Sam Lipworth
Clinical Lecturer and ID/Micro registrar in Oxford
- Reposted by Sam LipworthFirst 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...
- Reposted by Sam LipworthWhat 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
- Reposted by Sam LipworthWe are hiring for group leaders again — EBI is a great place to start your research group! embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
- Reposted by Sam Lipworth🧬 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...
- Reposted by Sam LipworthAre 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...
- Reposted by Sam LipworthOur 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...
- 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.
- Reposted by Sam LipworthNew 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.
- Reposted by Sam LipworthFrom 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
- Reposted by Sam LipworthNow 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!
- 🚨 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...
- Reposted by Sam LipworthPhD 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...
- Reposted by Sam LipworthNow 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...
- 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 🧬💻
- Reposted by Sam LipworthTo 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.
- 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!
- Reposted by Sam LipworthDelighted 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
- Reposted by Sam LipworthPleased 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!
- Reposted by Sam LipworthEver 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...
- Reposted by Sam LipworthIdentification of specific metabolic capacities associated with major extraintestinal pathogenic Escherichia coli lineages biorxiv.org/content/10.1101/202…
- 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...
- 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)
- 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!)
- Great collaboration with @ukhsa.bsky.social #HPRU colleagues #nicolestoesser and the NEKSUS consortium of 9 NHS trusts in England
- Reposted by Sam LipworthSometimes 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...
- Reposted by Sam LipworthVery 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 paper out! 🔈🔈📣📣 Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation. Combining experimental and computational approaches, we unveil how two of the most prevalent bacterial MGE accelerate the evolution of AMR. 🧵👇🏻 www.biorxiv.org/content/10.1...
- Reposted by Sam LipworthNew 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.
The hospital Sink-ome: Pathogen and antimicrobial resistance gene burden in sink-traps across 29 UK hospitals and associations with sink characteristics medrxiv.org/content/10.1101/202…
- Reposted by Sam LipworthThere are half a million cases of invasive non-Typhoidal Salmonella (iNTS) every year and while you might know S. Typhimurim and Enteritidis, you may not have heard of S. Panama 💩 🩸 🧫 💊 Check out our latest in @lancetmicrobe.bsky.social doi.org/10.1016/j.la... and the 🧵 below to find out more 1/n
- Reposted by Sam LipworthBEAST X v10.5.0 finally released – you can't just do beta releases forever. github.com/beast-dev/be... Details and instructions for installing on the BEAST website: beast.community
- Reposted by Sam LipworthDelighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well www.biorxiv.org/content/10.1...
- Reposted by Sam LipworthImportant paper by Lance Thurlow, @bconlon.bsky.social @sirmicrobe.bsky.social and others: Diabetes potentiates the emergence and expansion of antibiotic resistance. "hyperglycemia..facilitates.expansion and takeover of resistant mutants in diabetic infections." www.science.org/doi/10.1126/...
- Reposted by Sam LipworthAntimicrobial resistance data is now on the UKHSA data dashboard! 🧫 ukhsa-dashboard.data.gov.uk/antimicrobia...
