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
In our brand new 🥳 review, @hemaa-selvakumar.bsky.social & team pull a scattered literature in phage biology into a coherent framework for scaling up to engineering complex communities. We poured our hearts into this to share challenges & future opportunities for the nextGen!
September 29, 2026 at 7:42 PM
In our brand new 🥳 review, @hemaa-selvakumar.bsky.social & team pull a scattered literature in phage biology into a coherent framework for scaling up to engineering complex communities. We poured our hearts into this to share challenges & future opportunities for the nextGen!
Reposted by Lars Barquist
😮😮 Microbial community dynamics in a traditional Swiss mountain cheese over 142 years of cheesemaking: Current Biology www.cell.com/current-biol...
Microbial community dynamics in a traditional Swiss mountain cheese over 142 years of cheesemaking
How did modernizing cheesemaking change the microbes inside the cheese? By sequencing
preserved traditional Alpine cheese wheels spanning 142 years from a single Alpine
dairy, Somerville et al. trace ...
www.cell.com
September 25, 2026 at 3:47 PM
😮😮 Microbial community dynamics in a traditional Swiss mountain cheese over 142 years of cheesemaking: Current Biology www.cell.com/current-biol...
Reposted by Lars Barquist
This will be an amazing opportunity for the right person. The Department of Veterinary Medicine in Cambridge is recruiting for an established chair who will also be our Head of Department. Your research can be in any area of veterinary science.
Please circulate.
www.cam.ac.uk/jobs/profess...
Please circulate.
www.cam.ac.uk/jobs/profess...
Professorship of Veterinary Science
The Board of Electors to the Professorship of Veterinary Science invite applications for this Professorship from persons whose work is connected with veterinary science (ideally in research aligned wi...
www.cam.ac.uk
September 16, 2026 at 2:24 PM
This will be an amazing opportunity for the right person. The Department of Veterinary Medicine in Cambridge is recruiting for an established chair who will also be our Head of Department. Your research can be in any area of veterinary science.
Please circulate.
www.cam.ac.uk/jobs/profess...
Please circulate.
www.cam.ac.uk/jobs/profess...
Reposted by Lars Barquist
Our opinion piece on what you can do with tradis [tn-seq]. It's a shortish read, aimed at fellow daydreamers. Thank you @microbiologysociety.org for the invite and opportunity, this was surprisingly pleasant to research and write! www.microbiologyresearch.org/content/jour...
Applications of transposon-insertion sequencing for understanding bacterial physiology
Transposon-insertion sequencing (Tn-seq) couples transposon mutagenesis with next-generation sequencing to identify the transposon insertion site for thousands of mutants in parallel. It is a powerful...
www.microbiologyresearch.org
September 14, 2026 at 12:36 PM
Our opinion piece on what you can do with tradis [tn-seq]. It's a shortish read, aimed at fellow daydreamers. Thank you @microbiologysociety.org for the invite and opportunity, this was surprisingly pleasant to research and write! www.microbiologyresearch.org/content/jour...
Reposted by Lars Barquist
Kathrin Fröhlich @microberna.bsky.social on Global RNA interactomes discover new functions for bacterial small RNAs
#EMBOBacNet
See their @narjournal.bsky.social paper dissecting the role of AbnZ sRNA and its impact on cell morphology and vancomycin resist: academic.oup.com/nar/article/...
#EMBOBacNet
See their @narjournal.bsky.social paper dissecting the role of AbnZ sRNA and its impact on cell morphology and vancomycin resist: academic.oup.com/nar/article/...
An sRNA overexpression library reveals AbnZ as a negative regulator of an essential translocation module in Caulobacter crescentus
Abstract. Small RNAs (sRNAs) play a crucial role in modulating target gene expression through short base-pairing interactions and serve as integral compone
academic.oup.com
September 14, 2026 at 3:21 PM
Kathrin Fröhlich @microberna.bsky.social on Global RNA interactomes discover new functions for bacterial small RNAs
#EMBOBacNet
See their @narjournal.bsky.social paper dissecting the role of AbnZ sRNA and its impact on cell morphology and vancomycin resist: academic.oup.com/nar/article/...
#EMBOBacNet
See their @narjournal.bsky.social paper dissecting the role of AbnZ sRNA and its impact on cell morphology and vancomycin resist: academic.oup.com/nar/article/...
Reposted by Lars Barquist
#TrendingNow | Using a modified host, this study adds 36 new phages to the BASEL collection of phages that infect E. coli, revealing key roles of the O-antigen barrier in host recognition and restriction-modification systems in bacterial immunity. #ICYMI #MicroSky 🧪 buff.ly/grvuhX2
Completing the BASEL phage collection to unlock hidden diversity for systematic exploration of phage–host interactions
The BASEL collection of phages that infect E. coli has been a valuable resource, but is limited by the peculiarities of the host strain used. This study uses a modified host to expand the collection…
buff.ly
September 11, 2026 at 4:37 PM
#TrendingNow | Using a modified host, this study adds 36 new phages to the BASEL collection of phages that infect E. coli, revealing key roles of the O-antigen barrier in host recognition and restriction-modification systems in bacterial immunity. #ICYMI #MicroSky 🧪 buff.ly/grvuhX2
Reposted by Lars Barquist
I made a presentation to other faculty about recent progress in general AI, to facilitate the discussion around the impact for research and teaching in biology. It could be that the slides are useful for others trying to do that same. Feel free to re-use.
docs.google.com/presentation...
docs.google.com/presentation...
generalAI_for research_intro.pptx
Recent AI developments and what they mean for us Quick primer on general AI models* State-of-the-art in AI agent capabilities AI agents in biology (examples) Discussion - what does this mean for our r...
docs.google.com
September 9, 2026 at 10:53 AM
I made a presentation to other faculty about recent progress in general AI, to facilitate the discussion around the impact for research and teaching in biology. It could be that the slides are useful for others trying to do that same. Feel free to re-use.
docs.google.com/presentation...
docs.google.com/presentation...
Reposted by Lars Barquist
I have an open PhD position in my new Synthetic Phage Biology Lab at Research Centre Jülich. Join us to discover bacterial antiphage trickery! Please, apply and spread the word. recruiting.fz-juelich.de/jobposting/c...
PhD Position – Biology and application of bacterial antiphage defenses
recruiting.fz-juelich.de
September 1, 2026 at 10:49 AM
I have an open PhD position in my new Synthetic Phage Biology Lab at Research Centre Jülich. Join us to discover bacterial antiphage trickery! Please, apply and spread the word. recruiting.fz-juelich.de/jobposting/c...
Reposted by Lars Barquist
Thanks to Deutsche Bahn, the famous trolley problem is redundant! 🥳
September 1, 2026 at 2:17 PM
Thanks to Deutsche Bahn, the famous trolley problem is redundant! 🥳
Reposted by Lars Barquist
The use of Galleria mellonella to study microbial interactions, immune responses, & substrate interactions - super, comprehensive review from Evgenia Maslova, Ciaram Staber & @ronanmccarthy.bsky.social portlandpress.com/essaysbioche... #MicroSky
September 1, 2026 at 10:41 AM
The use of Galleria mellonella to study microbial interactions, immune responses, & substrate interactions - super, comprehensive review from Evgenia Maslova, Ciaram Staber & @ronanmccarthy.bsky.social portlandpress.com/essaysbioche... #MicroSky
Reposted by Lars Barquist
Big update to the seqproc paper (www.biorxiv.org/content/10.6...)! We've made seqproc even faster & more capable. We've also extended the analysis & tweaked & improved the configurations we used for other tools as well. Seqproc now has the beginnings of a graph optimization backend for its DSL!
August 31, 2026 at 11:04 PM
Big update to the seqproc paper (www.biorxiv.org/content/10.6...)! We've made seqproc even faster & more capable. We've also extended the analysis & tweaked & improved the configurations we used for other tools as well. Seqproc now has the beginnings of a graph optimization backend for its DSL!
Reposted by Lars Barquist
New Comment
From estimates to evidence: measuring the true burden of AMR
www.thelancet.com/journals/lan...
From estimates to evidence: measuring the true burden of AMR
www.thelancet.com/journals/lan...
From estimates to evidence: measuring the true burden of AMR
Antimicrobial resistance (AMR) is a major global health threat. A considerable challenge
has been generating robust evidence to define its true clinical and societal effect,
and to drive policy change...
www.thelancet.com
August 24, 2026 at 7:42 AM
New Comment
From estimates to evidence: measuring the true burden of AMR
www.thelancet.com/journals/lan...
From estimates to evidence: measuring the true burden of AMR
www.thelancet.com/journals/lan...
Reposted by Lars Barquist
"16S ribosomal RNA modification drives transcript-specific translation efficiency" pubmed.ncbi.nlm.nih.gov/42632017/
from @ramamurthilab.bsky.social lab #Ribosome #RNASky #MicroSky
from @ramamurthilab.bsky.social lab #Ribosome #RNASky #MicroSky
16S ribosomal RNA modification drives transcript-specific translation efficiency - PubMed
Bacterial ribosomal RNAs (rRNAs) are decorated with conserved nucleotide modifications, but the functionality of these modifications is often underexplored. MraW (RsmH) is a 16S rRNA methyltransferase. Here, we report that deletion of mraW corrects a late-stage sporulation defect in Bacillus subtili …
pubmed.ncbi.nlm.nih.gov
August 24, 2026 at 2:06 PM
"16S ribosomal RNA modification drives transcript-specific translation efficiency" pubmed.ncbi.nlm.nih.gov/42632017/
from @ramamurthilab.bsky.social lab #Ribosome #RNASky #MicroSky
from @ramamurthilab.bsky.social lab #Ribosome #RNASky #MicroSky
Reposted by Lars Barquist
Out Now! Colibactin beyond carcinogenesis #MicroSky
Colibactin beyond carcinogenesis
Nature Microbiology, Published online: 24 August 2026; doi:10.1038/s41564-026-02448-7Colibactin, a microbially produced genotoxin linked to colorectal cancer, can inhibit pathogen colonization while favouring bacteria that tolerate its genotoxic activity, uncovering an ecological role for colibactin in shaping microbial communities in the honey bee gut.
go.nature.com
August 24, 2026 at 10:09 AM
Out Now! Colibactin beyond carcinogenesis #MicroSky
Reposted by Lars Barquist
The first public release of seqproc is out! 🎉 v0.1.1, powered by ANTISEQUENCE v0.1.0.
seqproc let's you describe a sequencing protocol in EFGDL, compile it into a fast Rust pipeline for matching, filtering, correction, and FASTQ transformation. A powerful read pre-processing engine! 1/6
seqproc let's you describe a sequencing protocol in EFGDL, compile it into a fast Rust pipeline for matching, filtering, correction, and FASTQ transformation. A powerful read pre-processing engine! 1/6
August 23, 2026 at 6:39 PM
The first public release of seqproc is out! 🎉 v0.1.1, powered by ANTISEQUENCE v0.1.0.
seqproc let's you describe a sequencing protocol in EFGDL, compile it into a fast Rust pipeline for matching, filtering, correction, and FASTQ transformation. A powerful read pre-processing engine! 1/6
seqproc let's you describe a sequencing protocol in EFGDL, compile it into a fast Rust pipeline for matching, filtering, correction, and FASTQ transformation. A powerful read pre-processing engine! 1/6
Reposted by Lars Barquist
New paper day! What started as an overly ambitious summer student project is now published.
We asked which genomic signals best distinguish protein-coding, short ncRNA and long ncRNA genes from the genomic background.
doi.org/10.1093/g3jo...
We asked which genomic signals best distinguish protein-coding, short ncRNA and long ncRNA genes from the genomic background.
doi.org/10.1093/g3jo...
Genomic indicators of gene function: a systematic assessment of the human genome
Abstract. Proteins and non-coding RNAs are functional products of the genome that are central for crucial cellular processes. With recent technological adv
doi.org
August 23, 2026 at 10:27 PM
New paper day! What started as an overly ambitious summer student project is now published.
We asked which genomic signals best distinguish protein-coding, short ncRNA and long ncRNA genes from the genomic background.
doi.org/10.1093/g3jo...
We asked which genomic signals best distinguish protein-coding, short ncRNA and long ncRNA genes from the genomic background.
doi.org/10.1093/g3jo...
Reposted by Lars Barquist
Small proteins in prokaryotes, a fascinating world
#microbiology #proteins #prokaryotes #MicroSky
@femsjournals.bsky.social @femsmicro.org
doi.org/10.1093/fems...
#microbiology #proteins #prokaryotes #MicroSky
@femsjournals.bsky.social @femsmicro.org
doi.org/10.1093/fems...
Small proteins in prokaryotes, a fascinating world
Wolfgang R Hess, Kai Papenfort, Cynthia M Sharma, Franz Narberhaus, Ruth A Schmitz; Small proteins in prokaryotes, a fascinating world, microLife, , uqag02
doi.org
August 23, 2026 at 11:27 PM
Small proteins in prokaryotes, a fascinating world
#microbiology #proteins #prokaryotes #MicroSky
@femsjournals.bsky.social @femsmicro.org
doi.org/10.1093/fems...
#microbiology #proteins #prokaryotes #MicroSky
@femsjournals.bsky.social @femsmicro.org
doi.org/10.1093/fems...
Reposted by Lars Barquist
Decoding Bistability and Drivers of Phenotypic Variation in Bacteria
Annual Reviews in Microbiology by Jesús Cámara-Almirón, Milena Jaskólska, and @veeninglab.com at @dmf-unil.bsky.social
www.annualreviews.org/content/jour...
Annual Reviews in Microbiology by Jesús Cámara-Almirón, Milena Jaskólska, and @veeninglab.com at @dmf-unil.bsky.social
www.annualreviews.org/content/jour...
Decoding Bistability and Drivers of Phenotypic Variation in Bacteria
In a process known as phenotypic heterogeneity or phenotypic variation, bacteria can produce distinct phenotypes within an isogenic population in response to shifting environmental conditions. Noise i...
www.annualreviews.org
August 23, 2026 at 6:12 PM
Decoding Bistability and Drivers of Phenotypic Variation in Bacteria
Annual Reviews in Microbiology by Jesús Cámara-Almirón, Milena Jaskólska, and @veeninglab.com at @dmf-unil.bsky.social
www.annualreviews.org/content/jour...
Annual Reviews in Microbiology by Jesús Cámara-Almirón, Milena Jaskólska, and @veeninglab.com at @dmf-unil.bsky.social
www.annualreviews.org/content/jour...
Reposted by Lars Barquist
Excellent review article
Metabolic strategies of Enterobacteriaceae gut colonization | Nature Reviews Microbiology share.google/hKziCqmwDr3D...
Metabolic strategies of Enterobacteriaceae gut colonization | Nature Reviews Microbiology share.google/hKziCqmwDr3D...
Metabolic strategies of Enterobacteriaceae gut colonization - Nature Reviews Microbiology
In this Review, Schubert and Hardt explore the metabolic strategies that Enterobacteriaceae use to establish themselves in the gut, and how they adapt to inflammatory conditions in this environment.
share.google
August 22, 2026 at 9:49 PM
Excellent review article
Metabolic strategies of Enterobacteriaceae gut colonization | Nature Reviews Microbiology share.google/hKziCqmwDr3D...
Metabolic strategies of Enterobacteriaceae gut colonization | Nature Reviews Microbiology share.google/hKziCqmwDr3D...
Reposted by Lars Barquist
Remember this?
bsky.app/profile/did:...
Rigorous visualization of the structure in your high-dimensional data. Fantastic work by @dhdegroot.bsky.social
With help of the reviewers of Nat Biotech it is now updated, extended an officially published here:
www.nature.com/articles/s41... 1/n
bsky.app/profile/did:...
Rigorous visualization of the structure in your high-dimensional data. Fantastic work by @dhdegroot.bsky.social
With help of the reviewers of Nat Biotech it is now updated, extended an officially published here:
www.nature.com/articles/s41... 1/n
August 21, 2026 at 11:01 AM
Remember this?
bsky.app/profile/did:...
Rigorous visualization of the structure in your high-dimensional data. Fantastic work by @dhdegroot.bsky.social
With help of the reviewers of Nat Biotech it is now updated, extended an officially published here:
www.nature.com/articles/s41... 1/n
bsky.app/profile/did:...
Rigorous visualization of the structure in your high-dimensional data. Fantastic work by @dhdegroot.bsky.social
With help of the reviewers of Nat Biotech it is now updated, extended an officially published here:
www.nature.com/articles/s41... 1/n
Reposted by Lars Barquist
A new pre-print out - we show that promoters and terminators of transcription are frequently coupled, throughout the bacteria, and this is regulatory.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Widespread coupling of promoters and terminators of transcription in bacteria
Transcription underpins the expression of genetic information and is viewed as a series of independent initiation and termination events. In bacteria, promoters and terminators of transcription are th...
www.biorxiv.org
August 21, 2026 at 10:00 AM
A new pre-print out - we show that promoters and terminators of transcription are frequently coupled, throughout the bacteria, and this is regulatory.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Lars Barquist
These ratio outcome variables are a plague in the sciences. If your analysis treats 1/2 and 10/20 as the same evidence, then you have discarded uncertainty in the outcome. Model what you measure, not what you construct. Use the denominator as an exposure instead.
The study is based on the CD index, a citation-based measure of how much the successors of a work still rely on its predecessors, running from -1 (consolidating) to +1 (disruptive). Key detail: a paper with zero references automatically gets CD = +1 as soon as it is cited once.
August 13, 2026 at 2:27 PM
These ratio outcome variables are a plague in the sciences. If your analysis treats 1/2 and 10/20 as the same evidence, then you have discarded uncertainty in the outcome. Model what you measure, not what you construct. Use the denominator as an exposure instead.
Reposted by Lars Barquist
All four books I've co-authored are freely available online for non-commercial use:
- Bayesian Workflow at avehtari.github.io/Bayesian-Wor...
Links to other three books are in the quoted post 👇 (too many books to fit in one post!)
- Bayesian Workflow at avehtari.github.io/Bayesian-Wor...
Links to other three books are in the quoted post 👇 (too many books to fit in one post!)
August 13, 2026 at 6:57 AM
All four books I've co-authored are freely available online for non-commercial use:
- Bayesian Workflow at avehtari.github.io/Bayesian-Wor...
Links to other three books are in the quoted post 👇 (too many books to fit in one post!)
- Bayesian Workflow at avehtari.github.io/Bayesian-Wor...
Links to other three books are in the quoted post 👇 (too many books to fit in one post!)
Reposted by Lars Barquist
It took us two (2!) years to get our manuscript on resistance determinants to asobiotics published, and of course that had to happen during my summer vacation 🏝️🇪🇺
Thanks to @mulkern.bsky.social , @vuthuhien176.bsky.social and the other co-authors!
www.nature.com/articles/s41...
Thanks to @mulkern.bsky.social , @vuthuhien176.bsky.social and the other co-authors!
www.nature.com/articles/s41...
A systematic identification of resistance determinants to antisense antibiotics suggests adaptation strategies dependent on the delivery peptide - Nature Communications
In this study, authors investigate the evolution of bacterial resistance to antisense peptide nucleic acid (PNA) antibiotics. They observe that this typically occurs mainly by reducing drug uptake via...
www.nature.com
August 12, 2026 at 8:50 PM
It took us two (2!) years to get our manuscript on resistance determinants to asobiotics published, and of course that had to happen during my summer vacation 🏝️🇪🇺
Thanks to @mulkern.bsky.social , @vuthuhien176.bsky.social and the other co-authors!
www.nature.com/articles/s41...
Thanks to @mulkern.bsky.social , @vuthuhien176.bsky.social and the other co-authors!
www.nature.com/articles/s41...
Reposted by Lars Barquist
Out now in @natcomms.nature.com: how do bacteria evolve resistance to programmable antisense antibiotics?
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A systematic identification of resistance determinants to antisense antibiotics suggests adaptation strategies dependent on the delivery peptide - Nature Communications
In this study, authors investigate the evolution of bacterial resistance to antisense peptide nucleic acid (PNA) antibiotics. They observe that this typically occurs mainly by reducing drug uptake via...
www.nature.com
August 12, 2026 at 9:38 PM
Out now in @natcomms.nature.com: how do bacteria evolve resistance to programmable antisense antibiotics?
www.nature.com/articles/s41...
www.nature.com/articles/s41...