Fellow microbial immunity, mobile elements, and plasmid enthusiasts: the paper of our wonderful @BruriaSamuel on anti-defense genes in plasmids is now published in @Nature!!! Check out her thread below for highlights of our new results. 1/2

Genomes are full of dark matter of unknown functions. We present Minerva, a new method for discovery guided by genome language models. Minerva reveals the interactions hidden in non-coding DNA, pointing to hundreds of new putative RNAs and repetitive elements per bacterial genome. Minerva allows us to find and study elements invisible to traditional methods at orders of magnitude greater scale than before.

Excited to share Minerva, our approach using genome language models for biological discovery! Using Minerva, we find that UG27 reverse transcriptase systems encode variable arrays of diverse ncRNAs with a shared structure, each templating a short DNA hairpin. With @garykbrixi.

ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/BindCra…

VIPR is now out in @ScienceMagazine! What started with a mysterious RNA led us to an unexpected way of recognizing DNA, as well as some clues to CRISPR’s origins. So happy to share these two papers with an incredible team. Links below; original discovery thread here ↓

Chromatin structure controls defense island expression! Why do some systems defend on plasmids but fail natively? H-NS is key. Removing it boosts defense and beats anti-defense proteins but raises toxicity. Lab strains still hide novel immunity modules! biorxiv.org/content/10.64898…

Also a highly experimental port of these models into WebGPU, allowing direct prediction on your 💻: localfold.org WARNING: will drain battery🪫, overheat 🔥💻 & eat your data plan 📱 Started by Martin Steinegger as AF2 port to WebGPU martin-steinegger.github.io/… (3/3)

ColabFold 1.6.3 is out! 2.5x faster, pip-installable, ipSAE+pDockQ2 scores. Thanks Choonghwan Lee, Marielle Russo, Gyuri Kim, Martin Steinegger, Milot Mirdita 🐍 pip install colabfold[alphafold] (1/3)

Published now in @Nature - "Long-read sequencing reveals pre-meiotic gene conversion in sperm". We show an unexpected source of new genetic variation in human sperm, occuring earlier in development than previously thought. Check it out here: nature.com/articles/s41586-0… Thread: 1/

The leading region of many plasmids is adapted for translational efficiency doi.org/10.1093/nar/gkag810

Toxin-Antitoxin systems are thought to induce death or dormancy under some stress conditions. Focusing on the well studied MazEF system, we now show that this is not always the case. biorxiv.org/content/10.64898…

Riboseek encodes RNA and DNA sequences as overlapping di-mers and detects homologs more sensitively than BLASTN and nhmmer. It produces alignments 250-fold faster than nhmmer and 376-fold faster than rMSA. doi.org/10.64898/2026.07.31.…

Out now! In collaboration with Hiroshi Nishimasu's lab, we uncover how a dual reverse transcriptase immune system builds double-stranded DNA from both RNA and protein templates. sciencedirect.com/science/ar… Previous thread for the preprint:

קטע מדהים מיומן ברלין של חסידת אומות העולם רות אנדריאס-פרידריך. בכלל המלצת מעקב חמה על מני אדלר שמביא כל יום קטעים נפלאים מספרי הסטוריה והופך את הפיד למרתק

1/4 Every good defence needs a backup 🛡️⚔️ Out now in @NatureRevMicro our Comment on "𝗶𝗺𝗺𝘂𝗻𝗲 𝘀𝗮𝗳𝗲𝗴𝘂𝗮𝗿𝗱𝗶𝗻𝗴"! 🎉 🔗 nature.com/articles/s41579-0…

1/10 🚨Preprint! One RING to rule them all (phages)👑💍⚔️ Bacteria build giant DNA-scaffolded RNase rings (larger than the ribosome!) to shut down viral infection🧬🧵👇 🔗biorxiv.org/content/10.64898…

My paper on reduced amino acid alphabets for protein language models is out in Bioinformatics! I'll be giving a talk on this on Thursday at ISMB, would love to chat there. #ISMB2026 doi.org/10.1093/bioinformati…