It is almost five years since I first applied AlphaFold to a handful of viral proteins. Today, hundreds of thousands of predictions and many discoveries later, we are delighted to announce the integration of our Viro3D dataset into the @ebi.embl.org and Google DeepMind AlphaFold Database.

The AlphaFold Database, jointly developed with Google DeepMind, now contains datasets from specialist communities. This includes rich datasets for microbes, viruses & parasites associated with tropical diseases. Explore the new datasets in the AlphaFold Database. www.ebi.ac.uk/about/news/u...

Massive cuts to global health-care funding have had a huge impact on Africa, but a more resilient system can be built from within go.nature.com/46RnW0G

Staff at NIAID have been instructed to remove the words “biodefense” and “pandemic preparedness” from the US institute’s web pages, according to e-mails Nature has obtained. Read more about the shift in direction for NIAID. go.nature.com/4twztMV

After more than 1.2 Americans lost their lives to Covid, NIH director Jay Bhattacharya orders the agency to deprioritize pandemic preparedness & biodefense. Make it make sense. Scoop from @maxkozlov.bsky.social @nature.com www.nature.com/articles/d41...

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social a) correcting errors in 4.5 million genomes & their phylogeny b) improving representation of the Global South in public data www.nature.com/articles/s41... (thread 1/n)

We’re excited to announce our 9th Introduction to Viral #Bioinformatics course, starting 15 June 2026! 🧬 @cvrinfo.bsky.social Course information👉 tinyurl.com/yc8285zd

The US withdrawal from #WHO became official today, leaving the world less prepared for dangerous disease outbreaks. “When that will bite us in the ass, it’s impossible to predict. But there is a 100% certainty that it will bite us in the ass,” one expert told me. www.statnews.com/2026/01/22/u...

We've a computational PhD project available AI-DRIVEN DISCOVERY OF VIRUS–HOST MOLECULAR INTERACTIONS www.gla.ac.uk/colleges/mvl... as part of the University of Glasgow's MVLS Futures Themes PhD Programme. Deadline for applications is this Monday, 12th Jan 2026. Please apply!

We've a computational PhD project available AI-DRIVEN DISCOVERY OF VIRUS–HOST MOLECULAR INTERACTIONS www.gla.ac.uk/colleges/mvl... as part of the University of Glasgow's MVLS Futures Themes PhD Programme. Deadline for applications is this Monday, 12th Jan 2026. Please apply!

Review of 200 novel human #viruses over a century a reminder that pathogen emergence isn’t rare Increased human-animal interaction, driven by factors such as urbanization and deforestation, has created new opportunities for pathogens to jump species. www.cidrap.umn.edu/m...

How does fever work? Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence. This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵 www.science.org/doi/10.1126/...

A study on 1.7 million people in Hong Kong shows superior hybrid immunity to Covid in people who got vaccinated before infection vs. people who got infected first. "Our findings are a direct rebuttal to arguments for natural immunity," the authors write. doi.org/10.1016/j.va...

Never a good sign when I have a chance to post this. www.usatoday.com/story/travel...

A nice article, highlighting the important work our collaborators in South Africa are doing using wastewater to surveil a bunch of different vaccine preventable diseases (and finding a lot more of them than other reports would make you believe…). 💪🇿🇦 www.nature.com/articles/d44...

NEW: We traced out a devastating outbreak of bird flu to its source: an egg farm in Ohio. Where the wind blew, the virus followed. Within weeks, the farms downwind were about 20 times as likely to see outbreaks as those that weren’t.

Human #BirdFlu case in WA. #H5N5 not #H5N1. Patient is severely ill. Update coming. www.latimes.com/science/stor...

New paper👇

To summarise, PLM-interact extends single-protein PLMs to jointly encode interacting partners. It achieves state-of-the-art performance in cross-species and virus–host PPI prediction tasks and can be fine-tuned to predict mutation effects in human PPIs.

PLM-interact was applied to virus–human PPI prediction. The model outperforms existing approaches, achieving 5.7%, 10.9%, and 11.9% gains in AUPR, F1, and MCC, respectively — effectively capturing virus–host interactions at the protein level.

We further demonstrate examples where PLM-interact correctly predicts the effects of mutations on PPIs associated with human diseases. These results highlight its potential to identify whether disease-associated mutations weaken or strengthen protein interactions.

We fine-tuned PLM-interact to predict the effects of mutations on protein interactions — identifying whether mutations increase or decrease interaction strength. The fine-tuned model significantly outperforms zero-shot PPI models in the mutation-effect prediction task.

PLM-interact achieves state-of-the-art performance on a widely adopted cross-species PPI prediction benchmark — trained on human data and tested on mouse, fly, worm, yeast, and E. coli.

Existing PPI models use pre-trained PLMs to embed each protein separately, ignoring amino acid interactions between proteins. PLM-interact goes beyond single-protein encoding by jointly representing protein pairs to learn their relationships.

Protein language models trained on massive protein sequence datasets capture evolutionary, sequence and structural features — becoming the method of choice for representing proteins in state-of-the-art PPI predictors.

This work is a part of my viroinf PhD research, carried out under the supervision of Craig Macdonald, @davidlrobertson.bsky.social, and Ke Yuan, with HPC support from DiRAC (www.dirac.ac.uk).

New paper👇

A divergent betacoronavirus with a functional furin cleavage site in South American bats https://www.biorxiv.org/content/10.1101/2025.10.24.684489v1

1. We ( @jbakcoleman.bsky.social, @cailinmeister.bsky.social, @jevinwest.bsky.social, and I) have a new preprint up on the arXiv. There we explore how social media companies and other online information technology firms are able to manipulate scientific research about the effects of their products.

There is one point of agreement among both enthusiasts and sceptics: the future has already arrived go.nature.com/3WL73iS

And now NextStrain as well. Next up, will GISAID start charging open-source community tools to have access? That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.

We are at our future planning meeting with Genomics team at main campus of University 🏰 @cvrbioinfo.bsky.social

Chatbots are explicitly being designed “to elicit intimacy and emotional engagement in order to increase our trust in and dependency on them” (me in Wired magazine 🤭). This designed intimacy combined with AI sycophancy creates serious risks for delusional thinking www.wired.com/story/ai-psy...

Very nice reporting on the importance—and the vulnerability— of model organism databases www.nature.com/articles/d41...

New exciting resource published!! The Viro3D paper is out, describing our comprehensive database of predicted virus protein structures! 💻🧬 Work with @ulad-litvin.bsky.social , @grovearmada.bsky.social , Alex Jack, @bljog.bsky.social , @davidlrobertson.bsky.social www.embopress.org/doi/full/10....

🚨 New Web Resource Alert! 🚨 We're delighted to share Viro3D a database of >85000 viral protein structure predictions from >4400 human & animal viruses. 🔗 viro3d.cvr.gla.ac.uk 📄 www.embopress.org/doi/full/10.... @molsystbiol.org @cvrinfo.bsky.social @uofgmvls.bsky.social #Virology #AlphaFold 🧪 🦠

🌊 Coronaviruses likely acquired their spike proteins from aquatic herpesviruses. 4/5

🔍 Searches against structural network are extremely sensitive and allow to recover more RdRps than iterative profile-based searches. 3/5

🦠 The diversity of viral proteins can be reduced to 19,000 structural clusters. A structure-similarity network captures relationships between them. 2/5

Viro3D paper is out! We predicted 85,000 protein structures from human & animal viruses. 1/5 🧵 📑 Paper doi.org/10.1038/s443... 🔭 Explore virosphere viro3d.cvr.gla.ac.uk

Great to have this one published @cp-cellreports.bsky.social !! Some sarbecoviruses can use more ACE2 orthologs than others. The reason? A few sites in the RBD modulating the receptor usage of these viruses throughout their evolution! Worth a read 👇👇👇 www.cell.com/cell-reports...

@zachhensel.bsky.social and I have a new paper on the origin of SARS-CoV-2! 🧪 There are a lot of reviews on the topic already, so we tried to do something different: characterize "lab leak" scenarios, and directly address those on SARS-CoV-2's furin cleavage site.▫️1/9 doi.org/10.5802/crbi...

Mosquito-borne viruses surge in a warming Europe | Science | AAAS www.science.org/content/arti...

Really excited to have been a small part of this work investigating sarbecovirus host range, receptor usage and antigenicity! www.biorxiv.org/content/10.1101/2025.09.03.673949v1

A common type of ant in Europe breaks a fundamental rule in biology: its queens can produce male offspring that are a whole different species go.nature.com/4mOb5T9

Experimental infections reveal unexceptional viral tolerance in bats https://www.biorxiv.org/content/10.1101/2025.08.28.672855v1

🚨1000 authoritarian actions. 7 months🚨 I've been tracking Trump's authoritarian actions. From dismantling democratic institutions to militarising immigration enforcement, Trump is reshaping America. In my new post I highlight key authoriarian attacks christinapagel.substack.com/p/grand-desi... 1/2

📢 VACANCY | Research Assistant/Associate - Data Analysis Support @drtoniho.bsky.social & @louisapollock.bsky.social's Pfizer-funded research project focused on effectiveness of maternal #RSV vaccination in infants in Scotland. More: bit.ly/CVR-WorkWithUs Apply: gla.ac.uk/explore/jobs/ Ref 180274

Excited to share our work at the interface of virology and AI at two upcoming events! Will present Viro3D (our virus structure database: viro3d.cvr.gla.ac.uk), recent Nature paper on Flaviviruses (www.nature.com/articles/s41...), plus brand new work. #Virology #AI #Research

That's right. Gift link www.nytimes.com/2025/08/18/o...