Lars Barquist

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/s4158…

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/plosbiology/ar…

Research Highlight by @madhuramukho: Capturing host-microbe interactions nature.com/articles/s4159…

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/10.110…

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.

A study in @NatureGenet establishes the comprehensive genome-wide map of Shigella genes required to infect human intestinal epithelium. go.nature.com/3ZySYa8

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/s4158…

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/s4158… nature.com/articles/s4158…

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/gigasc…

New paper, discussing open problems in bacterial phenotype prediction with ML: arxiv.org/abs/2502.07749

I am happy to tell that our collaborative review article on #PhageTherapy has been just published in Nature Reviews Methods Primers rdcu.be/d9H92

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/ar…

🚀 New Paper Alert! 🚀 𝐑𝟐𝐃𝐓: a comprehensive platform for visualising RNA secondary structure Check it out in @NAR_Open: academic.oup.com/nar/article/53… Here’s why you should give it a try 🧵👇

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!

We've already applied this together with the @WestermannLab to build a web server for Bacteroides thetaiotaomicron (nature.com/articles/s4156…), you can check that out here: micromix.helmholtz-hiri.de/bacteroides/

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…