Heads-up! I’ll be starting my research group at MedUni Vienna in January 2027, with postdoc and PhD positions available soon. Looking for people interested in bacteria–phage interactions, bacterial defense systems, and phage anti-defense strategies. Please send your CV: anna.lopatina@univie.ac.at

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.

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 🧵

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...

biorxiv.org

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

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...

phylopic.org

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...

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

AlphaFold is being upgraded to better represent some of the least known and deadliest species: viruses go.nature.com/4cZivjx

AlphaFold 'goes viral': database adds protein complexes of common viruses

AI predictions could help with pandemic preparedness, but they will need experimental confirmation.

go.nature.com

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...

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

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 🧵

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.

doi.org

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.

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

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...

biorxiv.org

Gytis Dudas@evogytis.bsky.social · 3w ago

baltic v1.0.0 is live! Get it via pip or clone from Github repo. Now with documentation (baltic.readthedocs.io) & a gallery of tutorials & examples (phylo-baltic.github.io/baltic-gallery, still WIP). Huge thanks to @barney-potter.bsky.social for all the initiative & help along the way. #ViroSky

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/...

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 ...

science.org

Truly fantastic work 🤩 Congratulations to @eunbelivable.bsky.social and @martinsteinegger.bsky.social lab!

Martin Steinegger 🇺🇦@martinsteinegger.bsky.social · 3w ago

BFVD v3 contains 5.8M viral protein structures, 16× more than v2; 75% high quality, filling a major gap in AFDB coverage. It fully covers 72.6% of reference proteomes and spans 72.7% of ICTV species. Great work by @eunbelivable.bsky.social et al. 📄 www.biorxiv.org/content/10.6... 🌐 bfvd.foldseek.com

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!

Kathrine Dubla@kathrinemd.bsky.social · 3w ago

I’m slowly working to grow my network here and connect with people across aquaculture! I’ll be sharing bits of my work, along with some thoughts and commentaries, along the way. I’d be happy to hear about your work too and have a nice conversation about it. Say hi! 👋

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...

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"

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

Janani Durairaj (Jay)@ninjani.bsky.social · last mo.

Some exciting news: I'm joining the University of Lausanne @unil.bsky.social @dbc-unil.bsky.social as an Assistant Professor next month 🎉 My group will work on context-aware deep learning for protein structure, interaction & design. Postdoc and PhD openings coming soon - keep an eye out!

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 🧐

Martin Steinegger 🇺🇦@martinsteinegger.bsky.social · 4w ago

Fold Spacer lets you fly through protein structures (Weekend project #2). It’s my first game: I originally set out to build a racer with structures as the tracks, but was a little too crazy. So it became this instead. You can upload your own structures. 🌐 martin-steinegger.github.io/Fold-Spacer/

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

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...

biorxiv.org

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...

What a lovely addition to UniProt 🤩

Tatta Bio@tattabio.bsky.social · last mo.

UniProt is where most researchers start when they want to understand a protein. As of today, prokaryotic entries there will show something new: genomic context, powered by SeqHub, right in the Sequence section of the page.

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

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)

Nature@nature.com · 2mo ago

Nature research paper: Diverse bacterial pattern recognition receptors sense the core phage proteome go.nature.com/45fpXCZ

🚨 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

New review out! At @annualreviews.bsky.social for Virology! Check out the summary thread below 👇👇👇

Antigen Evolution & Design Lab@antigenevo.bsky.social · 3mo ago

First paper with the lab's affiliation!! ✨✨ summarising some of the cool concepts that the Antigen Evolution & Design Lab will be working on! Together with amazing collaborators @mghafari.bsky.social and @grovearmada.bsky.social www.annualreviews.org/content/jour...

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...

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-...

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...

pasteur.fr

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...

New Experimental Google Colab Notebook now integrates AlphaFold3 with OpenFold3 and py2Dmol: colab.research.google.com/github/sokry... (1/3)