Our structural core gene pipeline Unicode is now published at GBE 📄 doi.org/10.1093/gbe/... Please also check out @dongwookkim.bsky.social’s 🧵 bsky.app/profile/dong...

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

Can't wait for when I can vibe code a production recommender system. Until then, here's some system designs: • Retrieval vs. Ranking: eugeneyan.com/writing/syst... • Real-time retrieval: eugeneyan.com/writing/real... • Personalization: eugeneyan.com/writing/patt...

What industrial recsys papers have you enjoyed or found useful in the past year or two? Sharing my list: # 1. Integrating LLMs into recsys 1.1. LLM-augmented recommenders • Better Generalization with Semantic IDs: A Case Study in Ranking for Recommendations - arxiv.org/abs/2306.08121

SNU Profs Woon Ju Song & Martin Steinegger (Biology) developed the AI-based SeekRank algorithm to discover enzymes for cancer immunotherapy. doi.org/10.1093/nar/...

Unicore identifies single-copy protein structures across genomes using Foldseek, bypassing slow structure predictions by utilizing 3Di predictions from ProstT5, enabling rapid phylogenetic inference at the tree-of-life scale. 1/n 📄 www.biorxiv.org/content/10.1... 💾 github.com/steineggerla...

Unicore enables scalable and accurate phylogenetic reconstruction with structural core genes https://www.biorxiv.org/content/10.1101/2024.12.22.629535v1

And if you're looking for more learning over the long thanksgiving weekend, this could be a good place to start: eugeneyan.com/start-here/

Our Big Fantastic Virus Database (BFVD) is now published NAR! It contains protein structure predictions of major viral clades, enhanced by petabase-scale homology search and it's explorable on the web. 🌐 bfvd.foldseek.com 💾 bfvd.steineggerlab.workers.dev 📄 academic.oup.com/nar/advance-...