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🧵

New impact case study outlines the impressive economic & scientific value of UniProt - the world-leading open data resource for protein sequence & functional information. Users save up to 219 hours per year, equivalent to net benefits of up to €5,475 per user. www.ebi.ac.uk/about/news/a...

Excited for New Approaches and Concepts in Microbiology 2025 with sessions on Bacterial systems biology, Bacterial cell biology & protein machines, Microbiomes, Environment & evolution, Pathogenesis & phage, Antibiotic discovery, mechanisms, and resistance. #EESMicrobiology

Very excited to share our preprint on a new resource: the Encyclopaedia of Viral Anti-Defence Systems (EVADES)! This is the main result of my PhD at ‪EMBL-EBI (@ebi.embl.org)‬ and the University of Cambridge (@cam.ac.uk‬)! 🔗 www.biorxiv.org/content/10.1... 🧵1/n"

Want to know how the ligands interact with proteins beyond model cell lines, e.g., in tissues or bacteria? Interested in membrane targets? Check out our High-Throughput PELSA method which allows you do all these cool screenings for dozens of ligands within two hours! www.biorxiv.org/content/10.1...

And here it is, the completed BASEL collection finally published as early access in @plosbiology.org - see the thread for more details. 🤗🧬🎣

Now online! Jumbo phage killer immune system targets early infection of nucleus-forming phages

Join our favorite microbiology meeting! Fantastic talks, poster sessions, new technologies, and all the hot areas of microbiology in a great environment - experts in cell & systems biology, microbiomes, environment & evolution, pathogenesis, phage & antibiotics DON’T MISS abstract deadline, April 1

Updated validation reports are now available for structures determined using integrative & hybrid methods (IHM) that extends to structures derived from Crosslinking-MS data, along with previously supported Small Angle Scattering (SAS) data! ⬇️ Read more⬇️ www.wwpdb.org/news/news

🚀 #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

It is finally out! Muntathar Al-Shimary, @doudna-lab.bsky.social , @cresslab.bsky.social and I present a gene knockdown tool that works in diverse bacteriophages: CRISPRi through antisense RNA Targeting (CRISPRi-ART)! Check it out @naturemicrobiol.bsky.social www.nature.com/articles/s41...

In our latest review, we explore 12 deep-learning tools for metagenomic analysis, covering their strengths, limitations, and key applications. We hope it serves as both a resource and inspiration for new ways to analyze metagenomic data. Great work by Eli Levy Karin! 📄 doi.org/10.1093/nsr/...

New version of DefenseFinder available defensefinder.mdmlab.fr (& cli) Now encompassing 263 systems (+111 this year..!). Thanks @ftesson.bsky.social, DefenseFinder grandmaster. Full list of systems here: defense-finder-models/List_system_article.md at master · mdmparis/defense-finder-models

Excited to see this huge piece of work out 🎉 Congrats to everyone involved! If you ever wanted to read a 8in1 paper grab a cup of tea and enjoy 📖

We are very happy to present our work on N-glycoproteomics!🍬 Our method enables the selective enrichment and precise quantification of intact N-glycopeptides to explore the dynamics of glycosylation microheterogeneity. www.nature.com/articles/s41...

🚨 🧬 Updated preprint on the completed BASEL collection - what's new? Some fun with bacterial immunity and a new P22 relative infecting E. coli K-12. A thread 🧵

Excited to share our preprint with @savitski_lab led by @tarabartolec.bsky.social, @KMitosch & Clément Potel! We uncovered a mechanism by which the T7 phage broadly counteracts DNA-targeting bacterial defenses by deploying a loose cannon kinase in its genome @embl.org www.biorxiv.org/content/10.1...

1/11 - With Karin Mitosch and Clément Potel + colleagues in Savitski lab and @typaslab.bsky.social @embl.org, I’m very happy to share our discovery of a hyper-promiscuous phage protein kinase (T7K) which broadly deactivates bacterial defenses! 🦠 www.biorxiv.org/content/10.1...

You have to believe you can write a manuscript in a week, so that it will end up only taking three months.

Delighted to publish my new molecular animation: DNA Break Repair by Homologous Recombination youtu.be/Xe-83tBcxhs

The holobiont is more than just corals, and has spin off terms (can you say holoproteome? better than metaproteome imo). Makes sense and actually love the term is going places. (Michelle Heck, not here yet, just share this paper with me) #proteomics www.science.org/doi/10.1126/...

(BioRxiv All) Improving AlphaFold 3 structural modeling by incorporating explicit crosslinks: AlphaFold 3 has significantly advanced the modeling of macromolecular structures, including proteins, DNA, RNA, and their interactions with small molecules or… http://dlvr.it/TGZQsY #BioRxiv #MassSpecRSS

The eucaryote needs a bacteria which needa a phage which needs a kinase which needs a rna which needs a solvent molecule to steer the thing

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-...