Sam Lipworth

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...

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 ...

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...

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

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

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...

We are hiring for group leaders again — EBI is a great place to start your research group!

embl.wd103.myworkdayjobs.com/EMBL/job/Hin...

🧬 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

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...

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

Bash The Bug (@BashTheBug) / X Bash The Bug (@BashTheBug) / X

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

🔔🔔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...

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

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...

comparative genomics – Holt Lab Posts about comparative genomics written by kat

It's not a video, but @katholt.bsky.social's holtlab.net/tag/comparat... is a good place to start

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

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 …

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.

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.

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

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!

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...

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.

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!

you should be using pak

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 collaboration with @ukhsa.bsky.social #HPRU colleagues #nicolestoesser and the NEKSUS consortium of 9 NHS trusts in England

Overall, using R10.4.1, super-high accuracy basecalling and autocycler, we can reliably infer marker geens (MLST/ARGs etc) and feel that performance was good enough to drop Illumina sequencing for the NEKSUS study (more to follow in due course!)

Dot showed that overall, @rrwick.bsky.social Autocycler appears to outperform other long read assemblers and long read only assemblies are extremely accurate (median Q-score of 67). Long read polishing helps small amount + benefits from short read polishing are very small (only for worst assemblies)

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...

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...

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.

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...

Very happy to be a (small) part of this story!
The role of plasmid-encoded ISs in the acceleration of AMR evolution, through inactivation of different bacterial genes.

New analysis from Kevin Chau @modmedmicro.bsky.social for the SinkBug Consortium (a collaboration with teams across 29 UK hospitals, NITCAR, UKHSA): Pathogen and AMR gene burden in 287 hospital sink-trap metagenomes and factors associated with high burdens.