Lars Barquist

The pcnB gene sustains Shigella flexneri virulence Author summary Bacterial infections represent a major global threat. Understanding the genetic determinants promoting infections is crucial to overcome this threat. Shigella is an intracellular bacter...

Thrilled to share that our study on how the pcnB gene sustains Shigella virulence is now published in PLOS Pathogens: journals.plos.org/plospathogen...

In short: pcnB ➝increased virulence-plasmid replication ➝ elevated T3SS expression ➝ enhanced invasion/spread within the intestinal epithelium.

🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.

Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.

A thread 1/8

Identification and response to a putatively hypervirulent, carbapenem-resistant Klebsiella pneumoniae ST395 hospital outbreak in the UK Here, we describe a putatively hypervirulent, carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) outbreak. Nanopore sequencing guided the infection prevention and control (IPC) responses during the ...

Our latest is out tonight in @microbiologysociety.org MGen. Using long read seq to ID and then control hospital transmission of a CRKp we believe shows genomic and clinical signs of hypervirulence

www.microbiologyresearch.org/content/jour...

Evolution of hunt, kill, devour in a Vibrio ecospecies Bacterial ecospecies are a recently recognized genetic structure that is hypothesized to arise by complex adaptation to a new niche. Coadaptation within the “Molassodon” ecospecies of Vibrio parahaemo...

Sharing the link to our updated Vibrio preprint, where we compare and contrast Ecospecies with other genetic structures, and using the opportunity to fix typos and update some bluesky handles! with @danielfalush.bsky.social @whqqq.bsky.social @yjchao.bsky.social @chaooo.bsky.social

PhyloWeaver – Interactive phylogenetic tree editor Edit and visualize phylogenetic trees directly in your browser. PhyloWeaver lets you interactively rearrange tree topologies and export high-quality figures for publications and presentations.

I’ve released a tool to sketch and edit phylogenetic trees!
yawak.jp/PhyloWeaver/

Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.

What is that, an Aldi bargain bin? Look on my works, ye mighty, and despair.

The rise of ‘nightmare bacteria’: antimicrobial resistance in five charts Data reveal how the global challenge to reduce deaths and infections from drug-resistant bacteria is not going according to plan.

The rise of ‘nightmare bacteria’: antimicrobial resistance in five charts www.nature.com/articles/d41...

Genome sleuthing in hospitals: sequencing uncovered a Pseudomonas strain hiding in sink drains for years, and helped stop a long-running outbreak.

A slide with the text “This predictive task then motivates a natural variate-covariate decomposition of the full Bayesian model.” followed by equations for the six possible conditional decompositions of the probabilistic model p(y, x, theta). The conditional decomposition p( y, x, theta ) = p( y | x, theta ) p( x | theta ) p( theta ) is highlighted.

Wednesday, December 10!

Bayesian regression modeling!

Stan exercises!

Raising money for World Central Kitchen and United Farm Workers!

betanalpha.github.io/courses/!

Clostridial Cell Biology Group We are the Clostridial Cell Biology Group at the University of Sheffield. We study all aspects of cell biology, including the architecture and biogenesis of surface structures on both vegetative cells...

🚨 Fully funded PhD studentships 🚨

We have three fully funded PhD studentships available for Oct 26 start. Funded by the MRC DiMeN programme & the BBSRC Yorkshire Biosciences DTP. Details below as they are advertised. Contact me here or via email for more details or to discuss an application

You should apply to do an internship with us!

- Make sure you attach a research statement (we don't consider anybody with no statement for interviews)
- The application site will probably go down for a day or two on Nov 17, and the link may change

jobs.careers.microsoft.com/global/en/jo...

Colorful paper envelopes—pink, blue, beige, green, and cream—are neatly arranged in diagonal rows on a beige wall, creating a decorative geometric pattern.

#Dataviz newsletters! Here are the ones you shouldn't miss:

📩 Data Vis Dispatch, by Datawrapper - this is the one I never miss - my Nobel Prize visual was featured in a recent edition, I'm always super proud when that happens!
www.datawrapper.de/blog/newslet...

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Licence to knockdown — the phage gene silencer Nature Reviews Microbiology, Published online: 22 October 2025; doi:10.1038/s41579-025-01253-zThis Genome Watch explores how a new antisense oligomer-based approach enables functional genomics of genetically intractable bacteriophages, revealing essential genes and infection mechanisms without requiring genetic modification.

New online! Licence to knockdown — the phage gene silencer

If you’re interested in metals, microbes and maths 🤘 - please check out this PhD on the impact of metals on microbial communities with @thecopperdoctor.bsky.social @blindmath.bsky.social Denis Patterson and myself, you’d be based in Durham & be part of a vibrant interdisciplinary research group

🚨 Another funded PhD alert🚨

We are recruiting again! For a PhD student to start with us in the @langridgelab.bsky.social October 2026 - please share 👀

If you are interested in foodborne pathogens, public health and phage, look no further 🦠🏥🧬

➡️ tinyurl.com/3zvavp2t ⬅️

Apply by 6 Jan 2026 🗓️

Junior Group Leader for RNA-Biology, RNA-Technology or RNA-Medicine (f/m/d) - Würzburg (Stadt), Bayern (DE) job with Helmholtz-Institut für RNA-basierte Infektionsforschung (HIRI) | 12844907 #RNAexcellence Junior Group Leader Positions (f/m/d) Job advertisement no.:   089/2025 Starting date:                  As soon as possible. The con...

🚨 A fantastic opportunity to join HIRI to start your research group on RNA Biology 👇 www.nature.com/naturecareer...

The unique lipopolysaccharide composition of Salmonella Typhimurium ST313 dampens pyroptosis and inflammasome activation and suppresses host cell death https://www.biorxiv.org/content/10.1101/2025.09.29.679141v1

Deep-learning-based virtual screening of antibacterial compounds - Nature Biotechnology Antibacterial compounds are discovered by combining phenotypic screening with deep learning.

Deep-learning-based virtual screening of antibacterial compounds go.nature.com/47oIdKy

Using super-resolution microscopy to investigate the mechanistic principles of bacterial cell wall remodelling at University of Warwick on FindAPhD.com PhD Project - Using super-resolution microscopy to investigate the mechanistic principles of bacterial cell wall remodelling at University of Warwick, listed on FindAPhD.com

PhD project available in my lab. Email me with CV if interested
www.findaphd.com/phds/project...
#microsky #bioimaging

Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world Abstract. The increasing interest in finding new viruses within (meta)genomic datasets has fueled the development of computational tools for virus detectio

Interesting paper on bacteriophage genomics and bioinformatics

'Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world' by @sebwielgoss.bsky.social and colleagues

academic.oup.com/bib/article/...

Strong promoters are mutationally robust Mutational robustness is the persistence of a phenotype upon mutation. It facilitates molecular evolution and has been characterized in a variety of biological systems, but studies of prokaryotic prom...

A fun little side project I've been working on with @stepadenisov.bsky.social , Mato Lagator, and Andreas Wagner: "Strong promoters are mutationally robust". Briefly...

www.biorxiv.org/content/10.1...

Doesn't cover anything like the whole period, but The Thirty Years War by Veronica Wedgwood is an absolute classic, details a lot of the structure and politics of the Holy Roman Empire, and the writing is fantastic to read.

The new era of single-molecule RNA modification detection through nanopore base-calling models Nature Reviews Molecular Cell Biology, Published online: 13 October 2025; doi:10.1038/s41580-025-00896-3Nanopore RNA sequencing is a potent technology for the detection of RNA modifications. Nanopore modification-aware base-calling models have been recently developed, and this Progress article discusses their limitations, including modification cross-reactivities, variability in false positive rates and modification-calling threshold choices.

New Online! The new era of single-molecule RNA modification detection through nanopore base-calling models

😳

#phage #phagesky #microsky

Excited to share our preprint led by Carlos Voogdt et al

We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...

This is wonderful to play with, highly recommended for anyone who wants to understand the BWT

Two group leader positions available in the broader areas of RNA science, RNA technologies, and RNA medicine. Attractive packages and a great environment. Come and join us at Helmholtz RNA Würzburg, Bavaria.

tRNA-modifying enzymes in bacterial stress adaptation | Open Biology Transfer RNAs (tRNAs) and their modifications are central to bacterial translation and physiology, yet their roles in stress adaptation remain underexplored. While extensively studied in eukaryotes, a...

Happy to share our new review in Royal Society Open Biology 🎉
tRNA-modifying enzymes in bacterial stress adaptation:
How tRNA mods rewire translation under oxidative + antibiotic stress (MoTTs, moonlighting, therapy angles).
Read: doi.org/10.1098/rsob...
#RNAsky #microsky #AMR #RNAmodifications

All-at-once RNA folding with 3D motif prediction framed by evolutionary information - Nature Methods Structural RNAs exhibit a vast array of recurrent short three-dimensional (3D) elements found in loop regions involving non-Watson–Crick interactions that help arrange canonical double helices into tertiary structures. Here we present CaCoFold-R3D, a probabilistic grammar that predicts these RNA 3D motifs (also termed modules) jointly with RNA secondary structure over a sequence or alignment. CaCoFold-R3D uses evolutionary information present in an RNA alignment to reliably identify canonical helices (including pseudoknots) by covariation. Here we further introduce the R3D grammars, which also exploit helix covariation that constrains the positioning of the mostly noncovarying RNA 3D motifs. Our method runs predictions over an almost-exhaustive list of over 50 known RNA motifs (‘everything’). Motifs can appear in any nonhelical loop region (including three-way, four-way and higher junctions) (‘everywhere’). All structural motifs as well as the canonical helices are arranged into one single structure predicted by one single joint probabilistic grammar (‘all-at-once’). Our results demonstrate that CaCoFold-R3D is a valid alternative for predicting the all-residue interactions present in a RNA 3D structure. CaCoFold-R3D is fast and easily customizable for novel motif discovery and shows promising value both as a strong input for deep learning approaches to all-atom structure prediction as well as toward guiding RNA design as drug targets for therapeutic small molecules.

Integrated prediction of RNA secondary structure jointly with 3D motifs and pseudoknots guided by evolutionary information.
@aakaran31.bsky.social and @rivaselenarivas.bsky.social

link.springer.com/article/10.1...

🚨PHD PROJECT!🚨
Interested in #bacteria, #RNA, #evolution, #biotech, #EnvironmentalMicro?

Opportunity for a fully-funded #PhD with me, @rachelmwheatley.bsky.social, & @walllabuoglasgow.bsky.social via the NorthWestBio DTP:

www.gla.ac.uk/postgraduate...

Deadline 21 Nov. #MicroSky Please share!