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Lars Barquist

@lbarquist.bsky.social
4.6K followers 1.6K following 128 posts

Assistant prof @ UofT, associated scientist @ Helmholtz Institute for RNA-based Infection Research. Pathogen systems biology / informatics / functional genomics. Coastal New Hampshirite. Drink Moxie.

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Reposted by Lars Barquist
Vivek Mutalik @vivekmutalik.bsky.social · 29/09/2026
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!
Next generation application space with systematic characterization of phage-host interaction landscapes.
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Vivek Mutalik @vivekmutalik.bsky.social · 25/09/2026
😮😮 Microbial community dynamics in a traditional Swiss mountain cheese over 142 years of cheesemaking: Current Biology www.cell.com/current-biol...
cell.com
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 ...
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Reposted by Lars Barquist
Julian Parkhill @julianparkhill.bsky.social · 16/09/2026
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.uk
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...
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Reposted by Lars Barquist
Emily Goodall @emgoodall.bsky.social · 14/09/2026
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.org
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...
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Ákos T Kovács @evolvedbiofilm.bsky.social · 14/09/2026
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.com
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
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Reposted by Lars Barquist
PLOS Biology @plosbiology.org · 11/09/2026
#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.ly
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…
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Reposted by Lars Barquist
Pedro Beltrao @pedrobeltrao.bsky.social · 09/09/2026
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
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...
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Oleg Dmytrenko @olehdmy.bsky.social · 01/09/2026
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...
recruiting.fz-juelich.de
PhD Position – Biology and application of bacterial antiphage defenses
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www.slowtravelberlin.com @slowberlin.bsky.social · 01/09/2026
Thanks to Deutsche Bahn, the famous trolley problem is redundant! 🥳
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Freya Harrison @friendlymicrobe.bsky.social · 01/09/2026
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
Schematic representation of G. mellonella applications for investigating interbacterial interactions
The upper half (A) of the figure depicts experimental methods in which bacteria are introduced to G. mellonella larvae. These include force-feeding, injection, and burn models. The lower half (B) shows example interactions described in the literature within the G. mellonella model, including antagonistic, competitive, and cooperative co-infection outcomes.
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Rob Patro @robp.bsky.social · 01/09/2026
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!
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The Lancet Infectious Diseases @thelancetinfdis.bsky.social · 24/08/2026
New Comment From estimates to evidence: measuring the true burden of AMR www.thelancet.com/journals/lan...
thelancet.com
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...
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Frances Yap @ribo1214.bsky.social · 24/08/2026
"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.gov
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 …
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Reposted by Lars Barquist
Nature Microbiology @natmicrobiol.nature.com · 24/08/2026
Out Now! Colibactin beyond carcinogenesis #MicroSky
go.nature.com
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.
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Rob Patro @robp.bsky.social · 23/08/2026
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
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Paul Gardner @ppgardne.bsky.social · 23/08/2026
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.org
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
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Reposted by Lars Barquist
Evgenii Protasov @evgenii-protasov.bsky.social · 24/08/2026
Small proteins in prokaryotes, a fascinating world #microbiology #proteins #prokaryotes #MicroSky @femsjournals.bsky.social @femsmicro.org doi.org/10.1093/fems...
doi.org
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
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Ákos T Kovács @evolvedbiofilm.bsky.social · 23/08/2026
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.org
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...
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Willem van Schaik @wvschaik.bsky.social · 22/08/2026
Excellent review article Metabolic strategies of Enterobacteriaceae gut colonization | Nature Reviews Microbiology share.google/hKziCqmwDr3D...
share.google
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.
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Erik van Nimwegen @erikvannimwegen.bsky.social · 21/08/2026
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.com
Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data - Nature Biotechnology
High-dimensional data are visualized through representation on tree structures.
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Grainger Lab @graingerlab.bsky.social · 21/08/2026
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.org
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...
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Reposted by Lars Barquist
Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 13/08/2026
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.
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Aki Vehtari @avehtari.bsky.social · 13/08/2026
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.io
Bayesian Workflow book: Website – Bayesian Workflow book
Website for the Bayesian Workflow book by Gelman, Vehtari, McElreath, et al. — case studies, code, and exercises in R and Stan.
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Marco Galardini @mgalactus.bsky.social · 12/08/2026
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...
nature.com
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...
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Reposted by Lars Barquist
Adam Mulkern @mulkern.bsky.social · 12/08/2026
Out now in @natcomms.nature.com: how do bacteria evolve resistance to programmable antisense antibiotics? www.nature.com/articles/s41...
nature.com
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...
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Jens Hör @jenshoer.bsky.social · 10/08/2026
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.org
BactoMate: an integrated platform for reproducible bacterial microscopy analysis
Quantitative microscopy of microorganisms increasingly produces large, multidimensional datasets, yet their analysis often depends on fragmented workflows spanning file conversion, segmentation, quali...
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Reposted by Lars Barquist
Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 11/08/2026
Howdy, In my spare time I have been working on a modern web version of BRIG, and it is now in a state fit for public consumption. Please share with your team + students. And If they have feedback they can reach me on email. brigx.genomicx.org BRIGX is a modern implementation of BRIG […]
mstdn.science
Original post on mstdn.science
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Freya Harrison @friendlymicrobe.bsky.social · 10/08/2026
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.com
From sequence space to ecological function: microbiome-derived antimicrobial peptides as community effectors and therapeutic leads
Abstract. Antimicrobial peptide research has long centred on host defence molecules, yet microbiomes themselves encode a diverse and increasingly important repertoire of peptide-based antimicrobials. ...
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Philip Ball @philipcball.bsky.social · 10/08/2026
"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.org
Simulating is not always understanding: When model complexity obscures biology
In 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...
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Prof Paula Salgado @pssalgado.bsky.social · 05/06/2026
Our keynote speaker Franziska Faber on sRNAs in #Cdiff #sporulation @3cdf.bsky.social #3CdF2026
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Camilla Ciolli Mattioli @cciollimattioli.bsky.social · 04/08/2026
Offering 1 PhD position under the call in the link
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Camilla Ciolli Mattioli @cciollimattioli.bsky.social · 31/07/2026
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.org
Image-based transposon screening reveals a flavin reductase that restrains intracellular Salmonella replication in macrophages
Intracellular 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...
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NUCLEATE Cluster @nucleate-cluster.bsky.social · 20/07/2026
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
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Torsten Seemann @torstenseemann.bsky.social · 17/07/2026
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.gov
Now Available! NCBI Hidden Markov Models (HMM) Release 20.0 - NCBI Insights
Download 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...
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Josie Bryant @josiebryant.bsky.social · 08/07/2026
Very proud of this preprint out of my lab, our first (of hopefully many) host-microbe spatial transcriptomics paper. www.biorxiv.org/content/10.6... Amazing insights into P. aeruginosa biology and chronic airway disease @cysticfibrosis.org.uk @sangerinstitute.bsky.social @asthmaandlung.org.uk
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Adam Mulkern @mulkern.bsky.social · 07/07/2026
Why do some bacteria evolve antibiotic resistance more readily than others? Loved writing this one with @craigmaclean.bsky.social and Liam.
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Pedro Beltrao @pedrobeltrao.bsky.social · 08/07/2026
The @qedscience.bsky.social "impact" score generated a lot of discussion on ranking preprints, including ideas on multi-dimensional rankings that are user specific. Besides describing the ideas, we can now prototype them (with Claude in this case). Here is Salient salient-sgeu6fs5ua-uc.a.run.app
salient-sgeu6fs5ua-uc.a.run.app
Rising — Salient
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Elena Rivas @rivaselenarivas.bsky.social · 05/07/2026
New! R-scape version v2.6.11 github.com/EddyRivasLab... with drawings of R-scape annotated RNA consensus structures with many fewer overlaps!! Using RFview github.com/dincarnato/R... Shout out to @incarnatolab.bsky.social for displaying R-scape's covariation outputs + CaCoFold-R3D structures.
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A. Murat Eren (Meren) @merenbey.bsky.social · 04/07/2026
New study by Alexander Henoch (@ahenoch.bsky.social), a PhD student in our group @hifmb.de and @awi.de, shows what it takes to bring gene synteny into microbial pangenomes, and what we learn about the variability landscape of genomes when we do that. See the pre-print here: doi.org/10.64898/202...
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Jessica Blair @jessicamablair.bsky.social · 25/06/2026
"How to give a bad talk". Great commentary on how not to do this! www.nature.com/articles/s41...
nature.com
How to give a bad talk - Nature Reviews Cancer
Effective presentations require clarity and audience awareness. In this Comment, Itai Yanai outlines common misconceptions about presentations and how to address them to deliver more impactful and ins...
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Kym Deyn @kymdeyn.bsky.social · 19/06/2026
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
Jar of Moles (Grant Zoology Museum, London)
crittery dozened things each pink snout snootling
formaldehyde up it's bamboozler which poor fuck
had to collect them out in the dirt with a shovel
here moley moley  	BONK . I’m only gonna
put you in a jar and let tourists go eww at you
for the next two hundred years god look at me
for two hundred years I’d do anything look 
mummy, one of them’s licking the glass—
honey it's dead  velvety sweet sardined hope
their ghosts are friends teeming in a molish
afterlife dark and circular everything worm-
flavoured tasty buggy snackerels what if 
you smashed the mole jar? vinegared
moles spilling out flaccid & swimming
everyone screaming someone saying Freddy
you gotta get us a new jar of moles—
—goddammit boss I  never asked for any of this
A jar of wet preserved moles, the jar is very full and all the little hands, feet and snoots mark it as both upsetting and fascinating
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Helmholtz Institute Würzburg @helmholtz-hiri.bsky.social · 17/06/2026
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.de
Award-winning novel methods in RNA research
Patrick Bohn receives RNA Society Eclipse Award for Innovation in High Throughput Biology
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James Connolly @ruamicro.bsky.social · 02/06/2026
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.org
Yad fimbriae are triggered by host cues and enhance extraintestinal pathogenic Escherichia coli tissue colonisation during bloodstream infection
Author 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...
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Travis Wheeler @wheelerlab.org · 31/05/2026
Introducing nail - a Rust implementation of profile HMM sequence alignment for proteins. Near-HMMER sensitivity, but a lot faster: www.biorxiv.org/content/10.1... github.com/TravisWheele...
biorxiv.org
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Alicia Oshlack @aliciao.bsky.social · 27/05/2026
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.
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Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 15/05/2026
Growth-dependent tRNA Reprogramming and Codon Bias Link Translation to Metabolic State in Enterococcus faecalis 🦠 queuosine Q again... (Q is also a japanese anime character) www.biorxiv.org/content/10.6...
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Luis Pedro Coelho @luispedrocoelho.bsky.social · 13/05/2026
More details to follow later, but this has been in the works for almost 6 years, so it is great to finally see it in preprint form: "The elusive resistome: a global comparison reveals large discrepancies among detection pipelines" www.biorxiv.org/content/10.6...
biorxiv.org
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Kiabugboy @kiabugboy.bsky.social · 09/05/2026
Rugose coral video is done! Full video here: www.youtube.com/watch?v=dwkM... #SciArt #paleoart #3dAnimation #coral #reef
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Youssef El Mouali @youssefelmouali.bsky.social · 07/05/2026
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.com
Biogeography-associated emergence of enhanced oxygen tolerance in the abundant human gut commensal Segatella copri
El 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...
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Marco Galardini @mgalactus.bsky.social · 04/05/2026
Are you frustrated by how arbitrary fixed SNPs thresholds "feel"? Are you wondering if there are genetic differences between "promiscuous" and "shy" pathogens? If yes, then read our latest preprint to see what @jburgaya.bsky.social has been up to! www.medrxiv.org/content/10.6...
medrxiv.org
Coupling time-aware SNP thresholds with genetic markers to define bacterial transmission chains in hospital surveillance
Hospital settings can act as reservoirs for pathogens, with many nosocomial bacteria surviving for extended periods of time and spreading via contaminated environments, healthcare workers, or medical ...
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