Wrapping up an incredible final day at the APSPM meeting! Huge thanks to the organizers @cpuentelelievre.bsky.social @proteinmechanic.bsky.social Jordan Douglas and all the speakers for the brilliant talks and rich discussions. Beautiful Brisbane! #StrPhy #StrPhy26 #StructuralPhylogenetics

Indeed! Very nice collaboration with @irenedelrey.bsky.social @sebasn1.bsky.social @konsmitsi.bsky.social @jtrinidad13.bsky.social Montse Elias, Padhu & others to decipher the origin of the #plasmalogen biosynthesis pathway. @ibe-barcelona.bsky.social @icreacommunity.bsky.social @csic.es

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

FANTASIA's paper is finally out! Check it out if you're interested in alternative methods to homology for functional annotation in nonmodel organisms 🦐🐙🪱🧬🐝🪲 @gemmaeling.bsky.social @amrojasm.bsky.social @ibe-barcelona.bsky.social @cabd-upo-csic.bsky.social @csic.es www.nature.com/articles/s42...

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🧵

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/...

New paper from the lab from Sriram Garg in my group. We introduce a general substitution matrix for structural phylogenetics. I think this is a big deal, so read on below if you think deep history is important. academic.oup.com/mbe/advance-...

InterPro just got one of its biggest updates ever. Now with 1.8 billion AI-driven protein annotations, AlphaFold-based TED domains, and viral proteins from the Big Fantastic Virus Database (BFVD). See it all at www.ebi.ac.uk/interpro 🖥️🧬 @interprodb.bsky.social

Excited to share the results of my PhD! Using advanced protein structure comparisons, we uncovered remote homologs and revealed essential eukaryotic genes “lost” in kinetoplastids – what I like to call the “missing gears.” Discover more: journals.plos.org/plospathogen...

Not really my announcement to make--I am but a lesser co-author--but IQ-TREE 3 has just been released! (Most credit to Minh Bui and @roblanfear.bsky.social and their labs) ecoevorxiv.org/repository/v...

🚨 New paper alert! 🚨 A robustly rooted tree of eukaryotes sheds light on their deep evolutionary ancestry—suggesting that the Last Eukaryotic Common Ancestor (LECA) may have had an excavate-like cell architecture. 🧵🔬 (1/) www.nature.com/articles/s41...

🚀 #AlphaFold Database update AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures. www.ebi.ac.uk/about/news/u... @pdbeurope.bsky.social

Polarization has become a serious threat to shared reality, democracy, and even health "Thousands of people were dying needlessly because they didn’t trust medical advice, or their government, or mainstream media” Reducing partisan animosity is doable, but tricky: www.pnas.org/doi/epub/10....

📜 Yerba mate (Ilex paraguariensis) genome provides new insights into convergent evolution of caffeine biosynthesis 🧑‍🔬 Federico A. Vignale, Andrea Hernandez Garcia, Todd J. Barkman, Adrian G. Turjanski, et al. 📔 @elife.bsky.social 🔗 elifesciences.org/articles/104... #️⃣ #PlantSciene #PlantMetabolism

This week @science.org Sarfatis, Moffitt et al. from @bostonchildrens.bsky.social @harvardmed.bsky.social @broadinstitute.org Highly multiplexed spatial transcriptomics in bacteria | Science www.science.org/doi/10.1126/... #microsky #microbial #microbiology #genomics #transcriptomic 🦠🧫

The Foldseek webserver for fast protein structure searches now features a Sankey tree taxonomy visualization and filter, allowing to subset hits by clades. Developed by my talented student @sunjaelee.bsky.social. Try it out! 🌐 search.foldseek.com