Rapid release of multiplex PCR amplicon scheme for Andes hantavirus whole genome sequencing validated on control material: www.biorxiv.org/content/10.6... @scalene.bsky.social @stevepullan.bsky.social @ukhsa.bsky.social output from HPRU in Public Health Genomics

Bit of advice to Labour members. I’d treat any Streeting pledges as equivalent to Starmer pledges…

BBSRC Early Independence Fellowships had an Outline stage this year to try help with amount of peer review. Turns out they received 586 applications, a 110% increase on 2025, and only typically fund 15 a year. They are cancelling this stage and going straight to full app with an institutional sift.

Not long now until #ESCMIDGlobal2026. I will see you all there!

Working on bringing #genomics into diagnostics? 🧬 I’m presenting a poster at #ESCMIDGlobal2026 on some exciting work with @livuni-livsrf.bsky.social and Liverpool Clinical Laboratories, using nanopore sequencing for rapid fungal pathogen ID 🧬 📅 18 April | ⏰ 12:00–13:00 CEST See you there!

Working on bringing #genomics into diagnostics? 🧬 I’m presenting a poster at #ESCMIDGlobal2026 on some exciting work with @livuni-livsrf.bsky.social and Liverpool Clinical Laboratories, using nanopore sequencing for rapid fungal pathogen ID 🧬 📅 18 April | ⏰ 12:00–13:00 CEST See you there!

Big update for #gbdraw! - Multi-record circular plots: Genomes with multiple replicons can now be displayed in a single view! - Advanced linear plots: Focus on regions of interest with granular control over feature selection and color-coding! Try now: gbdraw.app #microbiology #bioinformatics

1/5 Introducing SimPlot-CL! 🧬 Recombination plays an important role in viral evolution. Similarity plots are a great way to visualize recombination patterns, but generating them across many genomes can be cumbersome (Work with my student, Keno Strotjohann!) 📂 github.com/hodcroftlab/simplot-cl

Over the years I’ve been willing to put up with quite a lot in order to go to football matches, but the possibility of being randomly scooped up & sent to a concentration camp for months is a bit too much of an inconvenience.

I watched much of Ian Chapman's (Head of @ukri.org) appearance this morning at @ukparliament.parliament.uk Science, Innovation and Technology Committee.. A few points and new information that bioscientists may find interesting... A 🧵

First day back @liverpooluni.bsky.social as Co-I on a Wellcome Discovery Award 🦠🏫 (in an exciting new office!) Grateful to have worked with @wvschaik.bsky.social @halllab.bsky.social & @pathogenomenick.bsky.social on public health genomics at @unibirmingham.bsky.social - papers to come! ✍️

Presenting my work in fabulous Newcastle for #VOMUK26! Come chat to me about my poster (or your opinions on The Traitors/Formula 1/crafting). #microsky #phagesky 🧪

New blog post with some thoughts on @nanoporetech.com and their recent announcement that the P2 Solo will be discontinued: rrwick.github.io/2026/01/21/p...

Love microbes & omics? 🦠🧬 We’re hiring a Postdoc in Public Health Genomics at @unibirmingham.bsky.social Work on cutting-edge research with wonderful people! @wvschaik.bsky.social @halllab.bsky.social @pathogenomenick.bsky.social @scalene.bsky.social @alanmcn1.bsky.social 📅 Closes 4th Feb

Subtweet: You do not feel safer in London *despite* it being more diverse than other towns. You feel safer in London because it is generally safe, and there being a lot of brown people here has LITERALLY NOTHING to do with how safe you are.

A wonderful way to start the year, with a new publication. We examine ethnic representation across UK bioscience by exploring the structural factors shaping career progression, and proposing recommendations for meaningful change. Full article: pubmed.ncbi.nlm.nih.gov/41474708/

New year, new PhD? 🧑‍🎓 If you’re fed up of leftovers, and out of ideas for festive fun, here’s a quick reminder to apply to these posts! 🧫 🧬 #PhD #Microbiology #Genomics

Happy holidays! 🦌🎄 A new chromosome-level genome assembly of Norwegian wild alpine reindeer was generated using #PacBio HiFi long reads, delivering accurate, haplotype-resolved results. See more HiFi-powered science at #PAG33 and visit us at booth 219! Read the paper: bit.ly/3Y0tEZu

‘Twas the night before Christmas, and all through the house, Not a creature was stirring… apart from journal editorial teams who have made this my final paper of the year! Happy to announce that this work has been published in Nature Comms. www.nature.com/articles/s41...

We’re hiring 2 Postdocs (f/m/d) in Drug–Microbiome–Host Interactions 🦠💊 Focus: how non-antibiotic drugs shape the gut microbiome, drug efficacy & side effects. #PostdocJobs #Microbiome #AcademicJobs Full job ad: lisamaierlab.com/wp-content/u...

💾 mlst 2.25.0 has been released! Fixed a bug that missed alleles in increasingly larger schemes like senterica (thanks @microbiologikat.bsky.social) and updated the databases. #bioinformatiocs #microbiology #genomics github.com/tseemann/mls...

UnigeneFinder: An automated pipeline for gene calling from transcriptome assemblies without a reference genome

This is not the first time RFK Jr or his fellow anti-vax travelers conducted a study they knew would harm or kill children in low-income countries. It is a dehumanizing, colonialist model of manufacturing evidence: sacrificing foreign kids for political pseudoscience. www.notus.org/health-scien...

Our new paper in MGen traces the evolution of a plasmid lineage associated with MDR in Enterococcus faecium, primarily driven by IS1216 For anyone interested in plasmid structures and the smaller MGEs that shape them 🧵👇 [1/14] @microbiologysociety.org www.microbiologyresearch.org/content/jour...

The first preprint from @izziepotterill.bsky.social PhD. A clone within ST131 clade C with a totally unique capsule region.

We are recruiting for a number of PhDs in the HPRU in Public Health Genomics, based at @unibirmingham.bsky.social, in collaboration with UKHSA. 🦠🧬 Apply below to work on cutting-edge science and public health priorities! (NB deadline of 9th January / UK only due to funding restrictions) (1/7)

Delighted to share Magda's new review in Annual Review of Food Science and Technology 🎉 We explore how microbe-diet interactions shape health across the life course and the promise (and challenges!) of microbiome-informed precision nutrition 👇 doi.org/10.1146/annu...

He really doesn’t understand any of the most basic biology concepts at all, huh

New PhD project, supervision by @alanmcn1.bsky.social and me. 'Nationwide Clostridioides difficile population dynamics' www.findaphd.com/phds/project... Deadline for applications 9 Jan 2026, UK students only.

I am pleased to share that my first postdoc paper from the @halllab.bsky.social is now on bioRxiv! 🎉 We used long-read #metagenomics to explore how the gut microbiome and #antimicrobialresistance landscape shift across advanced chronic #liverdisease (ACLD) www.biorxiv.org/content/10.6...

💾 ABRicate 1.2.0 has been released! This 'oversight' lasted 6 years, but with help from @finlaym.bsky.social we got CI working and updated all the databases. #bioconda #conda #bioinformatics #microbiology #genomics github.com/tseemann/abr...

Congrats @fullam.bsky.social @pangenomics.bsky.social @borklab.bsky.social & team(s). Great to see this published! proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes: academic.oup.com/nar/article/...

It is a disgrace that an alternative is even being entertained by the CDC

1/ 🚀 Big thanks to our community - since August we’ve added thousands of new sequences, rolled out major new features, and welcomed fresh faces into the #Pathoplexus world. Let’s dive into what’s new.👇🏻 Read the full update: pathoplexus.org/news/2025-11...

My account's upload and bulk download access were terminated permanently in 2021 without explanation after I published *checksums* of GISAID genomes. GISAID and its SAB have since ignored a dozen emails seeking explanation. 4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.

What a banger

Your daily reminder that the government continues to commercially support an individual who wants to destroy it through fascist violence.

I am delighted to be a co-investigator on this newly funded Wellcome Discovery Award. Excited to begin work with the team (including those not on Bluesky!) @jayhinton.bsky.social @roygoodacre.bsky.social @lisamaierlab.bsky.social @blancaps.bsky.social

Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it: www.biorxiv.org/content/10.1... Want to get started? github.com/rickbeeloo/b...

This remarkable therapy uses an approach the Trump administration just cancelled funding for.

Has anyone given this a go? Tempted to let Reviewer 2 weigh in on my hobbies..

A great reminder of why it's important to consider the shape of your data before diving into microbiome analysis!

🧬Viromics🧬 = using (meta-)genomics to study uncultivated viruses has yielded unprecedented insights into the diversity and global distribution of viruses @jgi.doe.gov's @simrouxvirus.bsky.social and Clement Coclet review the state of the field, available tools, and remaining challenges

Thank you to everyone who has used pyani over the years (I know it's thousands of people!) but we have now archived the repository. But we have replaced it with a completely rewritten and extended implementation: pyani-plus! github.com/pyani-plus/p... 1/

Yesterday was my last day after an exciting four years in @acdarby.bsky.social's lab at Liverpool. The lab photo below was taken in Birmingham, where I’ll soon be working! Excited to join @wvschaik.bsky.social, @pathogenomenick.bsky.social, @halllab.bsky.social to work on Public Health Genomics.

Plenty studies showing that your postcode is a better predictor of your health outcomes than your genome.

@andywatson on the NGS Sequencing market and the prisoner's dilemma

Keir Starmer, Yvette Cooper, David Lammy, and McSweeney @teamlabouruk.bsky.social should take note if what they really want is growth.

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io

🧵 You’re not behind in bioinformatics. The field just evolves faster than anyone can follow. 1/ It’s not you. Bioinformatics evolves too fast. And not just from new algorithms— But from how fast technology itself changes.