🚨New preprint out! We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8) www.biorxiv.org/content/10.1...

UniProt is changing its reference proteomes resource. Reference proteomes will remain in UniProtKB, while others will move to UniParc. Read more about these changes: www.ebi.ac.uk/about/news/u... 🧬 🖥️ Uniprot is a collaboration between EMBL-EBI, @sib.swiss & the Protein Information Resource.

🚀 Looking for talented PhD students! Join us in 🇸🇬 Singapore for 1-2 years to push the frontiers of AI for Genomics. Work on: 🧬 Cancer genome reconstruction 🧫 Cancer genome & cell foundation models 💊 RNA drug & mRNA therapeutic design #AI #Genomics #PhD 1/5

Excited to share: DNA glycosylases are diverse antiviral effectors. They recognize phage base modifications and initiate genome destruction. A structure‑guided approach made the scope of this discovery possible! 🧪 #phagesky doi.org/10.1101/2025... #phage #microbiology

#APSPM2026 is open to anyone curious about combining protein structure and evolution. Learn where to start in our workshops and discover how structure meets phylogenetics. Feb 15 - 18, 2026 Brisbane, Australia Register here: biosig.lab.uq.edu.au/strphy26/reg... (in-person only)

New lab preprint! @zestytoast.bsky.social tagged a scarce mycobacterial protein in M. smegmatis with TwinStep but got… something? @kjamali.bsky.social's ModelAngelo built models & @martinsteinegger.bsky.social's FoldSeek IDed them as the biotin-containing MCC & LCC complexes 🧵 tinyurl.com/ukny4ptz

OpenFold3-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👇

Our new preprint is out. Our group performed a comprehensive protein–protein complex prediction within 2,437 biosynthetic gene clusters. We predicted a total of 487,828 complexes for known BGCs, identifying 15,438 heteromeric interactions with an ipTM ≥ 0.6. (2/3) www.biorxiv.org/content/10.1...

Looks like OpenFold3 has been formally released in a public "preview". Not quite on parity with AlphaFold3 on a few benchmarks shown, in particular for antibody interactions. All info on the github link. I am sure we will hear more about this from the developers github.com/aqlaboratory...

We can’t wait to welcome you to sunny Brisbane. Home to world-class research and a vibrant scientific community. Join us at the University of Queensland for #APSPM2026 to discuss how protein structure and evolution come together #StrPhy26

Chris Sanders is now in bsky. Welcome!

We train machine learning models on millions of proteins. But when it comes to making predictions, do we need them to understand all proteins at once? Often, we need an accurate model for the specific protein we are studying or designing. We address this with ProteinTTT arxiv.org/abs/2411.02109 1/🧵

End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon. 🌐 evedesign.bio

Our Metabuli taxonomic classifier is now available as an app compatible with Windows, Linux, and macOS. It features an interactive visualization developed by @sunjaelee.bsky.social, along with improvements to Metabuli by @jbeom.bsky.social. 📄 academic.oup.com/bioinformati...

Easy and interactive taxonomic profiling with Metabuli App. It integrates database curation, read QC, taxonomic profiling, and visualization right on your desktop. No command line, server, or internet required. Now published in Bioinformatics! 🧵1/5 doi.org/10.1093/bioi... github.com/steineggerla...

Easy and interactive taxonomic profiling with Metabuli App academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/steineggerla...

Which mutations rewire function of regulatory DNA? Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models. Led by @EESetiz 1/N 🧵👇

You can get MSAs directly from AlphaFold DB now (alphafold.ebi.ac.uk). I also missed the FoldSeek implementation, which lets you search for structurally similar proteins direktly. This saves some clicking around. Neat!

AFDB v6 is already available in Foldseek! 🚀 search.foldseek.com foldseek databases Alphafold/UniProt50 afdb50 tmp foldseek easy-search query.cif afdb50 res.m8 tmp --cluster-search 0/1 (Reps only / all 241M) Thanks @ebi.embl.org and DeepMind for working with us to make it available to everyone.

#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!

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. www.biorxiv.org/content/10.1... (1/n)

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

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...

EcoFoldDB: Protein Structure-Guided Functional Profiling of Ecologically Relevant Microbial Traits at the Metagenome Scale enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

pip install ipsae from www.linkedin.com/in/ullah-sam... www.youtube.com/watch?v=A5ph... PyPI pypi.org/project/ipsae/ His github fork github.com/ullahsamee/I... My github github.com/DunbrackLab/... Paper www.biorxiv.org/content/10.1... For designed protein binders www.biorxiv.org/content/10.1...

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...

hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...

Does anyone know of a recent comparison of the main structural classification schemes of proteins and guidance on when to choose one? Something like this but including ECOD and perhaps seq-based schemes like Pfam, SUPERFAMILY and CDD. Img source (2020) pubmed.ncbi.nlm.nih.gov/32302382/

#structuralphylogenetics #strphy #3di

@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease. Details below careersearch.stanford.edu/jobs/computa... Plz RT

My favorite kinds of scientists are 1) Crazy enough to publish a paper where you give ecstasy to octopuses and study their social behavior 2) Detail-oriented enough to specify in the figure that 30 minutes is exactly 1800 seconds www.cell.com/current-biol...

If you use Boltz1/2, BioEmu, Chai1, or other MSA-dependent models, you’re likely using our ColabFold server. Please be considerate! Avoid large submissions across many IPs instead generate the MSA locally. Our server is an old-timer from 2014 and can’t handle that load.

An nf-core framework for the systematic comparison of alternative modeling tools: the multiple sequence alignment case study. #nfCore #ToolsComparison #MSA #NARgenomicsAndBioinformatics #Bioinformatics 🧬 🖥️ academic.oup.com/nargab/artic...

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...

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... & 🐍

The big difference is in the pairing. The MMseqs2 server pairs sequences based on species, while our old HHblits MSAs were paired based on genome proximity (number of genes apart). Working w/ @milot.bsky.social and @martinsteinegger.bsky.social we implemented the proximity filtering in server (3/4)

Beyond monomeric structures, accurate prediction of protein-protein interactions is crucial for understanding protein function. MSA Pairformer substantially outperforms all other methods in predicting residue-residue interactions at hetero-oligomeric interfaces

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

Yesterday @roman-bushuiev.bsky.social visited our lab. He gave a seminar talk about his recent work on DreaMS (www.nature.com/articles/s41...), and provided a hands-on training to my lab members. Looking forward to what we will discover using this awesome tool!

We are excited to share our preprint describing DirectContacts2! Here we develop a machine learning model to discriminate between direct and indirect protein interactions. We use our model to construct a highly accurate wiring diagram of the human cell. www.biorxiv.org/content/10.1...

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/...

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!

🌟 Exciting news! We’re launching three fully-funded postdoc positions for "New Horizons for Synthetic Phages” Join us in tackling antimicrobial resistance with cutting-edge synthetic biology + AI bioinformatics. Based at Flinders Uni in vibrant Adelaide. 👇 Read on for details! #Phage

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...

The seventh oral presentation of today with Michel van Kempen: "Extending 3Di: Increasing Protein Structure Search Sensitivity with a Complementary Alphabet" @iscb.bsky.social #ISMB_ECCB2025 #3DSIG

Nature Methods Senior Editor @drarunimasingh.bsky.social is currently attending the #ISMB2025 conference. If you'd like to meet her, send her an email!