics
🗓️Wednesday 19 November🕐 1–2pm 💻 Online
🎙️With Liam Shaw, Computational Biologist at University of Bristol
🔗Register now! www.targetamr.org.uk/hdrevents/ta...
Reposted by John Lees
Very happy about this work on phylogenetic neural inference, led by @lblassel.bsky.social :)
We’re very excited to finally share our latest work:
Phyloformer 2, a deep end-to-end phylogenetic reconstruction method: arxiv.org/abs/2510.12976
Using neural posterior estimation, it outperforms Phyloformer 1 and maximum-likelihood methods under simple and complex evolutionary models.
🧵1/17
Phyloformer 2, a deep end-to-end phylogenetic reconstruction method: arxiv.org/abs/2510.12976
Using neural posterior estimation, it outperforms Phyloformer 1 and maximum-likelihood methods under simple and complex evolutionary models.
🧵1/17
October 17, 2025 at 5:27 AM
Very happy about this work on phylogenetic neural inference, led by @lblassel.bsky.social :)
We are running a hackathon at EBI in Feb: biomics.bacpop.org
If you are at EMBL, ETH Zurich, GRC or GIMM working on a biological problem in data science or programming, consider putting a project forwards!
If you are at EMBL, ETH Zurich, GRC or GIMM working on a biological problem in data science or programming, consider putting a project forwards!
BIOMICS hackathon at EMBL-EBI
Hackathon held in Hinxton 2026
biomics.bacpop.org
October 15, 2025 at 4:29 PM
We are running a hackathon at EBI in Feb: biomics.bacpop.org
If you are at EMBL, ETH Zurich, GRC or GIMM working on a biological problem in data science or programming, consider putting a project forwards!
If you are at EMBL, ETH Zurich, GRC or GIMM working on a biological problem in data science or programming, consider putting a project forwards!
Reposted by John Lees
Proud to see my lab's work on M. tuberculosis and P. aeruginosa highlighted in this blog post
October 1, 2025 at 11:29 AM
Proud to see my lab's work on M. tuberculosis and P. aeruginosa highlighted in this blog post
Now published, our tool to run (almost) all biological models interactively in your web browser
Paper: academic.oup.com/bioinformati...
Website: biomodels.bacpop.org
Code: github.com/bacpop/SBMLt...
Paper: academic.oup.com/bioinformati...
Website: biomodels.bacpop.org
Code: github.com/bacpop/SBMLt...
September 29, 2025 at 9:49 AM
Now published, our tool to run (almost) all biological models interactively in your web browser
Paper: academic.oup.com/bioinformati...
Website: biomodels.bacpop.org
Code: github.com/bacpop/SBMLt...
Paper: academic.oup.com/bioinformati...
Website: biomodels.bacpop.org
Code: github.com/bacpop/SBMLt...
Reposted by John Lees
A new ggCaller version is out! v1.4 includes tweaks to improve efficiency, outputs Panaroo-friendly GFFs, and enables iterative gene calling; if you have already called a gene set, you can now add more genomes either one by one or in batches github.com/bacpop/ggCal...
GitHub - bacpop/ggCaller: Bifrost graph gene caller.
Bifrost graph gene caller. Contribute to bacpop/ggCaller development by creating an account on GitHub.
github.com
September 24, 2025 at 1:27 PM
A new ggCaller version is out! v1.4 includes tweaks to improve efficiency, outputs Panaroo-friendly GFFs, and enables iterative gene calling; if you have already called a gene set, you can now add more genomes either one by one or in batches github.com/bacpop/ggCal...
Reposted by John Lees
The EMBL PhD programme is open until 13th October (entry ~Sep 2026):
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
EMBL International PhD Programme – Unique in the world and waiting for you!
www.embl.org
September 17, 2025 at 3:49 PM
The EMBL PhD programme is open until 13th October (entry ~Sep 2026):
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
Thanks for all the trainers and attendees on this course, which was a lot of fun to run, and hopefully filled a gap in genomics/modelling training
And especially co-organisers @leonielorenz.bsky.social @sonjalehtinen.bsky.social Joel Hellewell
And especially co-organisers @leonielorenz.bsky.social @sonjalehtinen.bsky.social Joel Hellewell
Thank you to everyone who joined us this week for the @embo.org Practical Course 'Methods for infectious disease modelling using genomics'.
Join us for 2026's EMBO Practical Course. Sign up for 'Causality in biomedicine' alerts and hear as this new course develops: www.ebi.ac.uk/training/eve...
🧬🧫
Join us for 2026's EMBO Practical Course. Sign up for 'Causality in biomedicine' alerts and hear as this new course develops: www.ebi.ac.uk/training/eve...
🧬🧫
September 22, 2025 at 9:43 AM
Thanks for all the trainers and attendees on this course, which was a lot of fun to run, and hopefully filled a gap in genomics/modelling training
And especially co-organisers @leonielorenz.bsky.social @sonjalehtinen.bsky.social Joel Hellewell
And especially co-organisers @leonielorenz.bsky.social @sonjalehtinen.bsky.social Joel Hellewell
Reposted by John Lees
Thank you to everyone who joined us this week for the @embo.org Practical Course 'Methods for infectious disease modelling using genomics'.
Join us for 2026's EMBO Practical Course. Sign up for 'Causality in biomedicine' alerts and hear as this new course develops: www.ebi.ac.uk/training/eve...
🧬🧫
Join us for 2026's EMBO Practical Course. Sign up for 'Causality in biomedicine' alerts and hear as this new course develops: www.ebi.ac.uk/training/eve...
🧬🧫
September 19, 2025 at 8:33 AM
Thank you to everyone who joined us this week for the @embo.org Practical Course 'Methods for infectious disease modelling using genomics'.
Join us for 2026's EMBO Practical Course. Sign up for 'Causality in biomedicine' alerts and hear as this new course develops: www.ebi.ac.uk/training/eve...
🧬🧫
Join us for 2026's EMBO Practical Course. Sign up for 'Causality in biomedicine' alerts and hear as this new course develops: www.ebi.ac.uk/training/eve...
🧬🧫
Reposted by John Lees
Just launched an interactive Bayesian epidemic modelling platform that runs entirely in your browser!
No downloads, no installations, no expensive software licenses. Just open the link and start modelling disease dynamics with real-time parameter estimation.
>> widget-bayesian-sir.davidhodgson.me
No downloads, no installations, no expensive software licenses. Just open the link and start modelling disease dynamics with real-time parameter estimation.
>> widget-bayesian-sir.davidhodgson.me
Interactive Bayesian Epidemic Modelling
widget-bayesian-sir.davidhodgson.me
September 19, 2025 at 4:53 PM
Just launched an interactive Bayesian epidemic modelling platform that runs entirely in your browser!
No downloads, no installations, no expensive software licenses. Just open the link and start modelling disease dynamics with real-time parameter estimation.
>> widget-bayesian-sir.davidhodgson.me
No downloads, no installations, no expensive software licenses. Just open the link and start modelling disease dynamics with real-time parameter estimation.
>> widget-bayesian-sir.davidhodgson.me
The EMBL PhD programme is open until 13th October (entry ~Sep 2026):
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
EMBL International PhD Programme – Unique in the world and waiting for you!
www.embl.org
September 17, 2025 at 3:49 PM
The EMBL PhD programme is open until 13th October (entry ~Sep 2026):
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them