This is a metaphor for the tech industry overall circa 2025

Welcome to another member of the antiSMASH ecosystem of tools. When @marnixmedema.bsky.social and I were putting together antiSMASH version 1.0 15 years ago, I don't think our wildest dreams would have predicted where our little tool would go.

Metagenomics colleagues! Anybody know if a good piece of software to test whether Illumina contigs are circular? @antobeck.bsky.social?

Merry X-SMASH! My first first author paper is out on bioRxiv! 🖥 We present epsSMASH, a comprehensive and high-throughput tool for predicting exopolysaccharide (exoPS) biosynthetic gene clusters (BGCs) in bacterial genomes 🦠🧬🧫 1/8

All you want for christmas is.... transposon mutagenesis! Our new work at @cultivarium.bsky.social screening lots of transposon vectors in lots of bacteria, from @charliegilbert.bsky.social and team. Transposon and promoter modular parts available on Addgene (pooled library will be there soon too)

WATCH: Here's the segment CBS News pulled from "60 Minutes" last night

Former NSA employee (16 years) with a pro tip for you. Released controlled document on the left, Epstein on the right. See the difference? In real redactions, some words, headers, and bits will almost always still be visible, but especially classification headers. These documents are UNCLASSIFIED

Team, what tool do you use to adapter clip PacBio data? I’m used to using PoreChop for ONT, but not sure for PacBio.

💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...

Respiratory endosymbionts, that allow their ciliate hosts to breathe nitrate instead of (or in addition to) oxygen are frequent members of the wastewater microbiome. 🦠 🖥️🧬 Great to see this work by @louison-nicolas.bsky.social published in ISME coummuncations! doi.org/10.1093/isme...

The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource

The GTDB website now has an ANI calculator based on skani that supports uploading of user genomes. Try it at gtdb.ecogenomic.org/tools/skani. Find more information about @jimshaw.bsky.social fantastic tool at www.nature.com/articles/s41....

GTDB is now cross-referenced from ENA genome assembly pages. Check it out: www.ebi.ac.uk/ena/browser/.... Thank you to @ebi.embl.org for support with setting up these links!

🧬🦠🚨 Another new paper alert, this time led by @maureenbug.bsky.social ! In collaboration with the Emerson lab and @titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ? doi.org/10.1093/narg...

100%, both ONT and PacBio (although most of what we do is not marine / streamlined genome). We just published a specific study of soil metag short- vs long-read, and we see that, among other things, long-reads assemble regions too complex for short reads academic.oup.com/nargab/artic...

What would a marine microbiome observing system meant to last decades look like? 🌊🦠 We explored this at the recent MMOFF Workshop, which brought together diverse partners to envision the future of marine microbiome observations. merenlab.org/workshops/MM...

Holy crap And theoretically, if one size-selected, could even be better? 7kb N50 is good but we’ve seen ~20% output improvement after size selection before.

Microflora Danica: What can you learn from collecting and sequencing 10,000+ samples from a single country? Check out our new paper in @nature.com to find out. Incredible work led by Caitlin Singleton, Thomas B. N. Jensen, and Mads Albertsen from @aau.dk. 🦠🧫🧬 www.nature.com/articles/s41...

🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...

Symbiont-coral partnerships Hologenome of B. pseudoalternata reveals a division of labor between deep-sea coral & symbionts. Host provides habitat & manages immunity, while symbionts recycle waste, supply nutrients, resist viruses & produce antioxidants www.cell.com/cell-host-mi...

Enormous milestone. All thanks to vaccinations!!!

Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years #phagesky www.nature.com/articles/s41...

Hey Team! What do you think are the best free digital notebooks these days. I've used: Evernote--great, but now it's paid TiddlyWiki wasn't bad, but got rid of scrollable code blocks Obsidian--basic, and I don't like not being able to scroll my code blocks like OG Tiddlywiki. Suggestions?

proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes academic.oup.com/nar/advance-... #jcampubs

gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats

Starting this week, I set aside one hour each week to meet ECRs outside my group who want to discuss career development, mentorship, or any non-technical professional questions. Here is a blog that explains my motivation for this and how to schedule a meeting: merenlab.org/2025/11/16/E...

“My magic beans can work miracles, they’re different from all of the fake magic beans out there” has been the sales pitch of charlatans since time immemorial.

I just published my weekly newsletter to >10K subscribers: The truth about AI coding for bioinformatics divingintogeneticsandgenomics.kit.com/posts/ai-po...

The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity academic.oup.com/gbe/article/... 🧬🖥️🧪

Chemical richness and diversity of uncultivated ‘Entotheonella’ symbionts in marine sponges www.nature.com/articles/s41... #jcampubs

Thought i'd show a bit of personality outside of metagenomics talk here. Caught a bit of the aurora in Ohio yesterday. Was my first time seeing one, and also trying to photograph it. I love how these turned out. Anybody else see it?

A wonderful collaboration between my lab and Andy Ellington and Edward Marcotte here at UT. We obtained lots of thermal stable plastic degrading enzymes from the deep sea (Guaymas Basin, Gulf of California)

“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla. doi.org/10.1038/s415... @benjwoodcroft.bsky.social @rhysnewell.bsky.social 🧵1/6

Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic. We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.

Metagenomics colleagues! I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data. Please help and share!

1/ Working with big data in R? Your wrangling just got a massive upgrade. duckplyr is now in the tidyverse—and it’s fast. Really fast. 🧵

PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks www.nature.com/articles/s41... #jcampubs

Our new paper in @currentbiology.bsky.social, led by @renatoamorais.bsky.social, examined the history and veracity of the alleged paradox and its patron Charles Darwin. www.cell.com/current-biol... @oclaripv.bsky.social @paulinenarvaez.bsky.social @utaustin.bsky.social @psl-univ.bsky.social

Heard of "Darwin's paradox"? It refers to Charles Darwin's observation that coral reefs are wildly productive despite occurring in nutrient-poor tropical oceans. Reefs are, so the story goes, oases in marine deserts 🏝️... Turns out that 2/3 of these assertions are very wrong... 🌐 🦑🧪 🧵⬇️

#NewResearch Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes @rstepanauskas.bsky.social & co #microsky www.nature.com/articles/s41...

Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp.... genzplyr is dplyr, but bussin fr fr no cap.

🚨New preprint out! We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8) www.biorxiv.org/content/10.1...

This is a very informative read: Seven data-driven lessons from the 2025 elections open.substack.com/pub/gelliott...

Omg I’m dying 😂😂😂…so…So Emily Austin, a right wing 'influencer' who works for Bibi and the GOP, launched 'Hot Girls for Cuomo'. Guess who didn't bother to register the URL when she did that? What do you think Hot Girls for Cuomo dot com leads to now?... 😄 Enjoy. [ HotGirlsforCuomo.com ]

Australia has so much clean energy they're literally giving it away. Meanwhile, GOP is in all-out war to stamp out solar www.abc.net.au/news/2025-11...

Nature suggests you use their "Manuscript Adviser" bot to get advice before submitting I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:

GcMeta - a new global resource of metagenome-assembled genomes and their encoded functions with an easy to use, interactive and searchable website academic.oup.com/nar/advance-...

Don’t forget to register and join us for our ASM-QLD and BrisJAMS careers beyond academia session this Thursday 😎

Interesting. Glad they also mention the small METR study showing that AI agents slowed down experienced coders, despite reporting productivity increase. I’d guess agents will be like the internet and research—useful for diligent experts and detrimental to those to dabble and don’t recognize slop.

Happy to have been involved in this paper. @nanoporetech.com www.nature.com/articles/s41...