Ulad Litvin

A 3x3 grid of coloured images of influenza virus particles in the style of an Andy Warhol screen print. Image credit Naina Nair / Ed Hutchinson (MRC-University of Glasgow Centre for Virus Research)

🚨New Influenza Tool🚨
Interested in IAV mutations?
Looking for markers of mammalian adaptation?
Frustrated by converting between IAV numbering systems?
The #Flu-MutationExplorer, a new tool from @cvrbioinfo.bsky.social and @royalvetcollege.bsky.social, is here to help:
flu-gdb.cvr.gla.ac.uk
(1/n)

Out today: We discovered new viral proteins that target immune signaling molecules, solely based on their AlphaFold-predicted shapes

www.science.org/doi/10.1126/...

Congrats Nitzan Tal and coauthors! Thank you Kranzusch lab for the fun collaboration!

Linking below previous thread on our findings

Mapping the yeast atructural interactome with AlphaFold3: an open call for collaboration We are excited to announce the early-stage release of our S. cerevisiae  structural interactome mapping project. Using AlphaFold3 (AF3), w...

We have started a project trying to predic the interactions/structures of all yeast protein pairs using an AlphaFold pooling approach. We are making the current dataset open and we welcome collaborations.
www.evocellnet.com/2026/03/mapp...

🧵 FlashPPI (new model) is live in SeqHub. Proteome-wide PPI prediction in minutes, 2,400x faster than the next best sequence-based method, 4x better predictive performance. How it works: 👇

Predicting protein-protein interactions (PPIs) at proteome scale can take months with co-folding models due to the massive all-vs-all comparisons required.

We are excited to announce FlashPPI, a contrastive learning framework that predicts proteome wide physical interfaces in minutes. 1/🧵

With Eugene Koonin, we propose a concept of “the selfish ribosome”, under which evolution of life is viewed as a ribosomal takeover, where the ribosome evolved to consume most of the cell’s resources, while other cellular componentry ensures the propagation of the ribosome. arxiv.org/abs/2602.23268

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

Image of a herpesvirus structure

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...

The paradox of immune systems conservation between prokaryotes and eukaryotes - Nature Reviews Microbiology The widespread prokaryotic immune systems, in particular restriction–modification, CRISPR–Cas and defensive toxin–antitoxin systems, are absent in eukaryotes, whereas relatively rare ones, such as Arg...

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...

Multiple protein structure alignment at scale with FoldMason Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

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:

Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning Mirdita Lab builds scalable bioinformatics methods.

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

Dominant contribution of Asgard archaea to eukaryogenesis - Nature A survey of the reconstructed gene set of the last eukaryotic common ancestor shows a consistent link between Asgard archaea and the origin of numerous, functionally diverse&nbsp;eukaryotic genes, dem...

#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...

Genomic clues to the origin of eukaryotic cells How did eukaryotic cells with complex architecture evolve from simpler prokaryotic cells? DNA analyses offer possible answers.

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/...

Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes Nature Ecology & Evolution - Analysis of the 3D chromatin architecture and cis-regulatory elements in a sea urchin and a sea star reveals mechanisms of 3D chromatin organization in echinoderms...

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!

Global Landscape of Human Kinase Motifs in Viral Proteomes Viruses are classically viewed as targets of host sensing, yet whether they also sense and respond to host cues remains largely unexplored. We propose that host-driven post-translational modification ...

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 stamatak@ics.forth.gr

Computational Approaches to Early Evolution

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...

Decoding cnidarian cell type gene regulation - Nature Ecology & Evolution This study reconstructs the gene regulatory networks that define cell types in the sea anemone Nematostella vectensis, providing a valuable resource for comparative regulatory genomics and the evoluti...

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...

Genetic diversity in horseshoe bat ACE2 and sarbecovirus spike proteins mutually shape one another Angiotensin-converting enzyme 2 (ACE2) serves as the entry receptor for a wide diversity of sarbecoviruses naturally harboured by horseshoe bats (genus Rhinolophus ). Despite the extensive circulation...

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.