Ben Vezina
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
- Reposted by Ben Vezina[Not loaded yet]
- This behaviour is just going to embolden for-profit journals to move entirely to LLM-based reviews. Why do journals need 'reviewers' to unethically upload other people's IP to an LLM when they can do it themselves and rake in the 💰? Cringe self-own IMO www.nature.com/articles/d41...
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- Reposted by Ben VezinaOur report on the current state of preprinting in the life sciences is out! Read it here: zenodo.org/records/1... & watch our video on the key data: youtu.be/G_mmmkuBua8 #preprints #scicomm #academicsky
- Reposted by Ben VezinaFoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...
- This is the sort of strategic planning that should go into #vaccine design 💉 They analysed 1,930 #Klebsiella pneumoniae 🦠🧫🧬 neonate blood isolates from 13 countries and estimate that 20 antigens 🧪 could cover 72.9% of all infections for 5–10 years #IDSky #EpiSky journals.plos.org/plosmedicine...
- Reposted by Ben VezinaCheck out our review on emerging technologies for diet tracking in Nature Food. 👇 This paper was led by @catalinacuparencu.bsky.social, with @cdiener.com and others: www.nature.com/articles/s43... @isbscience.org @uwbioe.bsky.social @uwgenome.bsky.social
- Reposted by Ben Vezina3 weeks left to submit an abstract for the Klebsiella Seminar Series! It is FREE, but registration is required. #AMR #Microsky #UTIsky sites.google.com/view/klebclu...
- We’re excited to kick off a new season of the Klebsiella Seminar Series, held on Thursdays in April 🧫🧬! We have 3 sessions on pathogenesis, pediatric Klebsiella & translational approaches. We will also have an open session. Registration is mandatory & FREE in this link forms.gle/LhJu11WQN6Yy... 🔁
- Reposted by Ben VezinaPhD studentships available through our BBSRC-funded doctoral programme. 🦠🧫💻 Contact me if you're interested in using bioinformatics/lab-based approaches with cultivated and uncultivated bacteria of the human microbiome, to identify and characterize novel enzymes with potential biotech applications.
- Our new paper on Insertion Sequences (IS) in #Klebsiella - Lineages have vastly different IS loads and profiles - An inverse relationship between IS load and metabolic capacity, in particular phosphorus use, consistent with early reductive evolution. www.microbiologyresearch.org/content/jour...
- Reposted by Ben VezinaCost of being female lead/corresponding author in biomedical sciences: "[T]he median amount of time spent under review is 7.4%–14.6% longer for female-authored articles than for male-authored articles" even in disciplines where women well-represented. #AcademicSky journals.plos.org/plosbiology/...
- (1/2) I wanted to highlight a figure in our recent article on IMP carbapenemases. You may have heard of .newick files, but have you heard about .nhx? This format allows encoding of node AND branch info, meaning you can annotate mutational differences, for example. www.nature.com/articles/s41...
- (2/2) If you want to make trees like this, where you can see what mutations cause a tree to split at each node, try my open source tool TreeBranchLabeller. github.com/bananabenana...
- Reposted by Ben VezinaPhold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...
- Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...
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- Great data vis. Crisp!
- Reposted by Ben VezinaImportant reminder from @ourworldindata.
- Reposted by Ben VezinaA free, open-access library of high-quality organism illustrations for science communication
- Reposted by Ben VezinaAspect Ratio as Driver of Bacterial Competition! Our latest work uncovers this simple and powerful determinant of bacterial competition. We demonstrate that longer bacteria consistently dominate colony fronts—even when outnumbered. The mechanism? Collective alignment. www.nature.com/articles/s41...
- Reposted by Ben VezinaWhen we say "no, everything hasn't been digitized," I need you to understand that we really mean is that virtually nothing has been digitized. This is because the realm of primary sources that historians use is incomprehensibly large.
- Reposted by Ben VezinaNow published in @natcomms.nature.com 🎉 www.nature.com/articles/s41... With Gillian Rodger, @nstoesser.bsky.social, @samlipworth.bsky.social, @stat-sarah.bsky.social, and many others!
- 🚨 New preprint! 🚨 We reveal that blaTEM-1 expression varies across the E. coli phylogeny, driving differences in co-amoxiclav resistance: www.biorxiv.org/content/10.1...
- If you want an example of gold standard genomics across every aspect of a paper, read this. It levelled me up. Covers #Acinetobacter baumannii. Recontextualises the global pop + reveals genuine insights. Includes development of software which types genomes too. www.nature.com/articles/s41...
- I wish people uploaded reads instead of assemblies onto NCBI/ENA, if they're only gonna do one? Better yet, do both. More can be done with reads, and they can be reassembled when newer assemblers are written. I feel like this should be mandatory. No assembly upload without reads, IMO
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- Reposted by Ben Vezina#AMR #Klebsiella cause >100,000 neonatal deaths globally each year. Our new preprint shows more than half of #Klebsiella pneumoniae neonatal sepsis cases in African and South Asian are nosocomial, acquired through transmission in neonatal units. #WAAW doi.org/10.1101/2025...
- (1/7) Really pleased to have this published in @natcomms.nature.com We looked at all public genomes encoding blaIMP (carbapenem #AMR ) 🦠🧫🧬💊. We show 5 IMP variants achieved global endemicity while 2 are regionally endemic. www.nature.com/articles/s41... #MicroSky #microbiology #IDSky #EpiSky 🧪
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- Absolutely stoked to have this published in @plosbiology.org We looked at the metabolism of #Klebsiella pneumoniae 🦠🧫. We not only demonstrated lineage-specific #metabolism, but that lineages can cross-feed and support each other. journals.plos.org/plosbiology/... #MicroSky #microbiology 🧬 🧪 💊
- Read this if you: - Work on #colonisation resistance or #probiotic consortia against Kp: It's not enough to exclude 1x lineage due to the metabolic diversity across the population - Work on #Klebsiella - Want a gold-standard workflow for deep, quantitative metabolic analysis - Enjoy #DataVis
- So all those tet(A)'s you are seeing in public data is possibly encoding #tigecycline #AMR, yet only n=74 papers? It didn't used to be though: Tigecycline originally "showed good activity against strains expressing...tet(A) efflux resistance determinants" journals.asm.org/doi/10.1128/...
- ❤️ eggNOG
- From @jhcepas.bsky.social and colleagues in the @narjournal.bsky.social #NARDatabaseIssue | eggNOG v7: phylogeny-based orthology predictions and functional annotations | #Bioinformatics #ProteinCentric #Database #OpenScience 🧬 🖥️🧪🇨🇭🇪🇸🇩🇪🔓 ⬇️ academic.oup.com/nar/advance-...
- Reposted by Ben VezinaIs the human microbiome a source for hospital-associated infections (HAI) and are any genetic changes associated with HAI? In our new preprint, we longitudinally reconstruct the evolutionary processes within the human microbiome leading up to HAI: doi.org/10.1101/2025...
- Reposted by Ben VezinaArrows are tricky. For us, as the designer of the visual, it will be super clear what it means. But for someone looking at our visual for the first time, it can be highly ambiguous. Depending on the reader, the same arrow can mean sequence, zoom, range, label, movement,... 1/2
- Wanted to highlight a cool recent paper I read. If you work on #Pseudomonas 🦠🧫🧬 you should check this out. 39(!) P. aeruginosa strains tested via C. elegans slow-kill assays, followed by GWAS to identify novel accessory genome virulence factors #MicroSky #Microbiology doi.org/10.3389/fmic...
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- Reposted by Ben VezinaLondon 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`
- Reposted by Ben VezinaWe 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 VezinaNew 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.
