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
'Robust Aitchison PCA was not insensitive to uneven sequencing effort and did not perform as well as rarefaction. (...) Using the benchmarking framework from the original analysis, rarefaction outperformed robust Aitchison PCA, other compositional data analysis methods + other normalization methods'
New paper up on bioRxiv! This is my third and hopefully final paper on rarefaction. It's still better than the other available methods.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Rarefaction is better than robust Aitchison PCA and other compositional data analysis methods at controlling for uneven sequencing effort
Amplicon sequencing typically results in a wide distribution in the number of sequences obtained from each sample. How best to account for this variation has been a persistent problem in the microbial...
www.biorxiv.org
January 7, 2026 at 7:26 PM
'Robust Aitchison PCA was not insensitive to uneven sequencing effort and did not perform as well as rarefaction. (...) Using the benchmarking framework from the original analysis, rarefaction outperformed robust Aitchison PCA, other compositional data analysis methods + other normalization methods'
Reposted by Lars Barquist
3′UTR-derived small RNA couples acid resistance to metabolic reprogramming of Salmonella within macrophages url: academic.oup.com/nar/article/...
3′UTR-derived small RNA couples acid resistance to metabolic reprogramming of Salmonella within macrophages
Abstract. Acid resistance is crucial for enterobacteria to withstand host acidic environments during infection, including the gastrointestinal tract and ma
academic.oup.com
January 7, 2026 at 8:19 AM
3′UTR-derived small RNA couples acid resistance to metabolic reprogramming of Salmonella within macrophages url: academic.oup.com/nar/article/...
Reposted by Lars Barquist
Highly, highly recommended for persons interested in Bayesian methods and for persons not interested in Bayesian methods who should be.
And we're live, Lecture A1 is online. Introduction to Bayesian workflow, generative models, estimands, estimators, estimates, error checking, beginnings of probability theory and Bayesian updating. www.youtube.com/watch?v=ztbY...
January 6, 2026 at 12:21 PM
Highly, highly recommended for persons interested in Bayesian methods and for persons not interested in Bayesian methods who should be.
Reposted by Lars Barquist
Just a few hours left to apply for this #PhD!!
Do you like phages, genomes & public health impact?🦠🧬🏥
Wanna work in a cutting edge of science, with some awesome people @quadraminstitute.bsky.social?
🤔this could be just the project for you!!🧑🔬😎
Apply NOW before midnight
#PhDposition #academicsky
Do you like phages, genomes & public health impact?🦠🧬🏥
Wanna work in a cutting edge of science, with some awesome people @quadraminstitute.bsky.social?
🤔this could be just the project for you!!🧑🔬😎
Apply NOW before midnight
#PhDposition #academicsky
PhD Carrying a toxic burden: the continuing spread of “Shiga toxin stx2a”-harbouring phage in E. coli (LANGRIDGE_Q26MMB) 2026/27 | UEA
PhD Carrying a toxic burden: the continuing spread of “Shiga toxin stx2a”-harbouring phage in E. coli (LANGRIDGE_Q26MMB) 2026/27 | UEA
www.tinyurl.com
January 6, 2026 at 2:16 PM
Just a few hours left to apply for this #PhD!!
Do you like phages, genomes & public health impact?🦠🧬🏥
Wanna work in a cutting edge of science, with some awesome people @quadraminstitute.bsky.social?
🤔this could be just the project for you!!🧑🔬😎
Apply NOW before midnight
#PhDposition #academicsky
Do you like phages, genomes & public health impact?🦠🧬🏥
Wanna work in a cutting edge of science, with some awesome people @quadraminstitute.bsky.social?
🤔this could be just the project for you!!🧑🔬😎
Apply NOW before midnight
#PhDposition #academicsky
Reposted by Lars Barquist
And we're live, Lecture A1 is online. Introduction to Bayesian workflow, generative models, estimands, estimators, estimates, error checking, beginnings of probability theory and Bayesian updating. www.youtube.com/watch?v=ztbY...
January 6, 2026 at 11:02 AM
And we're live, Lecture A1 is online. Introduction to Bayesian workflow, generative models, estimands, estimators, estimates, error checking, beginnings of probability theory and Bayesian updating. www.youtube.com/watch?v=ztbY...
Reposted by Lars Barquist
Excited to share my publication, showing that co-residing bacteria in the gut alters population heterogeneity in C. difficile. Thank you to my co-author, Jilarie Santos-Santiago, and our collaborative team from the labs of @joeyzacks.bsky.social and @ritatamayo.bsky.social!
doi.org/10.1128/jb.0...
doi.org/10.1128/jb.0...
Enterococcus faecalis modulates phase variation in Clostridioides difficile | Journal of Bacteriology
Clostridioides difficile is an enteric pathogen with critical implications for public health. The microbial ecosystem in which C. difficile resides shapes the behavior and fitness of C. difficile; however, the mechanisms underlying these interactions are not well defined. Here, we demonstrate that Enterococcus faecalis, an opportunistic pathogen known to co-colonize the gut with C. difficile, influences phase variation and downstream growth phenotypes in C. difficile. This phenomenon represents a new paradigm by which co-residing bacteria can modulate phase variation dynamics in C. difficile or other enteric pathogens. Understanding factors that influence C. difficile behavior may elucidate new therapeutic strategies, especially in complex polymicrobial infections.
journals.asm.org
January 5, 2026 at 7:38 PM
Excited to share my publication, showing that co-residing bacteria in the gut alters population heterogeneity in C. difficile. Thank you to my co-author, Jilarie Santos-Santiago, and our collaborative team from the labs of @joeyzacks.bsky.social and @ritatamayo.bsky.social!
doi.org/10.1128/jb.0...
doi.org/10.1128/jb.0...
Reposted by Lars Barquist
Large-scale analysis of bacterial genomes reveals thousands of lytic phages | Nature Microbiology https://www.nature.com/articles/s41564-025-02203-4
Large-scale analysis of bacterial genomes reveals thousands of lytic phages - Nature Microbiology
Diverse genomes of lytic phages are found in bacterial assemblies, challenging assumptions about the nature of the lytic lifestyle.
www.nature.com
December 30, 2025 at 12:24 AM
Large-scale analysis of bacterial genomes reveals thousands of lytic phages | Nature Microbiology https://www.nature.com/articles/s41564-025-02203-4
Reposted by Lars Barquist
The sporulation phosphorelay protein Spo0B is membrane localized in Paenibacillus! The transmembrane domain appears to increase interaction with relay partners. Congrats to former lab undergrad @isabellalin.bsky.social and her grad mentor @cassidyprints.bsky.social
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
journals.asm.org
December 30, 2025 at 1:50 PM
The sporulation phosphorelay protein Spo0B is membrane localized in Paenibacillus! The transmembrane domain appears to increase interaction with relay partners. Congrats to former lab undergrad @isabellalin.bsky.social and her grad mentor @cassidyprints.bsky.social
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
Reposted by Lars Barquist
Available Postdoc position in my lab to advance ASO technology for biotechnology, food production, infectious diseases, environmental microbiology & more. Looking for specialists in these areas with an interest in RNA applications. Involves numerous national & international collaborations.
December 30, 2025 at 11:48 AM
Available Postdoc position in my lab to advance ASO technology for biotechnology, food production, infectious diseases, environmental microbiology & more. Looking for specialists in these areas with an interest in RNA applications. Involves numerous national & international collaborations.
Reposted by Lars Barquist
RIL-seq boosts the study of sRNAs. Here comes its first application to intracellular bacteria. Plus, 10 years after its characterization, we now present an RNA sponge of Salmonella PinT.
Congrats to @kooshapour.bsky.social & great collaboration w/ @jorg-vogel-lab.bsky.social!
doi.org/10.1093/nar/...
Congrats to @kooshapour.bsky.social & great collaboration w/ @jorg-vogel-lab.bsky.social!
doi.org/10.1093/nar/...
Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT
Abstract. Salmonella virulence chiefly relies upon two major pathogenicity islands, SPI-1 and SPI-2, which enable host cell invasion and intracellular surv
doi.org
December 27, 2025 at 2:06 PM
RIL-seq boosts the study of sRNAs. Here comes its first application to intracellular bacteria. Plus, 10 years after its characterization, we now present an RNA sponge of Salmonella PinT.
Congrats to @kooshapour.bsky.social & great collaboration w/ @jorg-vogel-lab.bsky.social!
doi.org/10.1093/nar/...
Congrats to @kooshapour.bsky.social & great collaboration w/ @jorg-vogel-lab.bsky.social!
doi.org/10.1093/nar/...
Reposted by Lars Barquist
Our preprint on predicting drug resistance in bacteria is now out in @plosbiology.org. We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. Work from @yanyingyu.bsky.social with @nwheeler443.bsky.social.
Biased sampling driven by bacterial population structure confounds machine learning prediction of antimicrobial resistance
Machine learning methods have emerged as promising tools to predict antimicrobial resistance (AMR) and uncover resistance determinants from genomic data. This study shows that sampling biases driven b...
journals.plos.org
December 17, 2025 at 2:55 PM
Our preprint on predicting drug resistance in bacteria is now out in @plosbiology.org. We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. Work from @yanyingyu.bsky.social with @nwheeler443.bsky.social.
Reposted by Lars Barquist
@peterfineran.bsky.social and colleagues develop Tn-seq for phages by leveraging anti-CRISPR (Acr) as a positive
selectable marker in the presence of CRISPR-Cas counter-selection, and identify essential genes in phage from non model orgs
www.biorxiv.org/content/10.6...
selectable marker in the presence of CRISPR-Cas counter-selection, and identify essential genes in phage from non model orgs
www.biorxiv.org/content/10.6...
December 20, 2025 at 11:34 PM
@peterfineran.bsky.social and colleagues develop Tn-seq for phages by leveraging anti-CRISPR (Acr) as a positive
selectable marker in the presence of CRISPR-Cas counter-selection, and identify essential genes in phage from non model orgs
www.biorxiv.org/content/10.6...
selectable marker in the presence of CRISPR-Cas counter-selection, and identify essential genes in phage from non model orgs
www.biorxiv.org/content/10.6...
Reposted by Lars Barquist
Looking for a POSTDOC to work on jumbo phages (those with large genomes and fascinating cell biology), using our latest ASO technology (Gerovac M et al. 2025 Nature) to define RNA export mechanisms as well as to help to advance phage therapy. Here's the job ad.
December 19, 2025 at 10:51 PM
Looking for a POSTDOC to work on jumbo phages (those with large genomes and fascinating cell biology), using our latest ASO technology (Gerovac M et al. 2025 Nature) to define RNA export mechanisms as well as to help to advance phage therapy. Here's the job ad.
Reposted by Lars Barquist
Do viruses use RNA to rewire bacteria?
Yes!
In our paper in @cp-molcell.bsky.social RIL-seq reveals interkingdom RNA interactions during λ infection. Phages don’t just encode proteins, they use small RNAs to hijack bacterial replication and fine-tune infection.
#RNA #Phage
doi.org/10.1016/j.mo...
Yes!
In our paper in @cp-molcell.bsky.social RIL-seq reveals interkingdom RNA interactions during λ infection. Phages don’t just encode proteins, they use small RNAs to hijack bacterial replication and fine-tune infection.
#RNA #Phage
doi.org/10.1016/j.mo...
Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle
Using RIL-seq, Silverman et al. map the RNA interactome of E. coli during phage lambda
infection and uncover a conserved phage-encoded sRNA that activates host replication
machinery. Their findings re...
www.cell.com
December 19, 2025 at 6:43 AM
Do viruses use RNA to rewire bacteria?
Yes!
In our paper in @cp-molcell.bsky.social RIL-seq reveals interkingdom RNA interactions during λ infection. Phages don’t just encode proteins, they use small RNAs to hijack bacterial replication and fine-tune infection.
#RNA #Phage
doi.org/10.1016/j.mo...
Yes!
In our paper in @cp-molcell.bsky.social RIL-seq reveals interkingdom RNA interactions during λ infection. Phages don’t just encode proteins, they use small RNAs to hijack bacterial replication and fine-tune infection.
#RNA #Phage
doi.org/10.1016/j.mo...
Reposted by Lars Barquist
Check out the Microbial Primers page. Short articles written to help people new to a field to get quickly up to speed. @microbiologysociety.org
www.microbiologyresearch.org/content/micr...
www.microbiologyresearch.org/content/micr...
Microbial Primers | Microbiology Society
In the constantly evolving world of microbiology, new research and discoveries can often be overwhelming. ‘Microbial Primers’ is a series of short articles designed to simplify and illuminate intricat...
www.microbiologyresearch.org
December 17, 2025 at 8:27 PM
Check out the Microbial Primers page. Short articles written to help people new to a field to get quickly up to speed. @microbiologysociety.org
www.microbiologyresearch.org/content/micr...
www.microbiologyresearch.org/content/micr...
Reposted by Lars Barquist
#MachineLearning methods are used to predict #AntimicrobialResistance #AMR from genomic data. @lbarquist.bsky.social &co show that sampling biases driven by population structure severely undermine the accuracy of AMR prediction models even with large datasets @plosbiology.org 🧪 plos.io/4iZ0zXQ
December 17, 2025 at 5:35 PM
#MachineLearning methods are used to predict #AntimicrobialResistance #AMR from genomic data. @lbarquist.bsky.social &co show that sampling biases driven by population structure severely undermine the accuracy of AMR prediction models even with large datasets @plosbiology.org 🧪 plos.io/4iZ0zXQ
Our preprint on predicting drug resistance in bacteria is now out in @plosbiology.org. We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. Work from @yanyingyu.bsky.social with @nwheeler443.bsky.social.
Biased sampling driven by bacterial population structure confounds machine learning prediction of antimicrobial resistance
Machine learning methods have emerged as promising tools to predict antimicrobial resistance (AMR) and uncover resistance determinants from genomic data. This study shows that sampling biases driven b...
journals.plos.org
December 17, 2025 at 2:55 PM
Our preprint on predicting drug resistance in bacteria is now out in @plosbiology.org. We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. Work from @yanyingyu.bsky.social with @nwheeler443.bsky.social.
Reposted by Lars Barquist
Our new paper from my PhD work is online. It shows how bacterial population structure can trick machine learning—sampling matters! Many thanks to @lbarquist.bsky.social for the support and guidance! dx.plos.org/10.1371/jour...
Biased sampling driven by bacterial population structure confounds machine learning prediction of antimicrobial resistance
Machine learning methods have emerged as promising tools to predict antimicrobial resistance (AMR) and uncover resistance determinants from genomic data. This study shows that sampling biases driven b...
dx.plos.org
December 16, 2025 at 8:49 PM
Our new paper from my PhD work is online. It shows how bacterial population structure can trick machine learning—sampling matters! Many thanks to @lbarquist.bsky.social for the support and guidance! dx.plos.org/10.1371/jour...
Reposted by Lars Barquist
🎉Our new paper out: the 6th update of MODOMICS, marking 20 years of our RNA 🧬modification database. Largest update so far, including >48,000 human RNAs with modification sites, collaboration with Sci-ModoM & Human RNome Project. NAR 2025 doi: 10.1093/nar/gkaf1284
#RNA #Epitranscriptomics #Databases
#RNA #Epitranscriptomics #Databases
The twentieth anniversary of the MODOMICS database coincides with its most extensive expansion to date. Prof. Janusz Bujnicki’s team has released 48,000 RNA sequences with modified residues.
Learn more: lnkd.in/ebfXGghx
Learn more: lnkd.in/ebfXGghx
December 16, 2025 at 4:52 PM
🎉Our new paper out: the 6th update of MODOMICS, marking 20 years of our RNA 🧬modification database. Largest update so far, including >48,000 human RNAs with modification sites, collaboration with Sci-ModoM & Human RNome Project. NAR 2025 doi: 10.1093/nar/gkaf1284
#RNA #Epitranscriptomics #Databases
#RNA #Epitranscriptomics #Databases
Reposted by Lars Barquist
Ditto, ditto, ditto!
We are thrilled this is now available in @plosbiology.org 🎉🎉🎉
Our analysis of metabolic diversity in #klebsiella pneumoniae, showing clone specific metabolism. 🦠
Fantastic work by @bananabenana.bsky.social, summarised beautifully below. 🤩
We are thrilled this is now available in @plosbiology.org 🎉🎉🎉
Our analysis of metabolic diversity in #klebsiella pneumoniae, showing clone specific metabolism. 🦠
Fantastic work by @bananabenana.bsky.social, summarised beautifully below. 🤩
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 🧬 🧪 💊
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 🧬 🧪 💊
A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and capacity for intra-species co-operation
Why are there so many co-circulating Klebsiella pneumoniae clones? Using genomics and large-scale metabolic modelling of >7000 isolates, this study identifies structured, clone-specific metabolic spec...
journals.plos.org
December 15, 2025 at 2:45 AM
Ditto, ditto, ditto!
We are thrilled this is now available in @plosbiology.org 🎉🎉🎉
Our analysis of metabolic diversity in #klebsiella pneumoniae, showing clone specific metabolism. 🦠
Fantastic work by @bananabenana.bsky.social, summarised beautifully below. 🤩
We are thrilled this is now available in @plosbiology.org 🎉🎉🎉
Our analysis of metabolic diversity in #klebsiella pneumoniae, showing clone specific metabolism. 🦠
Fantastic work by @bananabenana.bsky.social, summarised beautifully below. 🤩
Reposted by Lars Barquist
New PhD project, supervision by @alanmcn1.bsky.social and me.
'Nationwide Clostridioides difficile population dynamics'
www.findaphd.com/phds/project...
Deadline for applications 9 Jan 2026, UK students only.
'Nationwide Clostridioides difficile population dynamics'
www.findaphd.com/phds/project...
Deadline for applications 9 Jan 2026, UK students only.
Nationwide Clostridioides difficile population dynamics. at University of Birmingham on FindAPhD.com
PhD Project - Nationwide Clostridioides difficile population dynamics. at University of Birmingham, listed on FindAPhD.com
www.findaphd.com
December 13, 2025 at 4:59 PM
New PhD project, supervision by @alanmcn1.bsky.social and me.
'Nationwide Clostridioides difficile population dynamics'
www.findaphd.com/phds/project...
Deadline for applications 9 Jan 2026, UK students only.
'Nationwide Clostridioides difficile population dynamics'
www.findaphd.com/phds/project...
Deadline for applications 9 Jan 2026, UK students only.
Reposted by Lars Barquist
Franziska Faber and I are recruiting shared postdocs, PhD students to work on Fusobacterium & new BGCs. www.helmholtz-hiri.de/fileadmin/HI...
December 12, 2025 at 3:43 PM
Franziska Faber and I are recruiting shared postdocs, PhD students to work on Fusobacterium & new BGCs. www.helmholtz-hiri.de/fileadmin/HI...
Reposted by Lars Barquist
eggNOG v7: phylogeny-based orthology predictions and functional annotations academic.oup.com/nar/advance-...
December 11, 2025 at 5:03 PM
eggNOG v7: phylogeny-based orthology predictions and functional annotations academic.oup.com/nar/advance-...
Reposted by Lars Barquist
If you ever need to fuzzy search some DNA, sassy is your tool.
Please spread the word; I think many people just outside my own circle could benefit from this :)
cc @rickbitloo.bsky.social
github.com/RagnarGrootK...
Please spread the word; I think many people just outside my own circle could benefit from this :)
cc @rickbitloo.bsky.social
github.com/RagnarGrootK...
December 10, 2025 at 3:50 PM
If you ever need to fuzzy search some DNA, sassy is your tool.
Please spread the word; I think many people just outside my own circle could benefit from this :)
cc @rickbitloo.bsky.social
github.com/RagnarGrootK...
Please spread the word; I think many people just outside my own circle could benefit from this :)
cc @rickbitloo.bsky.social
github.com/RagnarGrootK...
Reposted by Lars Barquist
I'm teaching Statistical Rethinking again starting Jan 2026. This time with live lectures, divided into Beginner and Experienced sections. Will be a lot more work for me, but I hope much better for students.
I will record lectures & all will be found at this link: github.com/rmcelreath/s...
I will record lectures & all will be found at this link: github.com/rmcelreath/s...
December 9, 2025 at 1:58 PM
I'm teaching Statistical Rethinking again starting Jan 2026. This time with live lectures, divided into Beginner and Experienced sections. Will be a lot more work for me, but I hope much better for students.
I will record lectures & all will be found at this link: github.com/rmcelreath/s...
I will record lectures & all will be found at this link: github.com/rmcelreath/s...