New 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....

#RECOMB2026 will be in Thessaloniki, Greece on May 26-29, 2026. Satellites on May 24-25. Save the date! Το συνέδριο #RECOMB2026 θα πραγματοποιηθεί στη Θεσσαλονίκη, στις 26-29 Μαΐου 2026. Οι δορυφορικές εκδηλώσεις θα διεξαχθούν στις 24-25 Μαΐου 2026. Σημειώστε την ημερομηνία!

HHMI adopts Plan U journals.plos.org/plosbiology/...

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio www.nature.com/articles/s41...

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n 📄 www.nature.com/articles/s41... 💿 mmseqs.com

Happy to see that Spacedust is now published on Nature Methods! It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes. 1/6🧵

Preprint: Highly efficient protein structure prediction on NVIDIA RTX Blackwell and Grace-Hopper nvda.ws/4n4xzz9 Visit the NVIDIA Digital Biology Labs website to find more information like this: t.co/R9ufEZrGEA

Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data. @ruoshiz.bsky.social @milot.bsky.social www.nature.com/articles/s41...

www.nature.com/articles/s41... #microsky #genomics #phagesky #phage defense

👏👏👏 👏👏

**Please repost** If you're enjoying Paper Skygest -- our personalized feed of academic content on Bluesky -- we'd appreciate you reposting this! We’ve found that the most effective way for us to reach new users and communities is through users sharing it with their network

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...

Protein Structure Informed Bacteriophage Genome Annotation with Phold https://www.biorxiv.org/content/10.1101/2025.08.05.668817v1

MMseqs2 v18 is out - SIMD FW/BW alignment (preprint soon!) - Sub. Mat. λ calculator by Eric Dawson - Faster ARM SW by Alexander Nesterovskiy - MSA-Pairformer’s proximity-based pairing for multimer prediction (www.biorxiv.org/content/10.1...; avail. in ColabFold API) 💾 github.com/soedinglab/M... & 🐍

Thanks for tuning in--we've already received incredibly valuable feedback from the community and will continue to update our work! We're excited for all of MSA Pairformer's potential applications for biological discovery and for the future of memory and parameter efficient pLMs

Excited to share work with Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org biorxiv.org/content/10.1... TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵

Scaling down protein language modeling with MSA Pairformer https://www.biorxiv.org/content/10.1101/2025.08.02.668173v1

Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1... and GH repo: github.com/refresh-bio/...

Congratulations to Rayan Chiki, (Institut Pasteur) head of the “Sequence Bioinformatics” unit, for securing the ERC Proof of Concept 2025 for his project ENZYMINER! 👏 ‪@rayan.chiki.bsky.social #Bioinformatics

I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!

Really important points by @alexbateman1.bsky.social on the importance of curation, addressing some of the myths out there. Deeply resonates with the commentary Paul Thomas and I wrote last year www.nature.com/articles/s41...

Folddisco webserver result view update: - Added description texts for AFDB - Integrated TaxoView taxonomy visualization & filter by @sunjaelee.bsky.social - Inter-residue distance clustering by DBSCAN to explore motif diversity. 🌐 search.foldseek.com/folddisco 📄 www.biorxiv.org/content/10.1...

Recently I learnt that EMBL-EBI has a free online course about AlphaFold — how it works, strengths and limitations, how to use it — and it's very good! There are also little quizzes and interactives. www.ebi.ac.uk/training/onl...

Today at 5pm, @eunbelivable.bsky.social will present her work on the Big Fantastic Viral Database (BFVD) at #ISMB2025 in BOSC. She also has a poster B-123 (tomorrow, 22nd), so please drop by to have ta chat and grab some stickers! 📄 academic.oup.com/nar/article/...

FAMSA2 enables accurate multiple sequence alignment at protein-universe scale https://www.biorxiv.org/content/10.1101/2025.07.15.664876v1

BioEmu now published in @science.org !! What is BioEmu? Check out this video: youtu.be/LStKhWcL0VE?...

Unfortunately, the MLSB Workshop @ NeurIPS (@workshopmlsb.bsky.social) was rejected this year. Feedback from the deciding committee indicates it was a coin flip decision, with 283 proposals & a number related to “computational biology” More on the future of MLSB soon…

Noooo😭 This was the BEST workshop at NeurIPS!!

Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬 📄 www.biorxiv.org/content/10.1... 🌐 search.foldseek.com/folddisco

Structural motif search across the protein-universe with Folddisco https://www.biorxiv.org/content/10.1101/2025.07.06.663357v1

To learn more about the impact of MMseqs2-GPU and test it out (for free), here's a blog I wrote: developer.nvidia.com/blog/acceler...

Hello everyone! I am pleased to share information on the first ever Computational Structural Virology Symposium, conducted August 4th on zoom and highlighting work in this emerging field. You can register for this event here: forms.gle/CNiqskMwQEuV.... Please re-post!

Excited to unveil Boltz-2, our new model capable not only of predicting structures but also binding affinities! Boltz-2 is the first AI model to approach the performance of FEP simulations while being more than 1000x faster! All open-sourced under MIT license! A thread… 🤗🚀

Unicore is now published on GBE 🚀 Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n 📃 doi.org/10.1093/gbe/evaf109

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

The CoVFit paper is now published @natcomms.nature.com !! Exciting work led by Jumpei Ito really showing the potential of pLMs for genotype-2-phenotype predictions!! www.nature.com/articles/s41...

My student build a huge version of it! :D

We've updated our AFESM website to now include biome filtering, allowing exploration of protein structures adapted to specific environments. 🌐 afesm.foldseek.com Read more about the work in the skeetorial 🦋 bsky.app/profile/mart... or our preprint 📄 www.biorxiv.org/content/10.1...

Have we hit a "scaling wall" for protein language models? 🤔 Our latest ProteinGym v1.3 release suggests that for zero-shot fitness prediction, simply making pLMs bigger isn't better beyond 1-4B parameters. The winning strategy? Combining MSAs & structure in multimodal models!

Excited to share our new preprint on HLp—a bacterial histone from Leptospira perolatii that forms stable tetramers and wraps ~60 bp of DNA: "DNA Wrapping by a Tetrameric Bacterial Histone" www.biorxiv.org/content/10.1... @mpi-bio-fml.bsky.social

Our next keynote speaker, Rachel Kim, introduces us to BVFD. Now we know what the "F" stands for :) Truly FANTASTIC work! #RdRpSummit2025

Reinforcement learning with experimental feedback (RLXF) shifts protein language models so that they generate sequences with improved properties @nathanielblalock.bsky.social @philromero.bsky.social www.biorxiv.org/content/10.1...

Deep origin of eukaryotes outside Heimdallarchaeia within Asgardarchaeota www.nature.com/articles/s41... This paper is interesting, and provides evidence that several Njordarchaeales genomes were contaminated by TACK genomes. But from the peer review file, don't do this. Ignorance is not a virtue:

Clustering 821M structures (AFDB&ESMatlas) into 5.12M groups reveals biome-specific groups but only 1 new fold (many novel domain combinations though!). @jingiyeo.bsky.social @yewonhan.bsky.social @nbordin.bsky.social @hbkgenomics.bsky.social @milot.bsky.social @martinsteinegger.bsky.social

Today @yewonhan.bsky.social will give a flash talk about our metagenomic large-scale protein structure clustering and analysis at #RECOMB2025. Today (April 29) 1 p.m. at Global Lounge in “The Commons”

From Hong Kong, with Love 😉 @martinsteinegger.bsky.social @milot.bsky.social 7MB original file linktr.ee/carloshk

Boltz-1: Democratizing Biomolecular Interaction Modeling www.biorxiv.org/content/10.1... 🧬🖥️🧪

Our latest preprint is out on bioRxiv! A collaboration between the groups of @martinsteinegger.bsky.social , David Jones and Christine Orengo, we clustered AlphaFold Database and ESMatlas, a whopping 821 million proteins! We reveal biome-specific groups & over 11k novel domain combinations.