Ulad Litvin
@ulad-litvin.bsky.social
📤 166
📥 265
📝 17
PhD student (MRC-UofG CVR) 🏰 antiviral defence | 🧬 evolution | 🔮 protein structure prediction
pinned post!
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
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Viro3D: a comprehensive database of virus protein structure predictions | Molecular Systems Biology
imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for >4,400 viruses, allowing mapping of form and function across the human and animal virosphere. Viro3D i...
https://doi.org/10.1038/s44320-025-00147-9
8 months ago
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ESMFold2 👀
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8 days ago
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Yehlin Cho
13 days ago
🚀 Excited to share our new work: Absolute Stability Predictor! 📊:
forms.gle/4ZnXZSnTBvay...
Built the MGnify Stability Dataset (1.8M+ measurements) and developed stability prediction models, together with
@grocklin.bsky.social
@KotaroTsuboyama,
@sokrypton.org
and teams.
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CVR Bioinformatics
15 days ago
Congrats to
@ulad-litvin.bsky.social
on winning 2nd best talk at
#Vibiom2026
!
@cvrinfo.bsky.social
🏅
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Joseph Hughes
16 days ago
Fifth and final
@cvrinfo.bsky.social
talk at ViBioM 2026.
@ulad-litvin.bsky.social
presenting
viro3d.cvr.gla.ac.uk
and other applications of alphafold in virology.
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Ashar Malik
25 days ago
New work: Our earlier work showed that Foldseek characters could be adapted for phylogenetic alignment, treating each character as an evolutionary state. That part holds but there's a hidden assumption baked in that needed unpacking. So lets do that.🧵
#StructuralPhylogenetics
#Evolution
#Protein
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Mart Krupovic
24 days ago
With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the
#virosphere
. We describe all 10 viral realms and the logic behind them, and so much more. Check it out!
comptes-rendus.academie-sciences.fr/biologies/ar...
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Had a great time at the Microbiology Society Annual Conference! I gave a talk on modelling protein-protein interactions with AlphaFold3. A few lessons learned 🧬🧵
about 1 month ago
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Aris Katzourakis
about 1 month ago
Some bat alphacoronaviruses can exploit an entirely different receptor to enter human cells. This could lead to crossover events could be the first step in future epidemics, though we are not there yet and there would be many more barriers to overcome also.
www.nature.com/articles/s41...
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Heart-nosed bat alphacoronaviruses use human CEACAM6 to enter cells - Nature
Human CEACAM6, which is widely expressed in the lung, is identified as a receptor used by the spike proteins of Cardioderma cor (heart-nosed bat) alphacoronaviruses to enter cells.
https://www.nature.com/articles/s41586-026-10394-x
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Bohdana Hurieva🇺🇦
about 1 month ago
🎉Excited to share our new preprint! TIR domains from diverse animals, including human TLR4, are catalytically active and produce cyclic ADP-ribose (cADPR). This enzymatic activity is widespread in animals and conserved across the tree of life.
www.biorxiv.org/content/10.6...
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https://www.biorxiv.org/content/10.64898/2026.04.20.719644v1
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Minji Lee
about 1 month ago
We introduce ConforNets, a mechanism for conformational control in AlphaFold3 models - SoTA at producing diverse conformations on every multistate benchmark (N=104) - Novel capability: transfer state from one protein to another Outperforms BioEmu, ConforMix and AFsample3 🧵1/8
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Mart Krupovic
about 1 month ago
"The selfish ribosome" paper is now published in
@plosbiology.org
. Have a look! Many thanks to the editors and reviewers!
doi.org/10.1371/jour...
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Torsten Schwede
about 1 month ago
The CASP experiment is about to start - and is still short on challenging prediction targets. Ligand complexes, RNA, …
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Having fantastic time at
@microbiologysociety.org
annual conference in Belfast. Just gave a short talk on predicting protein-protein interactions with AlphaFold3 🔮 and all the tricks we’ve applied to make it work for challenging targets 👾
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about 2 months ago
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2 months ago
45 novel protein folds in the updated AFESM (AFDB + ESMatlas) manuscript: • 12 high-confidence folds in AFESM • 33 by ColabFold-repredicting 2.3M low-quality domains We show AFDB captures most domains already and ESMfold struggles with novelty 🌏
afesm.foldseek.com
📄
biorxiv.org/content/10.1...
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AFESM Clusters
Foldseek clustered 820M AlphaFold DB + ESMatlas structures
https://afesm.foldseek.com
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Vivek Mutalik
2 months ago
📣Huge preprint 🔔 Today we share something our group has been working toward for a long time, led by
@lucasmoriniere.bsky.social
We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.
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Aude Bernheim
2 months ago
How diverse is bacterial immunity ? We report in
@science.org
how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems. 👏
@emordret.bsky.social
,
@alexhv.bsky.social
& al
doi.org/10.1126/scie...
Explore them here
defensefinder.mdmlab.fr/wiki/refseq_...
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https://www.science.org/doi/10.1126/science.adv8275
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Stephan Hacker
3 months ago
How can we study the function of nucleotide-based
#SecondMessengers
?
@oliveiramann.bsky.social
presented her group's exciting findings in this field at
#Biochemistry2026
. She e.g. presented the
#cryoEM
structure of OAS2, which has key
#antiviral
functions.
linkinghub.elsevier.com/retrieve/pii...
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Martin Steinegger 🇺🇦
3 months ago
Kieran et al. trained a generative protein binder design model. The training is based on Teddymer, a dataset developed by
@sooyoung-cha.bsky.social
. By treating monomer domains as multimers and clustering them with Foldseek, she created a set that allowed Complexa to learn. 💾
teddymer.foldseek.com
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EMBL-EBI
3 months ago
You asked, we listened. Millions of AI-predicted protein complex structures are now available in the
#AlphaFold
Database. This spans homodimers from 20 of the most studied species, including humans, as well as the World Health Organization’s priority pathogens list.
www.ebi.ac.uk/about/news/t...
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Martin Steinegger 🇺🇦
3 months ago
AlphaFold database has entered the era of complexes. Together with NVIDIA, DeepMind and EBI, we use ColabFold, OpenFold and MMseqs2-GPU to predict ~31 million complexes (homo & hetro-dimers) resulting in 1.8 million high-quality predictions 📄
research.nvidia.com/labs/dbr/ass...
🌐
alphafold.ebi.ac.uk
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Brett Baker
3 months ago
Having a hard time keeping up with the fast-moving field of origin of eukaryotes/Asgards archaea? Our new perspective article can help, we review the status of research over the last decade and where it's going. The archaeal roots of eukaryotic life
www.pnas.org/doi/10.1073/...
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Mohammed AlQuraishi
3 months ago
New OpenFold3 preview out! (OF3p2) It closes the gap to AlphaFold3 for most modalities. Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9
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Ed Hutchinson
3 months ago
🚨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)
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Ulad Litvin
Sorek Lab
3 months ago
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
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Pedro Beltrao
3 months ago
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...
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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...
https://www.evocellnet.com/2026/03/mapping-yeast-atructural-interactome.html
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Tatta Bio
3 months ago
🧵 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: 👇
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Andre Cornman
3 months ago
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/🧵
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Mart Krupovic
3 months ago
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
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Sandy Hetherington
3 months ago
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...
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10th European Society for Evolutionary Developmental Biology Meeting 2026
The European Society for Evolutionary Developmental Biology is delighted to welcome you to the 10th biennial meeting, to be held at the University of Glasgow from June 9th - 12th in 2026.
https://www.evodevoconference26.com/important-dates
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Joe Grove
4 months ago
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.
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🦠 Viro3D and BFVD viral predictions are now available in the AlphaFold database
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4 months ago
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Soham Dibyachintan
4 months ago
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
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David Bhella
4 months ago
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...
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Ulad Litvin
Kranzusch Lab
4 months ago
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...
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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...
https://www.nature.com/articles/s41579-026-01284-0
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Martin Steinegger 🇺🇦
4 months ago
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...
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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...
https://www.science.org/eprint/4QQQFGCSQEGFJVGUESWN/full?activationRedirect=/doi/full/10.1126/science.ads6733
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Lars-Anders Carlson
4 months ago
Reminder with <2 weeks to deadline:
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Milot Mirdita
4 months ago
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
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Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning
Mirdita Lab builds scalable bioinformatics methods.
https://mirdita.org/
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Nature Microbiology
5 months ago
#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...
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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 eukaryotic genes, dem...
https://www.nature.com/articles/s41586-025-09960-6
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Sandra Álvarez
5 months ago
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...
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Waggoner Lab
5 months ago
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...
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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.
https://www.nature.com/articles/d41586-025-04094-1
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George Bouras
5 months ago
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/...
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Ulad Litvin
5 months ago
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
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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...
https://rdcu.be/eXX8l
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Robertson Lab
5 months ago
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!
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University of Glasgow - Colleges - College of Medical, Veterinary & Life Sciences - MVLS Graduate School - PhD Research Opportunities - College Futures Themes PhD Programme - Projects - Fundamentals o...
https://www.gla.ac.uk/colleges/mvls/graduateschool/phd-research-opportunities/futures-programme/projects/fundamentals-of-life/fol25davidrobertson/
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Mehdi Bouhaddou
5 months ago
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...
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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 ...
https://www.biorxiv.org/content/10.1101/2025.06.02.657064v2
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James Fraser
5 months ago
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...
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Know when to co-fold'em
This is the official web page for the James Fraser Lab at UCSF.
https://fraserlab.com/2025/12/29/know-when-to-co-fold-em/
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Alexis Stamatakis
6 months ago
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]
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Sandra Álvarez
5 months ago
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...
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Computational Approaches to Early Evolution
https://www.oist.jp/conference/computational-approaches-early-evolution
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Arnau Sebé-Pedrós
5 months ago
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...
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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...
https://www.nature.com/articles/s41559-025-02906-1
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Spyros Lytras
6 months ago
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...
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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...
https://www.biorxiv.org/content/10.1101/2025.10.26.684670v1
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Miguel Méndez Sandín
6 months ago
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...
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