Ulad Litvin
PhD student (MRC-UofG CVR)
🏰 antiviral defence | 🧬 evolution | 🔮 protein structure prediction
- Reposted by Ulad LitvinFoldMason 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...
- Reposted by Ulad LitvinReminder with <2 weeks to deadline:
- Reposted by Ulad LitvinMy 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
- Reposted by Ulad Litvin#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...
- Reposted by Ulad LitvinApplications 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...
- 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...
- Reposted by Ulad LitvinHow 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...
- Reposted by Ulad LitvinPhold'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/...
- 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...
- Reposted by Ulad LitvinOur 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
- Reposted by Ulad LitvinWe'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!
- Reposted by Ulad LitvinThrilled 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...
- Reposted by Ulad LitvinI'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...
- Reposted by Ulad LitvinPermanent 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
- Reposted by Ulad LitvinJoin 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...
- Reposted by Ulad LitvinExcited 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...
- Reposted by Ulad LitvinNew 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...
- Reposted by Ulad LitvinNew 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...
- Reposted by Ulad LitvinWhy 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.
- Reposted by Ulad LitvinI'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.
- Reposted by Ulad Litvinplease 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...
- Reposted by Ulad LitvinGardening in the Viral Genome Wilderness: Why virus genomics needs structure, not pipelines. gluetools.substack.com/p/the-sequen...
- Reposted by Ulad LitvinI’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...
- Reposted by Ulad LitvinViruses 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...
- Reposted by Ulad Litvin🦠🧪🧬🚨 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-...
- Reposted by Ulad LitvinReliable Identification of Homodimers Using AlphaFold biorxiv.org/content/10.1101/202…
- Reposted by Ulad LitvinAre 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...
- Reposted by Ulad LitvinA 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)
- Reposted by Ulad LitvinViro3D 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
- Reposted by Ulad LitvinOur 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
- Reposted by Ulad LitvinAI 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
- Reposted by Ulad LitvinExcited 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!
- Reposted by Ulad LitvinNew 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...
- Reposted by Ulad LitvinOur 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...
- Reposted by Ulad LitvinOpenFold3-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👇
- Reposted by Ulad LitvinAbstract 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
- Reposted by Ulad LitvinMy 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
- The Starting Principal Investigators at #AITHYRA the Research Institute for Biomedical Artificial Intelligence of the OeAW in Vienna invite outstanding candidates to apply for postdoctoral positions in the field of AI/ML & Life Sciences. www.oeaw.ac.at/aithyra/post... Please apply by 20 Nov 2025!
- Reposted by Ulad LitvinPerfect 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...
- Reposted by Ulad LitvinThe 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...
- Reposted by Ulad LitvinNew 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
- 🦠 The diversity of viral proteins can be reduced to 19,000 structural clusters. A structure-similarity network captures relationships between them. 2/5
- 🔍 Searches against structural network are extremely sensitive and allow to recover more RdRps than iterative profile-based searches. 3/5
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View full threadIt was a pleasure to work with @spyroslytras.bsky.social, Alex Jack, @davidlrobertson.bsky.social, @bljog.bsky.social and @grovearmada.bsky.social 5/5
