We are really excited that Euro Evo Devo will take place here in Scotland from the 9th-12th June, at the University of Glasgow! Deadline for Early Bird Registration and Abstract Submission are rapidly approaching in March so do register soon! www.evodevoconference26.com/important-da...

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.

🦠 Viro3D and BFVD viral predictions are now available in the AlphaFold database

Our new review about the evolutionary causes and consequences of gene duplication is out!!! We delve into the various adaptive and non-adaptive forces which shape the fate of gene duplicates uncovered across the last decade through cutting edge experimental and computational techniques

I am excited to share our latest preprint - An evolutionarily divergent herpesvirus with a giant tail. Featuring symmetry breaking and genome annotation from structure using ModelAngelo. doi.org/10.64898/202...

Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity! www.nature.com/articles/s41...

FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...

Reminder with <2 weeks to deadline:

My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring! mirdita.org

#NatMicroPicks Asgard archaea and the origin of eukaryotes! 🦠 Eukaryotic cellular complexity evolved largely within the Asgard lineage before mitochondrial endosymbiosis and later bacterial gene acquisitions #MicroSky www.nature.com/articles/s41...

Applications to join the Computational Approaches to Early Evolution workshop are still accepted! Do not miss your chance to attend this event full of discussions on the computational methods for studying early life! 🦠💻🧬 forms.oist.jp/form/computa...

How did eukaryotic cells with complex architecture evolve from simpler prokaryotic cells? DNA analyses offer possible answers @nature.com www.nature.com/articles/d41... www.nature.com/articles/s41... @bristoluni.bsky.social www.nature.com/articles/s41... www.nature.com/articles/s41...

Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...

Our work on the evolution of the regulatory genome of echinoderms is now out in @natecoevo.nature.com. Led by my former PhD Marta Magri, Danila Voronov & Saoirse Foley. Great collaboration of Arnone, Hinman & Maeso labs, started long time ago with our missed José Luis Gomez-Skarmeta: rdcu.be/eXX8l

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!

Thrilled to share the first major preprint from the lab. Viruses are classically viewed as targets of host sensing. Do viruses also sense and respond to the host? We propose viruses may act as “biosensors” of the host signaling state. A thread👇🏾 www.biorxiv.org/content/10.1...

I'm really excited to break up the holiday relaxation time with a new preprint that benchmarks AlphaFold3 (AF3)/“co-folding” methods with 2 new stringent performance tests. Thread below - but first some links: A longer take: fraserlab.com/2025/12/29/k... Preprint: www.biorxiv.org/content/10.6...

Permanent Research Group Leader Position, Crete, Greece: Interested to assume long-term responsibilities for the Biodiversity Computing Group www.biocomp.gr I have set up in Crete? Apply now via apella.minedu.gov.gr/en/node/5998 (PDF also in English) - for questions email to [email protected]

Join us for interesting discussions at the Computational Approaches to Early Evolution workshop next year in April at OIST in Onna, Okinawa! 🦠💻🧬 Registrations open until January 2nd '26, do not miss it! More info & registration details in the link below! 🔽 www.oist.jp/conference/c...

Excited to share the final version of our study on Nematostella cell type regulatory programs. Part of our @erc.europa.eu StG project, this was a challenging 5-year effort extraodinarily led by @aelek.bsky.social and @martaig.bsky.social. www.nature.com/articles/s41...

New preprint led by our MSc student Wenye Li!! 🎉 @systemsvirology.bsky.social What we find is a historic genetic interplay between sarbecoviruses and their horseshoe bat hosts' ACE2 receptor! 🦇 🧵... www.biorxiv.org/content/10.1...

New preprint out! Using ~75k environmental OTUs + 77 fossil calibrations, we reconstructed a Proterozoic timeline of eukaryote evolution. Our results show crown eukaryotes were already diversifying >1.6 Ga, long before the first undisputed fossils (~1.05 Ga). 🔗 DOI: www.biorxiv.org/content/10.6...

Why are virologists thinking and talking about this year's strain of influenza? We are dealing with a version of H3N2 that is unusual compared to what we might expect year on year. At the same time, it is not as unusual as, say, a novel pandemic strain, far from it.

I'm super excited to announce the first preprint of my PhD, together with Chenxi Ou and @sokrypton.org! ML has revolutionized protein modeling, but crucial challenges remain. For example, we can't reliably predict complicated protein structures without MSAs, which limits what we can design.

please share this postdoc job alert! come join the budding Biodiversity Cell Atlas initiative as a postdoc or senior postdoc at @sangerinstitute.bsky.social working closely with @arnausebe.bsky.social and me to make progress on what we cover in this paper www.nature.com/articles/s41...

Gardening in the Viral Genome Wilderness: Why virus genomics needs structure, not pipelines. gluetools.substack.com/p/the-sequen...

I’m happy to share our new preprint! We uncovered the full diversity of bacterial TIR-based antiviral immune signaling, massively expanded the known diversity of Thoeris systems, and revealed conservation of TIR-derived immune signals across the tree of life. www.biorxiv.org/content/10.6...

Viruses are found in almost every ecosystem across the planet. Now, researchers have released VIRE – a comprehensive viral genome database covering diverse ecosystems to advance understanding of viral evolution and ecosystem functions. Learn more: www.embl.org/news/science...

🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...

Reliable Identification of Homodimers Using AlphaFold https://www.biorxiv.org/content/10.1101/2025.11.27.691011v1

Are you fascinated by viruses? Would you like to design your own original research project in the UK's largest virology centre? Why not come and do a PhD @cvrinfo.bsky.social - application deadline 6th Jan 2026 (1/1): www.findaphd.com/phds/program...

A few py2Dmol updates 🧬 py2dmol.solab.org Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)

Viro3D delivers >85,000 AI-predicted protein structures for >4,400 viruses, expanding viral structural coverage 30-fold, enabling new insights to virus function/evolution. #VirusBioinformatics #StructuralBiology🧬🔍 📄 doi.org/10.1038/s443... 👤EVBC members: Spyros Lytras, David Robertson, Joseph Hughes

Our November issue is available at journals.iucr.org/d/issues/202... On the cover: recent studies demonstrate that the range of samples suitable for cryo-EM single-particle analysis is expanding towards increasingly more native samples. Read the review at shorturl.at/mitjg

AI in Protein Design: Hype vs. Reality Explained by David Baker In this GEN interview, he emphasizes that designing new proteins from scratch is now a reality. Whether AI transforms medicine will require improving our understanding of biology's complexity

Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!

New preprint alert!! 🚨🚨🚨in collaboration with the Letko @fviromics.bsky.social and Baric labs! Just in case you're tired of sarbecoviruses, this time we looked at ACE2-using merbecoviruses! specifically the first HKU5r-CoVs detected in mink a couple of years ago. www.biorxiv.org/content/10.1...

Our PLM-interact is out in Nature Communications! We show that jointly encoding protein pairs using protein language models improves protein–protein interaction prediction performance and enables fine-tuning to predict mutation effects in human PPIs. www.nature.com/articles/s41...

OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇

Abstract submissions are open for #APSPM2026! 🗓️ Deadline: Nov 28, 2026 📍 Brisbane + online 🎓 Travel grants for students & ECRs Join us to explore how protein structures and AI are reshaping evolutionary biology. @official-smbe.bsky.social #StrPhy26 #StrPhy

My lab is hiring postdocs! We combine AI, protein structure prediction and comparison, and high-throughput virology to study the virus-host conflict. You can read more about my lab's research here: jasonnomburg.com/research/ Apply here to join us in lovely Vienna! aithyra.onlyfy.jobs/job/0khkxp82

Perfect timing in the field for a beautiful review on NAD+ in bacterial immunity by @hugovaysset.bsky.social and @audeber.bsky.social @cp-molcell.bsky.social #MicroSky www.cell.com/molecular-ce...

The IFIT2–IFIT3 antiviral complex targets short 5’ untranslated regions on viral mRNAs for translation inhibition By Dustin Glasner, Matthew Daugherty & colleagues. #microsky www.nature.com/articles/s41...

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....

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

🚨 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 🧪 🦠

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n

The mechanism of STING NF-κB signaling has remained a mystery. An exciting new study from the Paludan lab now uses data throughout animal STING evolution to provide new answers – including isolating white blood cells from turtles and carp! www.nature.com/articles/s41...

How can we understand the earliest events in evolution of eukaryotic immunity? @yao-li.bsky.social reports incredible molecular fossils of complete bacterial-like operons in eukaryotes that illuminate how animal immunity was first acquired from anti-phage defense www.biorxiv.org/content/10.1...

More on the ancient foundation of animal development. Coyle & King illustrate how core regulatory modules were present in our pre-animal ancestors. The key was not invention, but recycling & new protein interactions. #CellBiology #multicellularity #protistsOnSky www.nature.com/articles/s41...