Eubiota: Modular Agentic AI for Autonomous Discovery in the Gut Microbiome https://www.biorxiv.org/content/10.64898/2026.02.27.708412v1
01.03.2026 01:47
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Eubiota: Modular Agentic AI for Autonomous Discovery in the Gut Microbiome https://www.biorxiv.org/content/10.64898/2026.02.27.708412v1
Introducing Seqera AI CLI, your AI-powered terminal assistant for @nextflow.io development. 🚀Build locally, deploy to the cloud, debug intelligently. All from one interface.🧵 hubs.la/Q045kK-10
Another product that is cancelled by @nanoporetech.com : ElysION, that was just introduced in September 2024. aseq.substack.com/p/oxford-fy2...
Nanopore sequencing reaches amplicon sequence variant (ASV) resolution https://www.biorxiv.org/content/10.64898/2026.02.26.708165v1
We've seen a big increase in the number of long-read #metagenomics publications, especially those using #PacBio HiFi data. Also very encouraging to all the new tools for long-read metagenome assembly & taxonomic profiling.
Complete list of publications: github.com/PacificBiosc...
Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025.
allthebacteria.readthedocs.io/en/latest/ov...
In case you missed it: our review titled "Spatial structure: shaping the ecology and evolution of microbial communities" is out! 🚨
Let me hit you with some highlights on why spatial structure matters. (and why you should care!)
Sharing is appreciated 🙏 🧵👇
doi.org/10.1093/fems...
Our perspectives piece on Agentic AI for biomedical research has been published in Nature Biotechnology www.nature.com/articles/s41... #agenticAI #artificialintelligence #agents
Our paper on foldback artifacts in long-read sequencing is now published in BMC Genomics!
We introduce Breakinator to flag foldback and chimeric artifacts across library types, sequencers, and chemistries.
Paper: link.springer.com/article/10.1...
With Matthew Meyerson and @lh3lh3.bsky.social
Claude Code just shipped "Remote Control" and it's a game-changer.
You can now control your local Claude Code session from your phone.
Here's how it works:
Comparison of read mappings at HG002 chr4:40,294,825-40,295,700, showing conventional (pbmm2) read mappings (above) and portello mappings (below). The same set of unaligned input reads were input into each mapping process.
What if you could improve small variant accuracy, CNV inference, and interpretability of your HiFi WGS data by taking a different approach to read mapping? Our new preprint describes portello, a method which demonstrates the potential for such improvements. (1/5)
How to get a universal vaccine vs respiratory threats?
Block via the nasal mucosa
@science.org
www.science.org/doi/10.1126/...
@natrevimmunol.nature.com
www.nature.com/articles/s41...
Every few months, I write an updated, idiosyncratic guide on which AIs to use right now.
My new version has the most changes ever, since AI is no longer just about chatbots. To use AI you need to understand how to think about models, apps, and harnesses. open.substack.com/pub/oneusefu...
Rapid dissemination of Staphylococcus aureus in the neonatal intensive care unit is associated with invasive infection www.nature.com/articles/s41...
New blog post: ONT read QC strategies for assembly
rrwick.github.io/2026/02/05/r...
Mini-study comparing a few QC/subsampling approaches, plus practical notes from my experience.
First evidence that healthy donor fecal microbiota transplant, added to immunotherapy, can enhance efficacy vs cancer
3 clinical trial reports (renal, small cell lung, melanoma)
nature.com/articles/s41...
nature.com/articles/s41...
nature.com/articles/s41...
Holy 💩!
Huh. At what point does an 800-pound gorilla officially become a monopoly?
The decrease in the price of the assets is interesting too - $60M cheaper than PacBio bought them. Tech that didn’t prove out? Or just a reflection on the market? 🦍🧪
A novel polyhydroxyalkanoate-storing bacterium Thauera carbonocopians sp. nov. isolated from a sequencing batch reactor fed with volatile fatty acids www.nature.com/articles/s41...
Genome contamination may lead to an overestimation of horizontal gene transfer inferences www.nature.com/articles/s41...
Aeromonas in South Asia: genomic insights into an environmental pathogen and reservoir of antimicrobial resistance www.nature.com/articles/s41...
Curious, what's the best-practice tool at this point for taxonomically classifying long reads from metagenomes from less well-characterised environments?
My impression is that Kraken will give lots of false positives and mis-classify taxa not in its database.
Please share around for visibility.
A comprehensive catalogue of receptor-binding domains in extracellular contractile injection systems www.nature.com/articles/s41...
alignment of reads to reference genome. a poly-t region was created by a single read in the dataset.
interesting nanopore sequencing experience. found this in the middle of my genome assembly. driven by a single read with a big homopolymer in the middle of it? pretty weird, something to look out for i guess (i wonder how many of these are in Genbank...)
Adding to the slew of recent articles about Claude Code. Not behind, but at the forefront: On feeling overwhelmed by AI progress, and why that means you're exactly where you need to be. doi.org/10.59350/gdj...
Two new studies that suggest an association between the consumption of preservative additives and an increased incidence of cancer (www.bmj.com/content/392/...) and type 2 diabetes (www.nature.com/articles/s41...)
Large-scale testing of antimicrobial lethality at single-cell resolution predicts mycobacterial infection outcomes www.nature.com/articles/s41...
Genomic dissection of the clonal background and global dissemination of hypervirulent Klebsiella pneumoniae CG23-KL57 lineage www.nature.com/articles/s41...
Bacterial chromatin remodeling associated with transcription-induced domains at pathogenicity Islands www.nature.com/articles/s41...
Exposure to natural daylight has important and salutary impact on our metabolism, and that's especially noted in people with Type 2 diabetes
cell.com/cell-metabol...
Now published in Nature Biotechnology:
go.nature.com/44P7nSm
If you missed it, the TL;DR is in my April thread below
