Lars Barquist
@lbarquist.bsky.social
Assistant prof @ UofT, associated scientist @ Helmholtz Institute for RNA-based Infection Research. Pathogen systems biology / informatics / functional genomics. Coastal New Hampshirite. Drink Moxie.
Pinned
Lars Barquist
@lbarquist.bsky.social
· Jun 12
A scalable gut epithelial organoid model reveals the genome-wide colonization landscape of a human-adapted pathogen - Nature Genetics
A genome-wide screen using human gut epithelial organoids combined with transposon-directed insertion sequencing identifies over 100 Shigella flexneri genes required for epithelial colonization.
www.nature.com
Very excited about our latest combining advanced cell culture, transposon-insertion sequencing, and statistical modeling to map Shigella virulence determinants in organoid models. Great collaboration w/ @mldm.bsky.social @sellinlab.bsky.social in @natgenet.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Lars Barquist
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.
In short: pcnB ➝increased virulence-plasmid replication ➝ elevated T3SS expression ➝ enhanced invasion/spread within the intestinal epithelium.
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...
journals.plos.org
November 21, 2025 at 11:28 AM
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.
In short: pcnB ➝increased virulence-plasmid replication ➝ elevated T3SS expression ➝ enhanced invasion/spread within the intestinal epithelium.
Reposted by Lars Barquist
🚨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
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
November 20, 2025 at 8:40 PM
🚨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
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
Reposted by Lars Barquist
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...
www.microbiologyresearch.org/content/jour...
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 ...
www.microbiologyresearch.org
November 20, 2025 at 4:56 PM
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...
www.microbiologyresearch.org/content/jour...
Reposted by Lars Barquist
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
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...
www.biorxiv.org
November 19, 2025 at 3:16 AM
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
Reposted by Lars Barquist
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.
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.
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.
yawak.jp
November 18, 2025 at 1:59 AM
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.
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.
Reposted by Lars Barquist
The rise of ‘nightmare bacteria’: antimicrobial resistance in five charts www.nature.com/articles/d41...
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.
www.nature.com
November 6, 2025 at 8:29 AM
The rise of ‘nightmare bacteria’: antimicrobial resistance in five charts www.nature.com/articles/d41...
Reposted by Lars Barquist
Genome sleuthing in hospitals: sequencing uncovered a Pseudomonas strain hiding in sink drains for years, and helped stop a long-running outbreak.
Client Challenge
Please enable JavaScript to proceed.
buff.ly
November 5, 2025 at 4:15 PM
Genome sleuthing in hospitals: sequencing uncovered a Pseudomonas strain hiding in sink drains for years, and helped stop a long-running outbreak.
Reposted by Lars Barquist
Wednesday, December 10!
Bayesian regression modeling!
Stan exercises!
Raising money for World Central Kitchen and United Farm Workers!
betanalpha.github.io/courses/!
Bayesian regression modeling!
Stan exercises!
Raising money for World Central Kitchen and United Farm Workers!
betanalpha.github.io/courses/!
November 4, 2025 at 2:33 PM
Wednesday, December 10!
Bayesian regression modeling!
Stan exercises!
Raising money for World Central Kitchen and United Farm Workers!
betanalpha.github.io/courses/!
Bayesian regression modeling!
Stan exercises!
Raising money for World Central Kitchen and United Farm Workers!
betanalpha.github.io/courses/!
Reposted by Lars Barquist
🚨 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
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
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...
sites.google.com
October 31, 2025 at 3:44 PM
🚨 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
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
Reposted by Lars Barquist
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...
- 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...
October 31, 2025 at 2:11 PM
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...
- 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...
Reposted by Lars Barquist
#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...
1/5
📩 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...
1/5
October 31, 2025 at 9:36 AM
#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...
1/5
📩 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...
1/5
Reposted by Lars Barquist
New online! Licence to knockdown — the phage gene silencer
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.
www.nature.com
October 22, 2025 at 4:29 PM
New online! Licence to knockdown — the phage gene silencer
Reposted by Lars Barquist
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
We're advertising a PhD at the intersection of mathematical ecology, metallobiology, and microbiology to study the impact of metals on microbial communities with @thecopperdoctor.bsky.social @kateduncan.bsky.social and Denis Patterson. Come join us in lovely Durham!
iapetus.ac.uk/studentships...
iapetus.ac.uk/studentships...
When nutrients turn toxic: how metals shape microbial coexistence
iapetus.ac.uk
October 29, 2025 at 2:49 PM
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
Reposted by Lars Barquist
🚨 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 🗓️
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 🗓️
October 28, 2025 at 1:17 PM
🚨 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 🗓️
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 🗓️
Reposted by Lars Barquist
🚨 A fantastic opportunity to join HIRI to start your research group on RNA Biology 👇 www.nature.com/naturecareer...
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...
www.nature.com
October 27, 2025 at 9:55 PM
🚨 A fantastic opportunity to join HIRI to start your research group on RNA Biology 👇 www.nature.com/naturecareer...
Reposted by Lars Barquist
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
September 30, 2025 at 3:18 AM
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
Reposted by Lars Barquist
Deep-learning-based virtual screening of antibacterial compounds go.nature.com/47oIdKy
Deep-learning-based virtual screening of antibacterial compounds - Nature Biotechnology
Antibacterial compounds are discovered by combining phenotypic screening with deep learning.
go.nature.com
October 24, 2025 at 3:39 PM
Deep-learning-based virtual screening of antibacterial compounds go.nature.com/47oIdKy
Reposted by Lars Barquist
PhD project available in my lab. Email me with CV if interested
www.findaphd.com/phds/project...
#microsky #bioimaging
www.findaphd.com/phds/project...
#microsky #bioimaging
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
www.findaphd.com
October 22, 2025 at 8:29 AM
PhD project available in my lab. Email me with CV if interested
www.findaphd.com/phds/project...
#microsky #bioimaging
www.findaphd.com/phds/project...
#microsky #bioimaging
Reposted by Lars Barquist
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/...
'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/...
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
academic.oup.com
October 21, 2025 at 1:45 PM
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/...
'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/...
Reposted by Lars Barquist
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
October 21, 2025 at 8:02 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Lars Barquist
New Online! The new era of single-molecule RNA modification detection through nanopore base-calling models
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.
bit.ly
October 13, 2025 at 12:21 PM
New Online! The new era of single-molecule RNA modification detection through nanopore base-calling models
Reposted by Lars Barquist
WHO reports 1 in 6 bacterial infections worldwide are antibiotic-resistant, with resistance rising sharply since 2018. Gram-negative bacteria like E. coli and K. pneumoniae pose the biggest threat. Action on #AMR surveillance and responsible antibiotic use is needed.
www.who.int/news/item/13...
www.who.int/news/item/13...
WHO warns of widespread resistance to common antibiotics worldwide
One in six laboratory-confirmed bacterial infections causing common infections in people worldwide in 2023 were resistant to antibiotic treatments, according to a new World Health Organization (WHO) r...
www.who.int
October 13, 2025 at 11:17 AM
Reposted by Lars Barquist
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...
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...
October 13, 2025 at 7:48 AM
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...
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...
Reposted by Lars Barquist
This is wonderful to play with, highly recommended for anyone who wants to understand the BWT
Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
October 9, 2025 at 8:31 PM
This is wonderful to play with, highly recommended for anyone who wants to understand the BWT
Reposted by Lars Barquist
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.
October 8, 2025 at 9:45 PM
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.