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Ulad Litvin

@ulad-litvin.bsky.social
198 followers 305 following 25 posts

PhD student (MRC-UofG CVR) 🏰 antiviral defence | 🧬 evolution | 🔮 protein structure prediction

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Reposted by Ulad Litvin
Nobel Prize @nobelprize.org · 15h
Peter Hegemann and Georg Nagel – awarded the 2026 medicine prize – discovered a remarkable protein, channelrhodopsin, in a single-celled alga. Hegemann wondered how Chlamydomonas, a single-celled alga, is able to swim towards a light source.
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Eirik Lågeide @eiriklag.bsky.social · 01/10/2026
Very excited to share the first preprint from my PhD with the community! This is also the first paper from the Plant Immunogenomics group with @galofir.bsky.social, so stay tuned for more! www.biorxiv.org/content/10.6... 1/n 🧵
biorxiv.org
NO VEIN is an ancestral immunity protein involved in plant-virus interaction
The conservation of immune systems from prokaryotes to eukaryotes can guide discovery of immunity genes across the tree of life. Most studies to date have focused on metazoan systems, while the extent...
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Mike Keesey @tmkeesey.bsky.social · 01/10/2026
PhyloPic is having an October fundraiser. The goal is to raise enough money to cover web hosting for the past six months. Please share the link, and chip in a bit if you can! www.phylopic.org
phylopic.org
PhyloPic
PhyloPic is an open database of free silhouette images of animals, plants, and other life forms, available for reuse under Creative Commons licenses. Download silhouettes for use in educational materi...
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Maksim Kalutskii @maksimkalutskii.bsky.social · 23/09/2026
Excited to share our new preprint! 📜 Here, we used CALVADOS and ultra-CG models to show how the kinetochore establishes a robust attachment to the dynamic microtubule end. Spoiler: IDRs 🧵 1/n www.biorxiv.org/content/10.6...
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Iñaki Ruiz-Trillo @multicellgenome.bsky.social · 28/09/2026
We have a new branch in the family tree of animals: Atreyea- a previously unrecognized lineage among the closest unicell relatives of animals. Led by @konsmitsi.bsky.social & @freejakoba.bsky.social together with a fantastic team of collaborators. 🔗 papers.ssrn.com/sol3/papers.... #protistsOnSky
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Nature @nature.com · 24/09/2026
AlphaFold is being upgraded to better represent some of the least known and deadliest species: viruses go.nature.com/4cZivjx
go.nature.com
AlphaFold 'goes viral': database adds protein complexes of common viruses
AI predictions could help with pandemic preparedness, but they will need experimental confirmation.
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EMBL-EBI @ebi.embl.org · 24/09/2026
Is the world prepared for a future pandemic? AI-predicted protein complex structures for 2,800 viruses known to infect humans are now openly available in the #AlphaFold Database, which could improve how we respond to emerging infectious disease outbreaks. Learn more: www.embl.org/news/science...
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 24/09/2026
AlphaFold Database is expanding into pandemic preparedness. Together with NVIDIA, DeepMind, EBI et al. we exhaustively predicted ~1.7 million homo- & heterodimers across 2,812 viral proteomes, resulting in 8,028 high-confidence predictions. 📄 research.nvidia.com/labs/dbr/ass... 🌐 alphafold.ebi.ac.uk
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Bat1K Genome Project @bat1kgenomes.bsky.social · 23/09/2026
Where did bats come from?🦇🌍 After decades of debate, the biggest bat genome + fossil study ever done has an answer - and it’s not where anyone expected! 🤩OUR PHASE 1 FLAGSHIP is out today in nature! doi.org/10.1038/s415... A thread 🧵
doi.org
Reference genomes and fossils revise bat family phylogeny and biogeography - Nature
An updated phylogeny of bats is presented, based on new genome assemblies and many ancient fossils and including all known bat families.
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Arc Institute @arcinstitute.org · 23/09/2026
Many important bacterial non-coding RNAs and structural elements remain undiscovered. To help, David Li, Garyk Brixi, Michael Fischbach, @brianhie.bsky.social & team introduce Minerva, which uses a genome language model to predict RNA base pairing, repeats, & other interactions from sequence alone.
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Gytis Dudas @evogytis.bsky.social · 23/09/2026
And here is the preprint, available online on Baltic Unity Day (Sep 22). Happy citing! www.biorxiv.org/content/10.6... Thanks again to @barney-potter.bsky.social, @gkarthik.com, @sidneymbell.bsky.social, and @mftorresj.bsky.social
biorxiv.org
baltic: the Backronymed Adaptable Lightweight Tree vIsualisation Code
For ten years, baltic (Backronymed Adaptable Lightweight Tree vIsualization Code) has been used to make annotated phylogeny figures in molecular epidemiology, including during the West African Ebola e...
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Ben Hale @benhale.bsky.social · 21/09/2026
Congrats to Samira Schiefer on her new paper in Science Advances! We analysed 70 natural human IFNB1 variants & found both loss- & gain-of-function IFNβ proteins, revealing unexpected diversity in antiviral immunity. Great effort with Dave Jones & Florence Kwaschik! www.science.org/doi/10.1126/...
science.org
Functional diversity of natural human IFNB1 variants in innate immunity
Human interferon-β (IFN-β), a type I IFN, is critical for effective innate immunity and is also an approved disease-modifying therapeutic. While genetic variations in several components of the type I ...
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Ulad Litvin @ulad-litvin.bsky.social · 19/09/2026
Truly fantastic work 🤩 Congratulations to @eunbelivable.bsky.social and @martinsteinegger.bsky.social lab!
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Ulad Litvin @ulad-litvin.bsky.social · 18/09/2026
Kath is an incredible scientist with experience in fieldwork, lab work & bioinformatics. She’s recently completed her MSc in Aquaculture and is now looking for PhD opportunities in aquatic animal health & virology 🐟🦠🔬 If you work in this space or know someone who does, don’t be shy to get in touch!
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Asher Leeks @asherleeks.bsky.social · 16/09/2026
Come work with @viromehunter.bsky.social and myself at UBC! We have a postdoctoral position available for someone with an interest in bioinformatics and genomics, using sociovirology to understand disease dynamics in plant viruses. Advert: ppvlab.sites.olt.ubc.ca/files/2026/0...
ppvlab.sites.olt.ubc.ca
Browser Verification | UBC Cybersecurity
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Milot Mirdita @milot.bsky.social · 16/09/2026
ColabFold 1.6.3 is out! 2.5x faster, pip-installable, ipSAE+pDockQ2 scores. Thanks Choonghwan Lee, Marielle Russo, Gyuri Kim 🐍pip install colabfold[alphafold] CF2 Sneak Peak with AF3/Boltz/Protenix/ESMFold2… 🐍pip install "colabfold[alphafold3]@git+https://github.com/sokrypton/ColabFold@af3-preview"
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Janani Durairaj (Jay) @ninjani.bsky.social · 16/09/2026
The PhD and Postdoc application links are now live! Come join me at UNIL to work on deep learning for protein structure, interactions & design. pickybinders.org#open-positions
career5.successfactors.eu
Career Opportunities: PhD student position in deep learning for enzyme structure & catalysis (22980)
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Ulad Litvin @ulad-litvin.bsky.social · 15/09/2026
It's a shame Foldseek is too fast 😅. I would love to play this game with my structures while waiting for search results. Maybe even have a leaderboard for people who managed to finish the race before Foldseek 🧐
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Alexis Stamatakis @stamatak.bsky.social · 12/09/2026
The RAxML-NG v2.0 preprint is out: www.biorxiv.org/content/10.6... v2.0 features integrated model testing, fast branch support metrics, automatic parallelization, phylogenetic difficulty prediction, genotype evolution models, to name but the most important features. And it is A LOT FASTER of course
biorxiv.org
RAxML-NG 2: Automatic model selection, novel tree search heuristics, and fast branch support metrics
RAxML-NG is a widely used tool for maximum likelihood based phylogenetic inference. In the seven years since the last RAxML-NG publication, we have continuously improved and extended the code. Here, w...
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Jumpei Ito @jampei2.bsky.social · 06/09/2026
New preprint! We show that poxvirus gene repertoires are shaped by expansion-biased birth-and-death dynamics and genome architectural constraints. Led by Arnon Plianchaisuk (@chainorato) in our lab. Please share! (1/10) www.biorxiv.org/content/10.6...
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Ulad Litvin @ulad-litvin.bsky.social · 04/09/2026
What a lovely addition to UniProt 🤩
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 26/08/2026
Foldseek-Interface enables fast search/clustering of the protein interface universe! We clustered 3.1M PDB dimers into 77,167 groups and found new interfaces keep appearing even as fold discovery plateaus. 🧵 📄 www.biorxiv.org/content/10.6... 🔎 search.foldseek.com/interface 🌐 interface.foldseek.com
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Sofia Luengo-Woods @sluengo.bsky.social · 30/07/2026
We’re so excited to share our new paper, where we tackle the wealth of structural and functional diversity of anti-phage sensors across bacteria (1/6)
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Antigen Evolution & Design Lab @antigenevo.bsky.social · 22/07/2026
🚨 JOB ALERT🚨 We are very excited to be hiring the lab's ✨very first postdoc✨! Work on new AI technologies for decoding antigen protein evolution in a fresh research environment, at the heart of Paris 🇫🇷 Details & link to apply: research.pasteur.fr/en/job/postd... Deadline: Sep 1st
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Spyros Lytras @spyroslytras.bsky.social · 14/07/2026
New review out! At @annualreviews.bsky.social for Virology! Check out the summary thread below 👇👇👇
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Martin Pacesa @martinpacesa.bsky.social · 07/07/2026
We often talk about complex protein folds but what does that really mean? Turns out we don't have a good metric for it. So we made a game to make one! Head over to our website to vote on which fold you think is more complex and why! pacesalab.com/foldcomplexi...
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Antigen Evolution & Design Lab @antigenevo.bsky.social · 07/07/2026
Inaugural post! We are a brand new lab @pasteur.fr studying how pathogen antigens evolve and how we can exploit these proteins' evolution to make better vaccines! Read a few words from the currently sole member of the lab @spyroslytras.bsky.social below! 😁 www.pasteur.fr/en/research-...
pasteur.fr
Predicting viral evolution with AI
Spyros Lytras is one of four young scientists selected in 2025 to lead new research groups at the Institut Pasteur. He has headed the “Antigen Evolution & Design laboratory” 5-year Group (G5) since Ju...
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 27/06/2026
I gave a workshop on AlphaFold & related programs @ the University of Utah. Part 1 covers protein structure prediction before/after AlphaFold & deep learning neural networks. Part 2 covers the math behind the scores. Part 3 covers PyMOL & the webservers. youtube.com/@rolanddunbr...
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Sergey Ovchinnikov @sokrypton.org · 15/06/2026
New Experimental Google Colab Notebook now integrates AlphaFold3 with OpenFold3 and py2Dmol: colab.research.google.com/github/sokry... (1/3)
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 06/06/2026
Folddisco is now published @natbiotech.nature.com. It’s a fast motif search for similar 3D DISCOntinuous residues like catalytic sites or zinc fingers across the entire protein universe. 📄 www.nature.com/articles/s41... 💾 folddisco.foldseek.com​​​​​​​​​​​​​​​​ 🌐 search.foldseek.com/folddisco
nature.com
Structural motif search across the protein universe with Folddisco - Nature Biotechnology
Folddisco enables protein structural motif search in million scale databases.
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Ulad Litvin @ulad-litvin.bsky.social · 27/05/2026
ESMFold2 👀
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Yehlin Cho @yehlincho.bsky.social · 21/05/2026
🚀 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 @cvrbioinfo.bsky.social · 20/05/2026
Congrats to @ulad-litvin.bsky.social on winning 2nd best talk at #Vibiom2026! @cvrinfo.bsky.social 🏅
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Joseph Hughes @bljog.bsky.social · 19/05/2026
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 @proteinmechanic.bsky.social · 10/05/2026
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 @mkrupovic.bsky.social · 11/05/2026
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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Ulad Litvin @ulad-litvin.bsky.social · 26/04/2026
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 🧬🧵
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Aris Katzourakis @ariskatzourakis.bsky.social · 23/04/2026
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...
nature.com
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.
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Bohdana Hurieva🇺🇦 @bhurieva.bsky.social · 23/04/2026
🎉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...
biorxiv.org
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Minji Lee @m1nj2.bsky.social · 21/04/2026
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 @mkrupovic.bsky.social · 22/04/2026
"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...
journals.plos.org
The selfish ribosome
In this Essay, the evolution of life is construed as a ribosomal takeover, whereby the ribosome evolved to consume most of the cell’s resources, while other cellular componentry ensured the propagatio...
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Torsten Schwede @torstenschwede.bsky.social · 21/04/2026
The CASP experiment is about to start - and is still short on challenging prediction targets. Ligand complexes, RNA, …
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Ulad Litvin @ulad-litvin.bsky.social · 14/04/2026
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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jingiyeo.bsky.social @jingiyeo.bsky.social · 03/04/2026
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...
afesm.foldseek.com
AFESM Clusters
Foldseek clustered 820M AlphaFold DB + ESMatlas structures
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Vivek Mutalik @vivekmutalik.bsky.social · 03/04/2026
📣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.
Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here
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Aude Bernheim @audeber.bsky.social · 02/04/2026
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_...
science.org
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Stephan Hacker @stephanhacker2.bsky.social · 18/03/2026
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 🇺🇦 @martinsteinegger.bsky.social · 17/03/2026
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 @ebi.embl.org · 16/03/2026
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 🇺🇦 @martinsteinegger.bsky.social · 17/03/2026
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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