Lars Barquist

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.

4.5K followers1.5K following128 posts

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Lars Barquist
@lbarquist.bsky.social

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...

nature.comA scalable gut epithelial organoid model reveals the genome-wide colonization landscape of a human-adapted pathogen - Nature GeneticsA genome-wide screen using human gut epithelial organoids combined with transposon-directed insertion sequencing identifies over 100 Shigella flexneri genes required for epithelial colonization.

Lars Barquist reposted

BF Francis Ouellette
@bffo.bsky.social

From @alexbateman1.bsky.social in #OUP 's @bioinfoadv.bsky.social journal | Peer Bork (1963-2026): pioneer of #ComputationalBiology, architect of #Bioinformatics #Resources, and visionary #Microbiome researcher | #OpenScience CC/ @embl.org @ebi.embl.org | 🧬🖥️🧪🔓❤️ ⬇️ academic.oup.com/bioinformati...

academic.oup.comPeer Bork (1963–2026): pioneer of computational biology, architect of bioinformatics resources, and visionary microbiome researcherPeer Bork, one of the most influential computational biologists of his generation, died on 16 January 2026 from natural causes (EMBL 2026). He was 62 years

Lars Barquist reposted

Vivek Mutalik
@vivekmutalik.bsky.social

😮😮 Microbial community dynamics in a traditional Swiss mountain cheese over 142 years of cheesemaking: Current Biology www.cell.com/current-biol...

cell.comMicrobial community dynamics in a traditional Swiss mountain cheese over 142 years of cheesemakingHow 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 ...

Lars Barquist reposted

Julian Parkhill
@julianparkhill.bsky.social

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...

cam.ac.ukProfessorship of Veterinary ScienceThe 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...

Lars Barquist reposted

Emily Goodall
@emgoodall.bsky.social

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...

microbiologyresearch.orgApplications of transposon-insertion sequencing for understanding bacterial physiologyTransposon-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...

Lars Barquist reposted

Ákos T Kovács
@evolvedbiofilm.bsky.social

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/...

academic.oup.comAn sRNA overexpression library reveals AbnZ as a negative regulator of an essential translocation module in Caulobacter crescentusAbstract. Small RNAs (sRNAs) play a crucial role in modulating target gene expression through short base-pairing interactions and serve as integral compone

Lars Barquist reposted

PLOS Biology
@plosbiology.org

#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

buff.lyCompleting the BASEL phage collection to unlock hidden diversity for systematic exploration of phage–host interactionsThe 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…

Lars Barquist reposted

Pedro Beltrao
@pedrobeltrao.bsky.social

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.comgeneralAI_for research_intro.pptxRecent 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...

Lars Barquist reposted

Rob Patro
@robp.bsky.social

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!

Lars Barquist reposted

The Lancet Infectious Diseases
@thelancetinfdis.bsky.social

Replying to @thelancetinfdis.bsky.social

New Comment From estimates to evidence: measuring the true burden of AMR www.thelancet.com/journals/lan...

thelancet.comFrom estimates to evidence: measuring the true burden of AMRAntimicrobial 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...

Lars Barquist reposted

Frances Yap
@ribo1214.bsky.social

"16S ribosomal RNA modification drives transcript-specific translation efficiency" pubmed.ncbi.nlm.nih.gov/42632017/ from @ramamurthilab.bsky.social lab #Ribosome #RNASky #MicroSky

pubmed.ncbi.nlm.nih.gov16S ribosomal RNA modification drives transcript-specific translation efficiency - PubMedBacterial 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 …

Lars Barquist reposted

Nature Microbiology
@natmicrobiol.nature.com

Out Now! Colibactin beyond carcinogenesis #MicroSky

go.nature.comColibactin beyond carcinogenesisNature 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.

Lars Barquist reposted

Rob Patro
@robp.bsky.social

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

Lars Barquist reposted

Paul Gardner
@ppgardne.bsky.social

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...

doi.orgGenomic indicators of gene function: a systematic assessment of the human genomeAbstract. Proteins and non-coding RNAs are functional products of the genome that are central for crucial cellular processes. With recent technological adv

Lars Barquist reposted

Ákos T Kovács
@evolvedbiofilm.bsky.social

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...

annualreviews.orgDecoding Bistability and Drivers of Phenotypic Variation in BacteriaIn 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...

Lars Barquist reposted

Willem van Schaik
@wvschaik.bsky.social

Excellent review article Metabolic strategies of Enterobacteriaceae gut colonization | Nature Reviews Microbiology share.google/hKziCqmwDr3D...

share.googleMetabolic strategies of Enterobacteriaceae gut colonization - Nature Reviews MicrobiologyIn 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.

Lars Barquist reposted

Erik van Nimwegen
@erikvannimwegen.bsky.social

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

nature.comBonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data - Nature BiotechnologyHigh-dimensional data are visualized through representation on tree structures.
Erik van Nimwegen@erikvannimwegen.bsky.social

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...

biorxiv.orgBonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics dataSingle-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...

Lars Barquist reposted

Grainger Lab
@graingerlab.bsky.social

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...

biorxiv.orgWidespread coupling of promoters and terminators of transcription in bacteriaTranscription 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...

Lars Barquist reposted

Richard McElreath 🐈‍⬛
@rmcelreath.bsky.social

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.

vincentholst.bsky.social@vincentholst.bsky.social

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.

Lars Barquist reposted

Aki Vehtari
@avehtari.bsky.social

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!)

avehtari.github.ioBayesian Workflow book: Website – Bayesian Workflow bookWebsite for the Bayesian Workflow book by Gelman, Vehtari, McElreath, et al. — case studies, code, and exercises in R and Stan.
Aki Vehtari@avehtari.bsky.social

All three books I've co-authored are freely available online for non-commercial use: - #Bayesian Data Analysis, 3rd ed (aka BDA3) at stat.columbia.edu/~gelman/book/ - #Regression and Other Stories at avehtari.github.io/ROS-Examples/ - Active Statistics at avehtari.github.io/ActiveStatis...

Lars Barquist reposted

Adam Mulkern
@mulkern.bsky.social

Out now in @natcomms.nature.com: how do bacteria evolve resistance to programmable antisense antibiotics? www.nature.com/articles/s41...

nature.comA systematic identification of resistance determinants to antisense antibiotics suggests adaptation strategies dependent on the delivery peptide - Nature CommunicationsIn 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...

Lars Barquist reposted

Jens Hör
@jenshoer.bsky.social

Do you need to analyze bacterial microscopy data and are looking for an all-in-one tool for Windows or macOS? Check out BactoMate by Lasse Hallenga and Philipp Popp! I'm happy that we were able to contribute to this great work. www.biorxiv.org/content/10.6...

biorxiv.orgBactoMate: an integrated platform for reproducible bacterial microscopy analysisQuantitative microscopy of microorganisms increasingly produces large, multidimensional datasets, yet their analysis often depends on fragmented workflows spanning file conversion, segmentation, quali...

Lars Barquist reposted

Freya Harrison
@friendlymicrobe.bsky.social

What do microbes actually use antimicrobial peptides for? How do they impact microbial communities? Thanks @lindaoyama.bsky.social for contributing this review to a special issue of Essays in Biochemistry on the social lives of bacteria #MicroSky portlandpress.com/essaysbioche...

portlandpress.comFrom sequence space to ecological function: microbiome-derived antimicrobial peptides as community effectors and therapeutic leadsAbstract. Antimicrobial peptide research has long centred on host defence molecules, yet microbiomes themselves encode a diverse and increasingly important repertoire of peptide-based antimicrobials. ...

Lars Barquist reposted

Philip Ball
@philipcball.bsky.social

"The central challenge is no longer building models that reproduce biological behavior, but building models from which causal structure can be inferred." Very sensible paper about not just throwing everything into your simulation or model. arxiv.org/abs/2608.06998

arxiv.orgSimulating is not always understanding: When model complexity obscures biologyIn cell biology, computational models of biological systems range from minimal representations with a handful of parameters to whole-cell simulations tracking thousands of molecular species across a c...

Lars Barquist reposted

Camilla Ciolli Mattioli
@cciollimattioli.bsky.social

Offering 1 PhD position under the call in the link

Helmholtz-Zentrum für Infektionsforschung (HZI)@helmholtzhzi.bsky.social

🚨 We're recruiting! The HZI is offering 16 fully funded PhD positions to tackle pressing challenges in infection research — from basic science to translational innovation. 📍 Braunschweig, Würzburg, Hannover or Saarbrücken 📅 Apply by September 11 Learn more: jobs.helmholtz-hzi.de/job/Braunsch...

Lars Barquist reposted

Camilla Ciolli Mattioli
@cciollimattioli.bsky.social

Preprint alert! Work from my postdoc in the lab of @roi1avraham.bsky.social In a collaboration with @danielschraivogel.bsky.social and Lars Steinmetz www.biorxiv.org/content/10.6...

biorxiv.orgImage-based transposon screening reveals a flavin reductase that restrains intracellular Salmonella replication in macrophagesIntracellular bacterial pathogens can survive and replicate within host cells, yet an isogenic population follows divergent fates: some bacteria are killed, some arrest growth, and others replicate to...

Lars Barquist reposted

NUCLEATE Cluster
@nucleate-cluster.bsky.social

Congrats to NUCLEATE PIs Jörg Vogel & Alexander Westermann on their new paper in PNAS! 👏 Alongside partners at Uni Marburg, they identified SAILR, a long non-coding RNA that acts as an apoptosis regulator. Read more: www.pnas.org/doi/10.1073/... #NUCLEATECluster

Helmholtz-Zentrum für Infektionsforschung (HZI)@helmholtzhzi.bsky.social

#Makrophagen sind die „Fresszellen“ des #Immunsystems, doch manche Erreger machen sich gerade diese Zellen als Versteck zunutze. Ein Team des @helmholtz-hiri.bsky.social hat mit Partnern eine #RNA gefunden, die ein "Notausschalter" für infizierte Immunzellen ist. www.helmholtz-hzi.de/media-center...

helmholtz-hzi.de„Notausschalter“ für FresszellenForschende identifizieren die lncRNA SAILR als Schlüsselregulator in Makrophagen. Sie könnte als Biomarker und Therapieansatz dienen.

Lars Barquist reposted

Torsten Seemann
@torstenseemann.bsky.social

NCBI Hidden Markov Models (HMM) Release 20.0 18,950 prokaryotic protein HMMs maintained by @ncbi ncbiinsights.ncbi.nlm.nih.gov/2026/07/01/h... #microbiology #bioinforbioinformatics #genomics

ncbiinsights.ncbi.nlm.nih.govNow Available! NCBI Hidden Markov Models (HMM) Release 20.0 - NCBI InsightsDownload release 20.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP). You can search this collection against your favorite prokaryoti...

Lars Barquist reposted

Adam Mulkern
@mulkern.bsky.social

Why do some bacteria evolve antibiotic resistance more readily than others? Loved writing this one with @craigmaclean.bsky.social and Liam.

Craig MacLean@craigmaclean.bsky.social

New Essay: 'Resistance potentiators: Evolutionary catalysts of antibiotic resistance' To understand the evolutionary drivers of #AMR we need to move beyond resistance genes to thinking about the ability of genomes to generate AMR variants. #microsky journals.plos.org/plosbiology/...

journals.plos.orgResistance potentiators: Evolutionary catalysts of antibiotic resistanceHow do bacteria evolve resistance to antibiotics? Drawing on evidence from experimental evolution, pathogen genomics, and molecular microbiology, this Essay argues that the evolution of antibiotic res...

Lars Barquist reposted

Kym Deyn
@kymdeyn.bsky.social

Rough day, so have a poem about the Jar of Moles in the Grant Zoology Museum in London that everyone has regarded as too thoroughly batshit to publish

Lars Barquist reposted

Helmholtz Institute Würzburg
@helmholtz-hiri.bsky.social

Congratulations to @nanopat.bsky.social on receiving the @rnasociety.bsky.social’s Eclipse Award for Innovation in High Throughput Biology! 🎉 The award recognizes the #RNA research methods he developed during his doctoral studies in #HIRI’s Smyth lab. Read more: www.helmholtz-hiri.de/en/newsroom/...

helmholtz-hiri.deAward-winning novel methods in RNA researchPatrick Bohn receives RNA Society Eclipse Award for Innovation in High Throughput Biology

Lars Barquist reposted

James Connolly
@ruamicro.bsky.social

Latest research from the lab out now. We examined the role and expression of fimbriae during UPEC bloodstream infection. A real team effort and brilliant collaboration with Mark Schembri’s lab in Brisbane. Thanks to the MRC and BBSRC for supporting our research @ukri.org

journals.plos.orgYad fimbriae are triggered by host cues and enhance extraintestinal pathogenic Escherichia coli tissue colonisation during bloodstream infectionAuthor summary Extraintestinal pathogenic Escherichia coli (ExPEC) colonise the human gut without causing disease but can disseminate to the urinary tract and bloodstream. Understanding the mechanisms...

Lars Barquist reposted

Alicia Oshlack
@aliciao.bsky.social

New paper from the lab! Spoiler: data driven methods performed better for normalisation than spike in CUT&RUN (again). Congratulations especially to Krutika Ambani for most of the work here now embarking on a PhD.

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social

Benchmarking normalisation methods for differential binding analysis in CUT&RUN https://www.biorxiv.org/content/10.64898/2026.05.24.727463v1

Lars Barquist reposted

Youssef El Mouali
@youssefelmouali.bsky.social

New paper out in @cp-cellhostmicrobe.bsky.social! Microbes evolving with modern lifestyles 🧬🦠 S. copri uses PerR to manage oxygen stress, but some strains acquired OxyR via HGT, boosting oxygen tolerance. These strains are enriched in industrialized populations. www.cell.com/cell-host-mi...

cell.comBiogeography-associated emergence of enhanced oxygen tolerance in the abundant human gut commensal Segatella copriEl Mouali and Tawk et al. characterize the oxygen-tolerance response in the human gut-residing bacterium Segatella copri. They identified a subset of strains that acquired an additional oxygen regulat...