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/)
Thank you for asking, yes Stubentiger does indeed stand for STUdying Balancing Evolution (Nfds) To Investigate GEnome Replacement
January 6, 2026 at 3:49 PM
Thank you for asking, yes Stubentiger does indeed stand for STUdying Balancing Evolution (Nfds) To Investigate GEnome Replacement
There's also an R package: github.com/bacpop/Stube...
So others can more easily apply/reuse/adapt this important model
So others can more easily apply/reuse/adapt this important model
GitHub - bacpop/Stubentiger: An R package for a negative frequency-dependent selection (NFDS) model to describe vaccine type replacement in Streptococcus pneumoniae populations
An R package for a negative frequency-dependent selection (NFDS) model to describe vaccine type replacement in Streptococcus pneumoniae populations - bacpop/Stubentiger
github.com
January 6, 2026 at 3:49 PM
There's also an R package: github.com/bacpop/Stube...
So others can more easily apply/reuse/adapt this important model
So others can more easily apply/reuse/adapt this important model
At least nothing else is getting worse
January 5, 2026 at 6:34 PM
At least nothing else is getting worse
It’s behind cloudflare captcha now (although I’m now wondering if that’s just the genome campus IPs) — so paperpile at least can’t auto download the pdf
January 5, 2026 at 6:06 PM
It’s behind cloudflare captcha now (although I’m now wondering if that’s just the genome campus IPs) — so paperpile at least can’t auto download the pdf
Looks very promising!!
One thing I didn't quite follow, when you mention 'a novel parameter for trait simulation that accounts for uncertainty in deep ancestral branches of a phylogeny' -- is that referring to the time to first event parameter?
One thing I didn't quite follow, when you mention 'a novel parameter for trait simulation that accounts for uncertainty in deep ancestral branches of a phylogeny' -- is that referring to the time to first event parameter?
January 5, 2026 at 5:45 PM
Looks very promising!!
One thing I didn't quite follow, when you mention 'a novel parameter for trait simulation that accounts for uncertainty in deep ancestral branches of a phylogeny' -- is that referring to the time to first event parameter?
One thing I didn't quite follow, when you mention 'a novel parameter for trait simulation that accounts for uncertainty in deep ancestral branches of a phylogeny' -- is that referring to the time to first event parameter?
The data was collected by the CABBAGE project, which has just been preprinted too: www.biorxiv.org/content/10.1...
www.biorxiv.org
November 19, 2025 at 12:27 PM
The data was collected by the CABBAGE project, which has just been preprinted too: www.biorxiv.org/content/10.1...