Ben Vezina
@bananabenana.bsky.social
Computational Biology | Microbiology | Molecular Biology postdoc.
Right now I do lots of stats, vis, metabolic modelling and quantitative genomics
can we pls fix greenhouse emissions, gov, pls
Right now I do lots of stats, vis, metabolic modelling and quantitative genomics
can we pls fix greenhouse emissions, gov, pls
Reposted by Ben Vezina
#NewResearch
A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people
@greening.bsky.social
#microsky
www.nature.com/articles/s41...
A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people
@greening.bsky.social
#microsky
www.nature.com/articles/s41...
A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people - Nature Microbiology
A previously uncharacterized microbial enzyme is responsible for the production of molecular hydrogen in the gut, which drives the growth of other bacteria and has implications for human health.
www.nature.com
November 5, 2025 at 3:40 PM
#NewResearch
A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people
@greening.bsky.social
#microsky
www.nature.com/articles/s41...
A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people
@greening.bsky.social
#microsky
www.nature.com/articles/s41...
Reposted by Ben Vezina
London interdisciplinary #PhD position now open with myself, @sergemostowylab.bsky.social, & @gmknght.bsky.social on #phage -bacteria-host immune dynamics for WHO priority bacterial pathogens #Klebsiella, #Shigella, and #Staph. Combines cellular microbiology, genomics, & mathematical modelling.
2026-27 Project (Dyson & Mostowy & Knight) - MRC London Intercollegiate Doctoral Training Partnership Studentships
PHACTS: Unravelling PHAge-baCTeria-host immune dynamicS to inform phage therapy SUPERVISORY TEAM Supervisor Dr Zoe Dyson...
mrc-lid.lshtm.ac.uk
November 13, 2025 at 11:11 AM
London interdisciplinary #PhD position now open with myself, @sergemostowylab.bsky.social, & @gmknght.bsky.social on #phage -bacteria-host immune dynamics for WHO priority bacterial pathogens #Klebsiella, #Shigella, and #Staph. Combines cellular microbiology, genomics, & mathematical modelling.
As part of leaving Windows 10 behind and refusing to upgrade to W11 spyware (Windows Recall, ads etc), I've moved everything over to Pop_OS!.
Moving OS has been challenging, even as someone familiar with Linux.
`echo 'echo This is the right move (and distro) and it will get easier' >> ~/.profile`
Moving OS has been challenging, even as someone familiar with Linux.
`echo 'echo This is the right move (and distro) and it will get easier' >> ~/.profile`
November 11, 2025 at 11:40 PM
As part of leaving Windows 10 behind and refusing to upgrade to W11 spyware (Windows Recall, ads etc), I've moved everything over to Pop_OS!.
Moving OS has been challenging, even as someone familiar with Linux.
`echo 'echo This is the right move (and distro) and it will get easier' >> ~/.profile`
Moving OS has been challenging, even as someone familiar with Linux.
`echo 'echo This is the right move (and distro) and it will get easier' >> ~/.profile`
Reposted by Ben Vezina
We strive to credit labs collecting specimens and generating sequence data prominently. But credit for data contributions is not zero sum – surfacing of data in popular tools generates visibility and does not infringe on future publications by the data generators. 2/5
November 6, 2025 at 9:46 PM
We strive to credit labs collecting specimens and generating sequence data prominently. But credit for data contributions is not zero sum – surfacing of data in popular tools generates visibility and does not infringe on future publications by the data generators. 2/5
Reposted by Ben Vezina
New paper: www.sciencedirect.com/science/arti...
Klebs can evolve resistance to Colistin through mgrB mutation or by acquiring the mcr-1 gene. Both routes have similar fitness costs against a bacterial competitor, but mgrB mutations are associated with enhanced virulence.
Klebs can evolve resistance to Colistin through mgrB mutation or by acquiring the mcr-1 gene. Both routes have similar fitness costs against a bacterial competitor, but mgrB mutations are associated with enhanced virulence.
mgrB inactivation confers enhanced pathogenicity and immune evasion over mcr-1 expression in colistin-resistant Klebsiella pneumoniae
Colistin is one of the last treatment options against human infections caused by multi-drug resistant Klebsiella pneumoniae. Colistin resistant K. pne…
www.sciencedirect.com
November 6, 2025 at 12:13 PM
New paper: www.sciencedirect.com/science/arti...
Klebs can evolve resistance to Colistin through mgrB mutation or by acquiring the mcr-1 gene. Both routes have similar fitness costs against a bacterial competitor, but mgrB mutations are associated with enhanced virulence.
Klebs can evolve resistance to Colistin through mgrB mutation or by acquiring the mcr-1 gene. Both routes have similar fitness costs against a bacterial competitor, but mgrB mutations are associated with enhanced virulence.
For the sake of the entire #biology 🧪🧬🦠🧫🔬💊and #medsky science 🩺community, I think @enasequence.bsky.social and the #bioinformatics community needs to prioritise development of new tools and functionality in-line with #NCBI and #Genbank, before it potentially goes down sometime in the near future.
November 5, 2025 at 11:54 PM
For the sake of the entire #biology 🧪🧬🦠🧫🔬💊and #medsky science 🩺community, I think @enasequence.bsky.social and the #bioinformatics community needs to prioritise development of new tools and functionality in-line with #NCBI and #Genbank, before it potentially goes down sometime in the near future.
- "This library appears to be damaged"
- "ImAgE mAdE WiTh BioReNDeR"
What is the obsession universities have with paying companies instead of supporting free, often better, open source? Paid software is scientifically undemocratic and goes against #OpenScience.
#SciSky 🧪
- "ImAgE mAdE WiTh BioReNDeR"
What is the obsession universities have with paying companies instead of supporting free, often better, open source? Paid software is scientifically undemocratic and goes against #OpenScience.
#SciSky 🧪
October 29, 2025 at 2:57 AM
- "This library appears to be damaged"
- "ImAgE mAdE WiTh BioReNDeR"
What is the obsession universities have with paying companies instead of supporting free, often better, open source? Paid software is scientifically undemocratic and goes against #OpenScience.
#SciSky 🧪
- "ImAgE mAdE WiTh BioReNDeR"
What is the obsession universities have with paying companies instead of supporting free, often better, open source? Paid software is scientifically undemocratic and goes against #OpenScience.
#SciSky 🧪
Reposted by Ben Vezina
#WHO report shows rising #antibiotic resistance in common bacteria
@katholt.bsky.social & @josebengoechea.bsky.social explain resistance worryingly high in #Klebsiella & E.coli as 1 in 6 lab-confirmed #bacterial infections in 2023 shown resistant to antibiotics.
www.lshtm.ac.uk/newsevents/n...
@katholt.bsky.social & @josebengoechea.bsky.social explain resistance worryingly high in #Klebsiella & E.coli as 1 in 6 lab-confirmed #bacterial infections in 2023 shown resistant to antibiotics.
www.lshtm.ac.uk/newsevents/n...
October 20, 2025 at 9:53 AM
#WHO report shows rising #antibiotic resistance in common bacteria
@katholt.bsky.social & @josebengoechea.bsky.social explain resistance worryingly high in #Klebsiella & E.coli as 1 in 6 lab-confirmed #bacterial infections in 2023 shown resistant to antibiotics.
www.lshtm.ac.uk/newsevents/n...
@katholt.bsky.social & @josebengoechea.bsky.social explain resistance worryingly high in #Klebsiella & E.coli as 1 in 6 lab-confirmed #bacterial infections in 2023 shown resistant to antibiotics.
www.lshtm.ac.uk/newsevents/n...
Reposted by Ben Vezina
Very excited to share the latest work from our lab, which was published today in Nature!
nature.com/articles/s41...
PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
nature.com/articles/s41...
PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
Isolation, engineering and ecology of temperate phages from the human gut - Nature
Human host-associated cellular products may act as induction agents for bacteriophages.
nature.com
October 15, 2025 at 9:41 PM
Very excited to share the latest work from our lab, which was published today in Nature!
nature.com/articles/s41...
PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
nature.com/articles/s41...
PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
Reposted by Ben Vezina
Research also shows that spreading smaller amounts of funding out over more researchers generally delivers better scientific outcomes per dollar spent than focusing bigger grants on fewer researchers.
journals.plos.org/plosone/arti...
journals.plos.org/plosone/arti...
Big Science vs. Little Science: How Scientific Impact Scales with Funding
Agencies that fund scientific research must choose: is it more effective to give large grants to a few elite researchers, or small grants to many researchers? Large grants would be more effective only...
journals.plos.org
October 4, 2025 at 5:50 PM
Research also shows that spreading smaller amounts of funding out over more researchers generally delivers better scientific outcomes per dollar spent than focusing bigger grants on fewer researchers.
journals.plos.org/plosone/arti...
journals.plos.org/plosone/arti...
Reposted by Ben Vezina
Unbelievable, Bakta reached its 1,000th citation!
A huge shout out and thank you to all Bakta users, bug reporters, those sharing ideas and suggesting features...
...just the entire incredibly supporting binfie community!
Without you, Bakta wouldn't be the same.
Thank you!
A huge shout out and thank you to all Bakta users, bug reporters, those sharing ideas and suggesting features...
...just the entire incredibly supporting binfie community!
Without you, Bakta wouldn't be the same.
Thank you!
October 6, 2025 at 8:11 AM
Unbelievable, Bakta reached its 1,000th citation!
A huge shout out and thank you to all Bakta users, bug reporters, those sharing ideas and suggesting features...
...just the entire incredibly supporting binfie community!
Without you, Bakta wouldn't be the same.
Thank you!
A huge shout out and thank you to all Bakta users, bug reporters, those sharing ideas and suggesting features...
...just the entire incredibly supporting binfie community!
Without you, Bakta wouldn't be the same.
Thank you!
reject chromatic aberration, embrace chromosomal aberration
October 3, 2025 at 11:52 AM
reject chromatic aberration, embrace chromosomal aberration
Reposted by Ben Vezina
Our new #klebsiella O type nomenclature, codesigned with Chris Whitfield, is now live in @pathogenwatch.bsky.social!
Need a quick explainer on the new names? Check out my blog post: tinyurl.com/y8yb3rbb (+link to full review article)
#MicroSky @klebnet.bsky.social @tomstantonmicro.bsky.social
Need a quick explainer on the new names? Check out my blog post: tinyurl.com/y8yb3rbb (+link to full review article)
#MicroSky @klebnet.bsky.social @tomstantonmicro.bsky.social
July 22, 2025 at 5:18 AM
Our new #klebsiella O type nomenclature, codesigned with Chris Whitfield, is now live in @pathogenwatch.bsky.social!
Need a quick explainer on the new names? Check out my blog post: tinyurl.com/y8yb3rbb (+link to full review article)
#MicroSky @klebnet.bsky.social @tomstantonmicro.bsky.social
Need a quick explainer on the new names? Check out my blog post: tinyurl.com/y8yb3rbb (+link to full review article)
#MicroSky @klebnet.bsky.social @tomstantonmicro.bsky.social
Reposted by Ben Vezina
And as for writing, don't get me started. Most often, the process of writing is not a laborious business of transcription, but a process of thinking itself. I'm not about to outsource my thinking to a machine.
September 26, 2025 at 10:50 AM
And as for writing, don't get me started. Most often, the process of writing is not a laborious business of transcription, but a process of thinking itself. I'm not about to outsource my thinking to a machine.
Staggering analysis here linking ciprofloxacin resistance to specific mutations in #Klebsiella.
In short, using ONLY genotype, one can reasonably predict phenotypic CIP MICs! See Fig 3 (below).
Loving the splitting of MIC and disk diffusion data as well.
#AMR #MicroSky #IDSky
In short, using ONLY genotype, one can reasonably predict phenotypic CIP MICs! See Fig 3 (below).
Loving the splitting of MIC and disk diffusion data as well.
#AMR #MicroSky #IDSky
September 27, 2025 at 6:07 AM
Staggering analysis here linking ciprofloxacin resistance to specific mutations in #Klebsiella.
In short, using ONLY genotype, one can reasonably predict phenotypic CIP MICs! See Fig 3 (below).
Loving the splitting of MIC and disk diffusion data as well.
#AMR #MicroSky #IDSky
In short, using ONLY genotype, one can reasonably predict phenotypic CIP MICs! See Fig 3 (below).
Loving the splitting of MIC and disk diffusion data as well.
#AMR #MicroSky #IDSky
Reposted by Ben Vezina
Celia also wrote about how we fitted 4.5 billion years in one image, at scale.
chezvoila.com/blog/saguenay/
chezvoila.com/blog/saguenay/
A data scale tested by time - Voilà:
Most of the time, the choice of scale is based on the data. Or not when the data you want to visualize are 4.5 billion years!
chezvoila.com
September 25, 2025 at 9:40 PM
Celia also wrote about how we fitted 4.5 billion years in one image, at scale.
chezvoila.com/blog/saguenay/
chezvoila.com/blog/saguenay/
Reposted by Ben Vezina
Reposted by Ben Vezina
In another preprint from the @brianhie.bsky.social Lab and @synbiogaolab.bsky.social, they introduce Germinal, a generative AI system for de novo antibody design.
Germinal produces functional nanobodies in just dozens of tests, making custom antibody design more accessible than ever before.
Germinal produces functional nanobodies in just dozens of tests, making custom antibody design more accessible than ever before.
September 24, 2025 at 3:07 PM
In another preprint from the @brianhie.bsky.social Lab and @synbiogaolab.bsky.social, they introduce Germinal, a generative AI system for de novo antibody design.
Germinal produces functional nanobodies in just dozens of tests, making custom antibody design more accessible than ever before.
Germinal produces functional nanobodies in just dozens of tests, making custom antibody design more accessible than ever before.
Reposted by Ben Vezina
Terrific @scientificdiscovery.dev post on randomized controlled trials in @ourworldindata.org.
Including this important chart on the impact of pre-registration.
Magically, when people had to pre-register outcomes, many of the benefits disappeared.
ourworldindata.org/randomized-c...
Including this important chart on the impact of pre-registration.
Magically, when people had to pre-register outcomes, many of the benefits disappeared.
ourworldindata.org/randomized-c...
September 24, 2025 at 5:52 PM
Terrific @scientificdiscovery.dev post on randomized controlled trials in @ourworldindata.org.
Including this important chart on the impact of pre-registration.
Magically, when people had to pre-register outcomes, many of the benefits disappeared.
ourworldindata.org/randomized-c...
Including this important chart on the impact of pre-registration.
Magically, when people had to pre-register outcomes, many of the benefits disappeared.
ourworldindata.org/randomized-c...
Automated, almost-error-free consensus #assemblies with Autocycler
Impressive benchmarks in Fig 2B (below): ≤10 median errors PER genome
Once again, incredible, landmark work from @rrwick.bsky.social
doi.org/10.1093/bioi...
Tool here: github.com/rrwick/Autoc...
#bioinformatics #genomics
Impressive benchmarks in Fig 2B (below): ≤10 median errors PER genome
Once again, incredible, landmark work from @rrwick.bsky.social
doi.org/10.1093/bioi...
Tool here: github.com/rrwick/Autoc...
#bioinformatics #genomics
September 22, 2025 at 3:02 PM
Automated, almost-error-free consensus #assemblies with Autocycler
Impressive benchmarks in Fig 2B (below): ≤10 median errors PER genome
Once again, incredible, landmark work from @rrwick.bsky.social
doi.org/10.1093/bioi...
Tool here: github.com/rrwick/Autoc...
#bioinformatics #genomics
Impressive benchmarks in Fig 2B (below): ≤10 median errors PER genome
Once again, incredible, landmark work from @rrwick.bsky.social
doi.org/10.1093/bioi...
Tool here: github.com/rrwick/Autoc...
#bioinformatics #genomics
Reposted by Ben Vezina
MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com
📄 www.nature.com/articles/s41...
💿 mmseqs.com
GPU-accelerated homology search with MMseqs2 - Nature Methods
Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...
www.nature.com
September 21, 2025 at 8:06 AM
MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com
📄 www.nature.com/articles/s41...
💿 mmseqs.com
Reposted by Ben Vezina
Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data.
@ruoshiz.bsky.social @milot.bsky.social
www.nature.com/articles/s41...
@ruoshiz.bsky.social @milot.bsky.social
www.nature.com/articles/s41...
De novo discovery of conserved gene clusters in microbial genomes with Spacedust - Nature Methods
This work presents Spacedust, a tool for de novo identification of conserved gene clusters from metagenomic data.
www.nature.com
September 16, 2025 at 1:25 PM
Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data.
@ruoshiz.bsky.social @milot.bsky.social
www.nature.com/articles/s41...
@ruoshiz.bsky.social @milot.bsky.social
www.nature.com/articles/s41...
Reposted by Ben Vezina
Thrilled to share this preprint on Klebsiella pneumoniae plasmids in a One Health setting 🦠 Fantastic work by @twinkler.bsky.social! 🎉 @irenlohr.bsky.social @margaretlam.bsky.social
A One Health study of Klebsiella pneumoniae species complex plasmids shows a highly diverse and ecologically adaptable plasmidome https://www.biorxiv.org/content/10.1101/2025.09.14.676155v1
September 16, 2025 at 9:40 AM
Thrilled to share this preprint on Klebsiella pneumoniae plasmids in a One Health setting 🦠 Fantastic work by @twinkler.bsky.social! 🎉 @irenlohr.bsky.social @margaretlam.bsky.social
Reposted by Ben Vezina
🎉 Delighted to share the first pre-print from my lab where we demonstrate that intergenic DNA repeats mediate phase variation of the mucoid phenotype in hypervirulent Klebsiella pneumoniae: www.biorxiv.org/content/10.1... #klebclub
Simple Sequence Repeats Mediate Phase Variation of the Mucoid Phenotype in Hypervirulent Klebsiella pneumoniae
Hypervirulent Klebsiella pneumoniae (HVKp) express a thick mucoid capsular polysaccharide which is essential for virulence and survival in the bloodstream but inhibits epithelial adhesion and invasion...
www.biorxiv.org
September 15, 2025 at 9:51 AM
🎉 Delighted to share the first pre-print from my lab where we demonstrate that intergenic DNA repeats mediate phase variation of the mucoid phenotype in hypervirulent Klebsiella pneumoniae: www.biorxiv.org/content/10.1... #klebclub