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...

Hey #rstats, #pydata, #julialang & #dataviz folks! 😊 What are some iconic data visualizations, similar to @edhawkins.org‘s warming strips & climate spiral?

🚨 New preprint out! Pan-Genus Analysis and Typing of AMR Plasmids in Acinetobacter Here, is the link: doi.org/10.21203/rs.... #AMR #Acinetobacter @liamtobin1.bsky.social @margaretlam.bsky.social @aimi-uts.bsky.social

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 🧪

From doi.org/10.1098/rsos... by Minocher, @rmcelreath.bsky.social, @babeheim.bsky.social... "The availability of social learning data decays exponentially with time since publication. The expected probability of finding material for any publication halves every 5.7 years on average (CI: 4.2–7.1)."

@danielleingle.bsky.social giving a great overview of genomics of emerging #antimicrobial resistance in #Australia @pasteur.fr

In my experience, "Data available on request" is a useless claim. I've reached out to a variety of academics that state this in their paper and one of the following things happen: - Their email address is no longer valid - Their whereabouts is unknown - They don't actually reply to the request ...

Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment. arxiv.org/abs/2506.12986

In 2005, 'tidal cycling', was proposed, where moon-driven tides enabled salt-based amplification of 🧬. Inter-tidal zones experience varying ionic cycles, mimicking thermal cycling. Long story short: Moon-based PCR. Interesting theory. Strong biochemistry. Weak earth science. doi.org/10.1016/j.ic...

Cool paper showing 🦠 recipient response to #plasmid conjugation Capsule blocks conjugation, preventing MPF between donor:recipient. However, conjugation exploits recipient strain heterogeneity of capsule thickness, conjugating to cells with less capsule #MicroSky 🧪 www.biorxiv.org/content/10.1...

Wild to think that the term 'residue' used in context of amino acids dates back to at least 1941 doi.org/10.1085/jgp..... Amino acid 'residues' were produced after acid-based hydrolysis of proteolytic enzyme chymotrypsin.

We’re pleased to share two new preprints with results from a structured survey of carbapenem- and/or colistin-resistant Enterobacterales (CCRE), conducted in 37 European countries in 2019. E. coli: papers.ssrn.com/sol3/papers.... K. pneumoniae: papers.ssrn.com/sol3/papers....

Very excited about our latest combining advanced cell culture, transposon-insertion sequencing, and statistical modeling to map Shigella virulence determinants in organoid models. Great collaboration w/ @mldm.bsky.social @sellinlab.bsky.social in @natgenet.nature.com www.nature.com/articles/s41...

🚀 New paper led by Dr Becks Spake! We make the case for precision ecology—using big data & predictive tools to tailor conservation actions to local contexts. Can ecology learn from medicine & marketing to boost impact? We think so. Read it here: rdcu.be/eoaR4 #Conservation #Ecology #BigData

Integration of metatranscriptomics data improves the predictive capacity of microbial community metabolic models #ISMEJournal from Zoran Nikoloski @mpi-mp-potsdam.bsky.social academic.oup.com/ismej/advanc...

New #antibiotic class 'gromomycins' discovered, produced by a Streptomyces spp Very comprehensive work from compound ID -> genetic determinants of gromomycin biosynthesis -> prevalence of the biosynthetic gene cluster variants in public data! onlinelibrary.wiley.com/doi/10.1002/... #AMR #microsky

ClaPNAC: a Classifier of Protein - Nucleic Acid Contacts www.biorxiv.org/content/10.1101/2025.05.30.657037v1 #cryoem

One of the coolest papers I've ever read: www.nature.com/articles/s41... Within-colony bacterial dynamics. And the figures are absolutely striking and clear.

Our new paper on the global epi of IMP carbapenemases. We originally called this paper: ‘Planet of the IMPs’ as IMPs are now everywhere. We found IMP variant-specific distributions across species, plasmids, mobile elements and geography www.medrxiv.org/content/10.1... #amr #amrsky #IDsky

New preprint: we used k-mer matching with suffix match length information to create an assembly-to-assembly alignment algorithm + software, kbo. We wanted to create a reference-based aligner and variant caller that scales to at least 10-100k bacterial queries. www.biorxiv.org/content/10.1...

Masterclass of applied quantitative #genomics - cool study design, findings and ties into real biology. Unclear if statistical comparisons controlled for clonal population bias though? Figure 4C is 👌👌 - using the upper tri for positive associations, and lower tri for negative associations.