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Excited to share “Bin Chicken”, substantially improving genome recovery through rational metagenomic assembly. Applied to public 🌍 metagenomes, it recovered 24,000 novel species 🦠, including 6 novel phyla. doi.org/10.1101/2024.1… Ben WoOdcroft Rhys Newell Centre for Microbiome Research 🧵1/6

Can LLM agents discover novel protein functions? Introducing Gaia Agent 🌎 🤖: an AI biologist capable of reasoning across genomic contexts to predict functions of proteins! Gaia Agent is now integrated with Gaia Search at gaia.tatta.bio

New year, new assemblies! I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes! It's the successor to Trycycler, designed to be faster and less reliant on user intervention. Check it out: github.com/rrwick/Autocyc… (1/5)

I'm very happy to report that Matthew S. Schechter's PhD work is now online as a pre-print: "Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities" biorxiv.org/content/10.110… Aaand here's a little 🧵 about it.

In Science Advances: a microbial genome census from publicly available databases using publicly available genome sequence data generated over the past three decades. Nikos Kyrpides Integrated Microbial Genomes & Microbiomes (IMG/M) DOE Office of Science biosciences.lbl.gov/2025/01/17/tak…

This is such an interesting study and important overview of the metagenomic sequence diversity! There is a huge discrepancy in the distribution of diversity between cultivated microbes and metagenomes. i.e. Over 95% of the isolated species can't be recovered from metagenomes.😮

OMG/gLM2 has been accepted at #ICLR2025! Congratulations to the team 🥳

One of the great things about bioinformatics is how open it can be. Contributing to a project you admire can actually get you involved in it :)

Publishing a paper in Nature while based in Brazil is an incredible achievement. Huge congratulations to the authors! I'm excited to give this a proper read :)

💛LoVis4u - a visualisation tool for comparative genomics and sequencing coverage profiles is now published! See our paper in NAR GB: doi.org/10.1093/nargab…

Dive into our lab’s first peer-reviewed publication—co-led with our friends Ben Adler and Muntathar Al-Shimary from the Doudna lab! If you’ve already read the preprint, don’t miss the new updates: doi.org/10.1038/s41564… Nature Microbiology

Updates coming to #NCBITaxonomy! We are introducing two new ranks, domain and realm, and discontinuing the rank superkingdom. Learn more: ow.ly/Nn8050V7Hfv

CoverM is published! CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformatics…

🚨 Just out in Science: 2/3 of bacterial gene families have a preferred position on the chromosome—and natural selection put them there! science.org/doi/10.1126/sc… Heinrich-Heine-Universität Düsseldorf CEPLAS

Is the genome just a bag of genes? A new paper in Science Magazine now reports that for two thirds of an organisms' genes the position along the chromosome is actually very tightly constrained! Amazing work from my favorite night scientist Martin Lercher and his team!

Small Things Considered! schaechter.asmblog.org/schaechter/202…

🔥 Pfam 37.3 just dropped! 🚀 353 incredible new protein families + 7 new clans! 🧬✨ Revolutionise your research NOW via InterPro website: ebi.ac.uk/interpro/entry…, API & Pfam FTP!

Episode 4 introduces our latest preprint! schaechter.asmblog.org/schaechter/202…

Just published! Even NASA cleanrooms—designed to be ultra-clean—harbor resilient, novel bacteria. 26 new species were found, some forming biofilms, resisting radiation, and producing biotech-relevant compounds. Check it here: microbiomejournal.biomedcentral.com/articles/10.11…

🦠💐🦠 人生一報目のプレプリントが公開されました！ I'm thrilled to share the first-first preprint in my life! Host range and ARG dissemination are shaped by distinct survival strategies of conjugative plasmids biorxiv.org/content/10.110… (1/🧵, Japanese follows English) 💐🦠💐