@LBarquist

Assistant Prof @UofT, research group leader @Helmholtz_HIRI. Pathogen systems biology / informatics / functional genomics. Coastal New Hampshirite. Drink Moxie.

scholar.google.com/citations?hl=en&user=9MYn5q8AAAAJ&view_op=list_works&sortby=pubdate
Joined October 2016
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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/ @dimartino_ml @SellinLab, out in @NatureGenet nature.com/articles/s41588-0…
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Our paper on predicting drug resistance in bacteria is out @PLOSBiology. We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. From @YanyingYu w/ @nwheeler443. journals.plos.org/plosbiolog…

Biased sampling driven by bacterial population structure confounds machine learning prediction of...

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...

journals.plos.org
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Research Highlight by @madhuramukho: Capturing host-microbe interactions nature.com/articles/s41592-0…

Capturing host–microbe interactions

Nature Methods - A combination of organoid technology and genetic methods enables studies of human pathogens.

nature.com
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Lars Barquist retweeted
Severin Ronneau@SRonneau30 Jul 2025
Happy to share our lastest story (with @HallezLab, @LBarquist, @CMichaux13) ! We show how host-relevant stress disrupts Fe-S cluster stability, tuning (p)ppGpp levels to control bacterial adaptation and trigger virulence. Read more here 👉 biorxiv.org/content/10.1101/…

Stress-Induced Iron-Sulfur Cluster Damage as a Conserved Trigger of the Stringent Response

Pathogenic bacteria rely on the stringent response to adapt to the complex and fluctuating conditions encountered within the host. However, the mechanisms by which the stringent response senses...

biorxiv.org
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Could lab-grown mini-organs help scientists research a range of infections? A new study published in @Nature Genetics shows how researchers have mapped how the Shigella bacterium infects the human gut. Read our interview with study co-author @LBarquist: uoft.me/bI7.
Lars Barquist, Assistant Prof at the Department of Biology at UTM

ALT Lars Barquist, Assistant Prof at the Department of Biology at UTM

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A study in @NatureGenet establishes the comprehensive genome-wide map of Shigella genes required to infect human intestinal epithelium. go.nature.com/3ZySYa8
This is figure 2, which shows a genome-wide map of the Shigella geneset required to invade the human enteroid infection model.

ALT This is figure 2, which shows a genome-wide map of the Shigella geneset required to invade the human enteroid infection model.

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Lars Barquist retweeted
Lars Barquist@LBarquist12 Jun 2025
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/ @dimartino_ml @SellinLab, out in @NatureGenet nature.com/articles/s41588-0…
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Lars Barquist retweeted
Waggoner Lab@LabWaggoner13 Jun 2025
Large-scale organoid models, combined with genome-wide mutagenesis screening, reveals virulence factors required for Shigella colonization @dimartino_ml @NatureGenet @SellinLab @LBarquist nature.com/articles/s41588-0… nature.com/articles/s41588-0…
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GigaScience@GigaScience19 Feb 2025
Presenting a new flexible web platform for sharing and integrating microbial omics data, including RNA-seq and transposon-insertion sequencing. Micromix: web infrastructure for visualizing and remixing microbial ‘omics data doi.org/10.1093/gigascience/…
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New paper, discussing open problems in bacterial phenotype prediction with ML: arxiv.org/abs/2502.07749

Whole-Genome Phenotype Prediction with Machine Learning: Open...

How can we identify causal genetic mechanisms that govern bacterial traits? Initial efforts entrusting machine learning models to handle the task of predicting phenotype from genotype return high...

arxiv.org
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I am happy to tell that our collaborative review article on #PhageTherapy has been just published in Nature Reviews Methods Primers rdcu.be/d9H92
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Lars Barquist@LBarquist4 Feb 2025
Interested in collecting, sharing, and interacting with large collections of bacterial functional genomics data (RNA-seq, Tn-seq/TraDIS, etc.)? Check out our new web platform, Micromix, with case studies for Salmonella and Bacteroides! Thread 1/n academic.oup.com/gigascience…

Micromix: web infrastructure for visualizing and remixing microbial ‘omics data

Abstract. Micromix is a flexible web platform for sharing and integrating microbial omics data, including RNA sequencing and transposon-insertion sequencin

academic.oup.com
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Lars Barquist retweeted
Anton Petrov@AntonIPetrov10 Feb 2025
🚀 New Paper Alert! 🚀 𝐑𝟐𝐃𝐓: a comprehensive platform for visualising RNA secondary structure Check it out in @NAR_Open: academic.oup.com/nar/article… Here’s why you should give it a try 🧵👇
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Interested in collecting, sharing, and interacting with large collections of bacterial functional genomics data (RNA-seq, Tn-seq/TraDIS, etc.)? Check out our new web platform, Micromix, with case studies for Salmonella and Bacteroides! Thread 1/n academic.oup.com/gigascience…

Micromix: web infrastructure for visualizing and remixing microbial ‘omics data

Abstract. Micromix is a flexible web platform for sharing and integrating microbial omics data, including RNA sequencing and transposon-insertion sequencin

academic.oup.com
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more replies
We've already applied this together with the @WestermannLab to build a web server for Bacteroides thetaiotaomicron (nature.com/articles/s41564-0…), you can check that out here: micromix.helmholtz-hiri.de/b…

An expanded transcriptome atlas for Bacteroides thetaiotaomicron reveals a small RNA that modulates...

Nature Microbiology - Integration of differential and conventional RNA sequencing and transposon mutant fitness data for Bacteroides thetaiotaomicron grown under 15 different conditions provides an...

nature.com
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Anyway, we hope to build this out into a series of community resources -- hope people find it useful and feel free to get in touch if you're interested in using it!
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Paperpile
@paperpile25 Jan 2025
When you find a key paper, the last thing you want is to miss related studies that could strengthen your literature review. Connected Papers can help you uncover related research. You can now save references discovered in @ConnectedPapers directly to Paperpile. Learn more in our blog post 🔽 paperpile.com/blog/connected…

Paperpile’s Connected Papers integration - Paperpile

We announce Paperpile’s Connected Papers integration, a literature discovery tool.

paperpile.com
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