Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback. rdcu.be/famFj

High-resolution metagenome assembly for modern long reads with myloasm

Nature Biotechnology - A long-read metagenome assembly method recovers circular and complete genomes better than existing tools.

rdcu.be

Nature Biotechnology@natbiotech.nature.com · 5mo ago

High-resolution metagenome assembly for modern long reads with myloasm - @lh3lh3.bsky.social @jimshaw.bsky.social @danafarber.bsky.social @harvardmed.bsky.social go.nature.com/3PBEwvR

🚨 New paper! Very excited to have been part of this collaborative work looking at the effect of antibiotics on the gut microbiota even years after prescription. Amazing effort led by Gabriel @tovefall.bsky.social and many others published today in Nature Medicine! 🔗 www.nature.com/articles/s41...

Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals - Nature Medicine

Using individual-level data from the Swedish Prescribed Drug Register and fecal metagenomes of 14,979 individuals in Sweden, the authors examined the association between oral antibiotic use over 8 yea...

nature.com

Deacon can now run in the browser using WebAssembly. Sequence data never leaves your machine. It currently supports FASTA/Q filtering using indexes up to 1GB in size. Demo: bede.im/deacon

New preprint from us @modmedmicro.bsky.social where we validate the diagnostic accuracy of a metagenomic nanopore sequencing method for respiratory RNA viruses. www.medrxiv.org/content/10.6...

Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study

Background Clinical metagenomics (CMg) offers high-throughput respiratory pathogen detection with a wider range than targeted, probe-dependent diagnostics. Sequencing cost and the challenges of high h...

medrxiv.org

🔔👇🔔

@nstoesser.bsky.social · 6mo ago

Are you a post-doctoral microbiologist interested in characterising bacterial resistance evolution and want to apply your knowledge and expertise to developing new therapeutics for Klebsiella (and other Enterobacterales) infections? Then we need you! Apply now bit.ly/3MX39Ce close date March 13th 👀

New pre-print with @wtmatlock.bsky.social!!! www.biorxiv.org/content/10.6... What shapes the distribution of plasmids across bacteria? Our paper shows that conjugative plasmids actually have a very narrow distribution compared to mobilizable plasmids. Conjugative systems restrict plasmid transfer!

At long last, my final PhD chapter is out: we developed a novel evolutionary simulator of bacterial pangenomes, Pansim, fitting it to data from >600K genomes using a likelihood-free framework, PopPUNK-mod, to explore neutral and adaptive pangenome dynamics www.biorxiv.org/content/10.6...

First paper of my PhD @doerrlab.bsky.social is up! We characterized meropenem tolerance in Enterobacterales species, and then further dissected tolerance mechanisms in Klebsiella pneumoniae. journals.plos.org/plospathogen...

Prevalence and mechanisms of high-level carbapenem antibiotic tolerance in clinical isolates of Klebsiella pneumoniae

Author summary Bacteria can survive exposure to antibiotics by constantly repairing cellular damage induced by the drug. This “antibiotic tolerance” enables diverse bacteria to survive long enough to ...

journals.plos.org

What if your dplyr pipelines ran on GPU? That's what I built with cuplyr! A CUDA-powered backend for #rstats data manipulation. Looking for testers and feedback! github.com/bbtheo/cuplyr

GitHub - bbtheo/cuplyr: GPU powered dataframes in R

GPU powered dataframes in R. Contribute to bbtheo/cuplyr development by creating an account on GitHub.

github.com

We are hiring for group leaders again — EBI is a great place to start your research group! embl.wd103.myworkdayjobs.com/EMBL/job/Hin...

Research Group Leader

Do you want to lead groundbreaking research in computational biology? Join us at EMBL-EBI! EMBL's European Bioinformatics Institute (EMBL-EBI) is seeking talented and highly-motivated scientists to jo...

embl.wd103.myworkdayjobs.com

🧬 Free @microbesng.bsky.social PopUp ECR symposium 🧬 UK-based MRes or PhD student, research assistant or postdoc working on microbial genomics or metagenomics? Present your work and/or chair a session, plus excellent keynote speakers: @halllab.bsky.social and @alexmsalmeida.bsky.social. #MNGPopUp

"Me and the boys during advent"... www.instagram.com/reel/DSSWRyc...

Daily Choirs on Instagram: "“O Adonai” comes from Arvo Pärt’s ‘Seven Magnificat Antiphons’, a cycle where time seems to slow down and every sound feels intentional. Here, performed by the men of the ...

1,433 likes, 9 comments - dailychoirs on December 15, 2025: "“O Adonai” comes from Arvo Pärt’s ‘Seven Magnificat Antiphons’, a cycle where time seems to slow down and every sound feels intentional. H...

instagram.com

Are you interested in infections, the micro-organisms that cause them and antimicrobial resistance? So are @bashthebug.net and they're looking for new members to join their patient & public group. More info: bashthebug.net/lay-represen... Deadline 27 Nov @ouhospitals.bsky.social @medsci.ox.ac.uk

Bash The Bug (@BashTheBug) / X

Bash The Bug (@BashTheBug) / X

x.com

🔔🔔Post-doc in microbial genomics with @modmedmicro.bsky.social🧬 - deadline tomorrow! Big genomic and clinical datasets to play with, friendly and very multidisciplinary team! my.corehr.com/pls/uoxrecru...

Our recent paper on rifampicin resistant subpopulations in M. tuberculosis (M. tb) has been published at JAC-antimicrobial resistance. I am really happy to see this work published just hours before submitting my DPhil thesis! 🔗👇 doi.org/10.1093/jaca...

Subpopulations in clinical samples of M. tuberculosis can give rise to rifampicin resistance and shed light on how resistance is acquired

AbstractObjectives. WGS has become a key tool for diagnosing Mycobacterium tuberculosis infections, but discrepancies between genotypic and phenotypic drug

doi.org

We have a fully funded PhD studentship available @modmedmicro.bsky.social in Oxford to work on a really cool project looking at population heterogeneity in bloodstream infections www.ndm.ox.ac.uk/study/dphil-... Please spread the word/get in touch if you'd like to chat.

New research article Estimating the association of antimicrobial resistance genes with minimum inhibitory concentration in Escherichia coli: an observational study www.thelancet.com/journals/lan... #IDSky #ClinMicro #AMR #WGS #OpenAccess #OA

Pleased to see this out today in @lancetmicrobe.bsky.social www.sciencedirect.com/science/arti.... We estimate the independent effects of AMR genes on MIC at a drug-bug level and challenge the idea that resistance is a binary phenomenon.

Estimating the association of antimicrobial resistance genes with minimum inhibitory concentration in Escherichia coli: an observational study

Surveillance and prediction of antibiotic resistance in Escherichia coli relies on curated databases of genes and mutations. We aimed to quantify the …

sciencedirect.com

From Pipettes to Pipelines: Greening a Multidisciplinary Research Lab. @dotnagy.bsky.social writes about the experiences from the Modernising Medical Microbiology (MMM) research group on engaging wet lab, computer lab, and office teams on the #sustainability agenda. #GreenLab #SustainableScience

From Pipettes to Pipelines — Oxford Climate Society

Dorottya Nagy writes about the experiences from the Modernising Medical Microbiology (MMM) Unit research group on engaging wet lab, computer lab, and office teams on the sustainability agenda.

oxfordclimatesociety.com

Now published in @natcomms.nature.com 🎉 www.nature.com/articles/s41... With Gillian Rodger, @nstoesser.bsky.social, @samlipworth.bsky.social, @stat-sarah.bsky.social, and many others!

Escherichia coli phylogeny drives co-amoxiclav resistance through variable expression of TEM-1 beta-lactamase - Nature Communications

This study found E. coli phylogenetic background shapes TEM-1 beta-lactamase expression and co-amoxiclav resistance. Phylogeny alone shifted isolates from susceptible to resistant, stressing a need for lineage-sensitive genotype-phenotype prediction.

nature.com

Will Matlock@wtmatlock.bsky.social · 2y ago

🚨 New preprint! 🚨 We reveal that blaTEM-1 expression varies across the E. coli phylogeny, driving differences in co-amoxiclav resistance: www.biorxiv.org/content/10.1...

PhD opportunity to come and work in Glasgow, developing advanced tissue culture models to study Staphylococcus aureus colonisation and infection #microsky #PhD #DTPprogram Enquiries from potential applicants are welcome. www.gla.ac.uk/postgraduate... www.findaphd.com/phds/program...

Now published, our tool to run (almost) all biological models interactively in your web browser Paper: academic.oup.com/bioinformati... Website: biomodels.bacpop.org Code: github.com/bacpop/SBMLt...

SBMLtoOdin and Menelmacar: interactive visualisation of systems biology models for expert and non-expert audiences

AbstractSummary. Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predi

academic.oup.com

EMBL-EBI@ebi.embl.org · 12mo ago

Mathematical models in biology are powerful, but often hard to run, visualise, or reuse without specialist skills. Menelmacar is a new platform that makes biological models interactive and easy to explore directly in the browser: biomodels.bacpop.org 🧬💻

To summarise our recent pre-print: Autocycler, the automated consensus assembler, when used with Nanopore long-read only Enterobacterales assemblies, produces more complete chromosomes and plasmids, with an accuracy comparable to hybrid assemblies.

Dorottya Nagy@dotnagy.bsky.social · 11mo ago

Pleased to see this pre-printed, highlighting the completeness/accuracy of @nanoporetech.com long-read genome assembly for clinical Enterobacterales: www.biorxiv.org/content/10.1... Thanks to colleagues @modmedmicro.bsky.social, @ukhsa.bsky.social, @genewiz.bsky.social and @oxfordbrc.bsky.social!

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n

Pleased to see this pre-printed, highlighting the completeness/accuracy of @nanoporetech.com long-read genome assembly for clinical Enterobacterales: www.biorxiv.org/content/10.1... Thanks to colleagues @modmedmicro.bsky.social, @ukhsa.bsky.social, @genewiz.bsky.social and @oxfordbrc.bsky.social!

Ever run `install.packages()` and wish it were faster, smarter, and more reliable? The {pak} package speeds things up with parallel downloads, dependency solving, and reproducible installs. 📦 pak.r-lib.org #RStats

Come and work with Nicole Stoesser and I in Oxford with the fantastic team @modmedmicro.bsky.social - great opportunity for a postdoc in microbial genomics to do some creative research with great datasets as part of our HPRU. my.corehr.com/pls/uoxrecru...

Identification of specific metabolic capacities associated with major extraintestinal pathogenic Escherichia coli lineages https://www.biorxiv.org/content/10.1101/2025.09.14.675865v1

Great new work from #DotNagy @modmedmicro.bsky.social - she tool 96 clinical isolates from the NEKSUS study and sequenced with both Illumina and Nanopore - question was, can we do away with hybrid sequencing for the rest of the study? www.biorxiv.org/content/10.1...

Nanopore long-read only genome assembly of clinical Enterobacterales isolates is complete and accurate

Whole bacterial genome sequence reconstruction using Oxford Nanopore Technologies ('Nanopore') long-read only sequencing may offer a lower-cost, higher-throughput alternative for pathogen surveillance...

biorxiv.org

Sometimes you meet absolutely incredible bioinfo-magicians. It was a huge privilege when @shenwei356.bsky.social joined our group for a year on an @embl.org sabbatical. While here, he developed a new way of aligning to millions of bacteria, called LexicMap 1/n www.nature.com/articles/s41...

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology

LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

nature.com