We strive to credit labs collecting specimens and generating sequence data prominently. But credit for data contributions is not zero sum – surfacing of data in popular tools generates visibility and does not infringe on future publications by the data generators. 2/5

New paper: www.sciencedirect.com/science/arti... Klebs can evolve resistance to Colistin through mgrB mutation or by acquiring the mcr-1 gene. Both routes have similar fitness costs against a bacterial competitor, but mgrB mutations are associated with enhanced virulence.

For the sake of the entire #biology 🧪🧬🦠🧫🔬💊and #medsky science 🩺community, I think @enasequence.bsky.social and the #bioinformatics community needs to prioritise development of new tools and functionality in-line with #NCBI and #Genbank, before it potentially goes down sometime in the near future.

- "This library appears to be damaged" - "ImAgE mAdE WiTh BioReNDeR" What is the obsession universities have with paying companies instead of supporting free, often better, open source? Paid software is scientifically undemocratic and goes against #OpenScience. #SciSky 🧪

#WHO report shows rising #antibiotic resistance in common bacteria @katholt.bsky.social & @josebengoechea.bsky.social explain resistance worryingly high in #Klebsiella & E.coli as 1 in 6 lab-confirmed #bacterial infections in 2023 shown resistant to antibiotics. www.lshtm.ac.uk/newsevents/n...

Very excited to share the latest work from our lab, which was published today in Nature! nature.com/articles/s41... PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.

Research also shows that spreading smaller amounts of funding out over more researchers generally delivers better scientific outcomes per dollar spent than focusing bigger grants on fewer researchers. journals.plos.org/plosone/arti...

Unbelievable, Bakta reached its 1,000th citation! A huge shout out and thank you to all Bakta users, bug reporters, those sharing ideas and suggesting features... ...just the entire incredibly supporting binfie community! Without you, Bakta wouldn't be the same. Thank you!

reject chromatic aberration, embrace chromosomal aberration

Our new #klebsiella O type nomenclature, codesigned with Chris Whitfield, is now live in @pathogenwatch.bsky.social! Need a quick explainer on the new names? Check out my blog post: tinyurl.com/y8yb3rbb (+link to full review article) #MicroSky @klebnet.bsky.social @tomstantonmicro.bsky.social

Happy to share that the paper describing Autocycler is now 100% up: doi.org/10.1093/bioi... (1/3)

And as for writing, don't get me started. Most often, the process of writing is not a laborious business of transcription, but a process of thinking itself. I'm not about to outsource my thinking to a machine.

Staggering analysis here linking ciprofloxacin resistance to specific mutations in #Klebsiella. In short, using ONLY genotype, one can reasonably predict phenotypic CIP MICs! See Fig 3 (below). Loving the splitting of MIC and disk diffusion data as well. #AMR #MicroSky #IDSky

Celia also wrote about how we fitted 4.5 billion years in one image, at scale. chezvoila.com/blog/saguenay/

journals.plos.org/plosgenetics... #MicroSky

In another preprint from the @brianhie.bsky.social Lab and @synbiogaolab.bsky.social, they introduce Germinal, a generative AI system for de novo antibody design. Germinal produces functional nanobodies in just dozens of tests, making custom antibody design more accessible than ever before.

Terrific @scientificdiscovery.dev post on randomized controlled trials in @ourworldindata.org. Including this important chart on the impact of pre-registration. Magically, when people had to pre-register outcomes, many of the benefits disappeared. ourworldindata.org/randomized-c...

Automated, almost-error-free consensus #assemblies with Autocycler Impressive benchmarks in Fig 2B (below): ≤10 median errors PER genome Once again, incredible, landmark work from @rrwick.bsky.social doi.org/10.1093/bioi... Tool here: github.com/rrwick/Autoc... #bioinformatics #genomics

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n 📄 www.nature.com/articles/s41... 💿 mmseqs.com

Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data. @ruoshiz.bsky.social @milot.bsky.social www.nature.com/articles/s41...

Thrilled to share this preprint on Klebsiella pneumoniae plasmids in a One Health setting 🦠 Fantastic work by @twinkler.bsky.social! 🎉 @irenlohr.bsky.social @margaretlam.bsky.social

🎉 Delighted to share the first pre-print from my lab where we demonstrate that intergenic DNA repeats mediate phase variation of the mucoid phenotype in hypervirulent Klebsiella pneumoniae: www.biorxiv.org/content/10.1... #klebclub

"Paying the filter tax" - Honours student Josh on how volume is lost during syringe filtration.

For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny www.biorxiv.org/content/10.1... github.com/iqbal-lab-or...

A deadly tropical disease known as sleeping sickness has been eliminated from Kenya in a significant public health triumph. Uganda, Rwanda, Benin, Ghana, Cote d’Ivoire, Guinea, Equatorial Guinea, Chad, & Togo have also eliminated sleeping sickness. www.goodnewsnetwork.org/who-declares...

New blog post! I added a new feature to @gbouras13.bsky.social's Pypolca: homopolymer-only polishing. Potentially useful for cross-sample polishing - early test on Cryptosporidium looks promising. Check it out here: rrwick.github.io/2025/09/04/h...

The people have spoken: Best Lightning Talk goes to @bananabenana.bsky.social and Best Medium Talk goes to @munazzahmaqbool.bsky.social. Congratulations winner and winner, it was a pleasure listening to your talks! #MicroSeq2025

🌏Jocelyn Hume shows us how #sequencing was able to characterise the evolutionary trajectory and driving forces behind IMP-4 transmission. Delve into one of the largest global and regional #epidemiology studies of blaIMP-4 in #bacterial isolates! #MicroSeq2025 #plasmid

"For pathogen surveillance, we identify the trapped mosquitos morphologically, painstakingly individually" - Peter Mee #MicroSeq2025

github.com/matevz-kovac... Incredible work. Someone made a word square with 10 words. Had to be done algorithmically and involved citations to species names.

Will they ever fix these issues? We pay to publish Pay to read Write for free Edit for free Proofread for free And they won’t even give us a single login across journals 🤪

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...

Fantastic paper that benchmarks all the things you’d want to know for rolling out Oxford Nanopore sequencing for rapid, clinical diagnostics. They looked at time to results and quality trade-offs #IDSky #MicroSky #AMR #AMRSky #MedSky www.medrxiv.org/content/10.1...

New preprint where we analysed IS loads in 🦠 #Klebsiella pneumoniae lineages and found they're inversely associated with nutrient usage. We propose an insertional tolerance model, whereby IS can only insert into metabolically-tolerable sites. #IDSky #MicroSky 🧪 www.biorxiv.org/content/10.1...

Citrobacter freundii ain't ever been a friend of ours... now becoming even more hostile! #IDSky #ClinMicro #AMR #MedSky @lancetmicrobe.bsky.social www.thelancet.com/journals/lan...

LibreOffice Writer imports SVGs while Microsoft Word compresses images. LibreOffice Writer makes formatting easy while Microsoft Word anchors images 5 pages down. I've made the switch and about to donate. Now LibreOffice Writer is my new best friend ❤️

Day 3 at #fems2025 started with an exciting and inspiring keynote by Chris @greening.bsky.social on microbes living out of thin air @femsmicro.org

I find it hard to understand what grant 'rubrics' actually want. How come I'm expected to write in clear language but have to decode bureaucratic hieroglyphics first? Sorry, I mean: navigating the layered pathway to significant impact buzzword frameworks.

📣Calling Australian/NZ ECRs and PhD Students 📣 Abstract submission and registration for MicroSeq2025 opens July 21! Abstracts for both medium-length and lightning talks will be welcome.

We have already seen these features unlock new capabilities. For example because Boltz-2 was trained on thousands of short MD simulations, conditioning on MD captures local dynamics competitively with specialized models like AlphaFlow or BioEmu, demonstrating Boltz-2’s power as a foundation model.

BioEmu now published in @science.org !! What is BioEmu? Check out this video: youtu.be/LStKhWcL0VE?...

A @csisingapore.bsky.social team showed D-I-Tasser can outperform AlphaFold2/3, elevating high-accuracy protein structure & function predictions. We wonder if this moves us closer to resolving protein–protein complex structure prediction? @natbiotech.nature.com www.nature.com/articles/s41...

I've been trying to articulate the 'modern' research biology 🧬🧪 process loop that I use/aspire to, where large-scale data is leveraged in it's own right while also driving experimental design. The idea is to minimise risk, cost and time at experimental stages while maximising outputs and yield.

We should really find a way to save CASP

A lot of sepsis cases are caused by bacterial outbreaks in neonatal units, which can hugely skew the estimated antigen prevalence. So we adjust for localised clustering at each site, to reduce this bias in our prevalence estimates. Turns out this makes a big difference to estimates for some K types.

I'm super happy to share this preprint on ‘Distribution of capsule and O types in #Klebsiella pneumoniae causing neonatal sepsis in Africa and South Asia: meta-analysis of genome-predicted serotype prevalence and potential vaccine coverage’ doi.org/10.1101/2025...

Fantastic article about the logical steps current #AI systems self-reason their way into blackmailing and harming people. This feels like a warning to consider what we might create and the power that we give it - because it may try to harm us to protect itself. venturebeat.com/ai/anthropic...

What are some of best graphical abstracts you've seen? Looking for some inspo #scisky 🧪