Kat Holt

Fungal genome sequencing for free! 👇🏼 #GGFungi2026

Very cool - thanks Rob!

Oh wow, I knew Mike Manefield back in Aus but didn’t know he wrote kids books! Thanks for this!

Ooh looks cool - thanks!

Any recommendations for books / vids for little ones interested to learn about microbiology?

My 5yo has picked up on work chatter and keeps asking “Tell me about Klebsiella?” and I am running out of ideas! 😂

#MicroSky

AI Keeps Failing at Microbiome Prediction Why simple models keep winning, where deep learning still shines, and where the field is headed

AI has huge promise for genomics -- but it has consistently failed at microbiome-based prediction.

My new post on why simple models keep winning, where deep learning actually earns its place, and where the field is headed

blekhman.substack.com/p/ai-keeps-f...

I love this spring weather ☀️🌷 but yikes I can feel the histamine pumping thru me!! 🤧

rambaut/figtree Automatically exported from code.google.com/p/figtree - rambaut/figtree

The first version of FigTree was released nearly 20 years ago and it is still widely used (including by me). But there are currently 85 issues on the GitHub repo (github.com/rambaut/figt...) and some of them I don’t really like the look of.

Statement from Dario Amodei on our discussions with the Department of War A statement from our CEO on national security uses of AI

When even the AI company CEOs say “what you want is unethical and a bad idea”, it’s time to sit the fuck down and have a serious think about what you wanted.

Formalizing our commitment to code sharing In support of open science, PLOS Biology routinely asks authors to openly share their research code before publication. We are now formalizing this practice with a mandatory code sharing policy and…

In support of #OpenScience, we routinely ask authors to openly share their #research #code before publication.

We are now formalizing this practice with a mandatory #CodeSharing policy and clarifying what we mean by code sharing.

BioAIrepo: EMBL-EBI’s hub for life science AI models New EMBL-EBI repository helps researchers share and reuse machine learning models trained on life science data.

📢 We want your feedback on our new pilot project for sharing AI models in life science research.

Finding, reusing and citing machine learning models remains a major challenge in the life sciences.

BioAIrepo is here to help.

www.ebi.ac.uk/about/news/t...

Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025.
allthebacteria.readthedocs.io/en/latest/ov...

@wytamma.bsky.social 's WASM tools have transformed my experience of teaching Python to first year undergraduate biologists this year. Since last year, I've been teaching ~400 undergrads how to code (functions, lists, dictionaries, loops) over (one hour intro lecture +) two 2-hour practicals. 1/n

We are excited to be recruiting a new tenure track group leader in the Structural Studies Division at MRC LMB! It is an amazing place to start your own lab.
@mrclmb.bsky.social

Please get in touch if you have any questions.
www.nature.com/naturecareer...

Postdoc Ad Postdoctoral Position in Computational Phage Biology Microbial Genomics Group, Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków PL Summary We are seeking a postdoctoral rese...

📢 Hiring a Postdoc in Computational Phage Biology (Kraków, Poland)

We study the evolution & structural modularity of prophage-encoded glycan-degrading enzymes in Klebsiella pneumoniae — combining genomics and AlphaFold-based analyses.

Details in attached PDF 👇

Postdoctoral Research Associate at University of Bath Searching for an academic job? Explore this Postdoctoral Research Associate opening on jobs.ac.uk! Click to view more details and browse other academic jobs.

New postdoc position available in the Tooke lab in our department. Perfect if you like molecular microbiology, structural biology and biochemistry!
www.jobs.ac.uk/job/DQP592/p...

🚨 Places are going fast!
🎉 Over 100 people have already signed up for the TARGetAMR Conference 2026
🗓️ Join us at our FREE event, on 14–15 May in Birmingham to explore the future of AMR Genomics
✨ Don’t miss out!
👇 Register now www.targetamr.org.uk/hdrevents/ta...
#TARGetAMR26

🆕 at @naturemedicine.bsky.social
How does ChatGPT Health do for appropriately triaging a person as to whether to go to the emergency room or stay home? www.nature.com/articles/s41...
Not very well. Under-triaged 52% of case vignettes that are considered gold-standard emergencies

Make no mistake this is a concerted and organised attempt to completely undermine science and expert opinion. This is Covid denialism on steroids and it’s on all of academia to see this for what it is and push back as strongly as possible

The fundamental premise behind AI-enabled cheating is that coursework is merely busy work, because your'e just doing it for professors.

We would never say that showing up for football practice is merely busy work because you're just doing it for your coaches.

"Tech killed online education" is a heck of an outcome.

Recurrent and chronic UTIs have a huge impact on patient's quality of life and is an area of research which is often overlooked and understudied. There are massive gaps in our understanding which we can fill to... (1/3)

See all images in this post and that follow for the top 10!

#MicroSky #UTISky

Except literally every data analysis or model I've ever asked AI to build has contained at least one error: www.nature.com/articles/d41...

Common response: "But someone just needs to give AI detailed instructions..."

But who is the "someone" in that sentence? And how did they get their expertise?

"Precarity is the one constant of academic science. Themes of instability thread themselves through everything we do."

A brief blog post from me about the @ukri.org funding pause and who the real victims will be.

occamstypewriter.org/mindthegap/2...

#AcademicSky

Before the vaccine, 10% of measles infections resulted in deafness. Measles currently causes 100K children/yr to become blind. Even those who recover completely can later develop the fatal encephalitis. Every infection disrupts the immune system and can cause loss of all immunity to other infections

Danika Mason: Australian presenter apologises for drinking before slurred Winter Olympics report Danika Mason also blamed the cold, after talking about coffee and iguanas in her live cross.

Still waiting for the BBC to show an interest in the retired British woman incarcerated in the US for a couple of months, but they obviously think this is more important…

www.bbc.co.uk/news/article...

‘Don’t go to the US – not with Trump in charge’: the UK tourist with a valid visa detained by ICE for six weeks Karen Newton was in America on the trip of a lifetime when she was shackled, transported and held for weeks on end. With tourism to the US under increasing strain, she says, ‘If it can happen to me, i...

As she says, ‘If it can happen to her, it can happen to anyone’...

‘Don’t go to the US – not with Trump in charge’: the UK tourist with a valid visa detained by ICE for six weeks

www.theguardian.com/us-news/2026...

How does treatment induced antibiotic resistance happen in real-world infections? We analysed 25k Pseudomonas isolates from 180 patients in a clinical trial to find out! TLDR: The ecological and evolutionary paths are surprisingly diverse & complex even in patients receiving identical treatment…

Economic impact of a maternal Klebsiella pneumoniae vaccine: estimates for 107 low- and middle-income countries
https://doi.org/10.1098/rstb.2025.0002

A One Health study of Klebsiella pneumoniae species complex plasmids shows a highly diverse and ecologically adaptable plasmidome Plasmids play a pivotal role in the horizontal gene transfer (HGT) of antimicrobial resistance (AMR) and virulence determinants among bacteria. Members of the Klebsiella pneumoniae species complex (Kp...

Fascinating and important study on Klebsiella plasmid diversity

'Plasmids from human, animal and marine [Klebsiella pneumoniae complex] isolates formed shared genetic clusters spanning ecological boundaries'

www.microbiologyresearch.org/content/jour...