iiinova — where your digital self keeps evolving

Reposted by Jaebeom Kim

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 01/08/2026

Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek

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Jaebeom Kim @jbeom.bsky.social · 22/07/2026

Metabuli GTDB232 database is now available. Try this to classify your metagenomc reads using 199,923 GTDB species, NCBI RefSeq viruses, and a human T2T genome. jaebeom-kim.github.io/metabuli-doc...

jaebeom-kim.github.io

New Databases - Metabuli - Sensitive and Specific Taxonomic Classification

Sensitive and specific metagenomic classification via joint analysis of amino acid and DNA

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Jaebeom Kim @jbeom.bsky.social · 21/07/2026

Results of the first ICTV Computational Virus Taxonomy Challenge are out! Metabuli was among the most accurate and fastest classifiers evaluated. doi.org/10.64898/202... Try Metabuli App, a desktop GUI for DB curation, read QC, classification, and visualization: jaebeom-kim.github.io/metabuli-doc/

doi.org

First community challenge for automated virus taxonomy

The rapid rate of virus discovery renders manual curation by taxonomy experts increasingly impractical, creating a need for reliable software that can reproducibly assign viral contigs to taxa at all ...

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Reposted by Jaebeom Kim

hbkgenomics.bsky.social @hbkgenomics.bsky.social · 06/06/2026

Does your designed active site already exist in nature? Is an uncharacterized protein hiding a catalytic site or a pocket? Folddisco answers both, searching millions of structures for a 3D motif in seconds. @natbiotech.nature.com 🧬 📄 www.nature.com/articles/s41... 🧵1/7👇

nature.com

Structural motif search across the protein universe with Folddisco - Nature Biotechnology

Folddisco enables protein structural motif search in million scale databases.

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Jim Shaw @jimshaw.bsky.social · 30/05/2026

Our method, savont, for generating amplicon sequence variants (ASVs) for long-read amplicons is now on bioRxiv. Work with @lh3lh3.bsky.social and help from @mkddueholm.bsky.social and team (Marie Riisgaard-Jensen, @kirk3gaard.bsky.social, Kasper Skytte Andersen) github.com/bluenote-157... 1/6

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Sholto David @sholtodavid.bsky.social · 17/05/2026

Surprised to discover that Thermo Fisher appears to show a fake western blot for the validation of one of their p53 antibodies. I've added a diagram to show the very similar bands. This does not appear to be one of the "published figures" but their own internal data.

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Jaebeom Kim @jbeom.bsky.social · 09/04/2026

Metabuli & Metabuli App v1.2 improve novel species classification with higher precision and recall. New light mode is 1.8× faster and requires 50% less storage while keeping precision. New RefSeq, GTDB, HRGM, and HROM databases added. 💾 github.com/steineggerla... 📄 doi.org/10.64898/2026.03.13.711249

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jingiyeo.bsky.social @jingiyeo.bsky.social · 03/04/2026

45 novel protein folds in the updated AFESM (AFDB + ESMatlas) manuscript: • 12 high-confidence folds in AFESM • 33 by ColabFold-repredicting 2.3M low-quality domains We show AFDB captures most domains already and ESMfold struggles with novelty 🌏 afesm.foldseek.com 📄 biorxiv.org/content/10.1...

afesm.foldseek.com

AFESM Clusters

Foldseek clustered 820M AlphaFold DB + ESMatlas structures

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Jaebeom Kim @jbeom.bsky.social · 03/04/2026

As an organizer, it was great to see such a large student participation! As a metagenomics researcher, learning about reference microbiome/virome was very helpful to my studies.

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Reposted by Jaebeom Kim

RSG Korea @rsg-korea.bsky.social · 15/03/2026

<RSG Korea 2026 1st Webinar> Human Reference Microbiome for the Era of Microbiome Medicine Prof. Insuk Lee (Yonsei University) March 24th, 2026, 17:00-18:00 (KST) Register here: docs.google.com/forms/d/e/1F... The Zoom link will be emailed before the webinar. #Microbiome #Metagenomics

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Reposted by Jaebeom Kim

EMBL-EBI @ebi.embl.org · 18/11/2025

Antimicrobial resistance (AMR) is a growing health threat, making infections harder to treat and complicating routine medical care. EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform. #WAAW2025 #ActOnAMR www.ebi.ac.uk/about/news/t... 🧬💻

ebi.ac.uk

A new gateway to global antimicrobial resistance data

New online portal connects bacterial genomes with experimental resistance data to support antimicrobial resistance research.

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Jaebeom Kim @jbeom.bsky.social · 16/10/2025

Easy and interactive taxonomic profiling with Metabuli App. It integrates database curation, read QC, taxonomic profiling, and visualization right on your desktop. No command line, server, or internet required. Now published in Bioinformatics! 🧵1/5 doi.org/10.1093/bioi... github.com/steineggerla...

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Reposted by Jaebeom Kim

Ben Langmead @benlangmead.bsky.social · 14/10/2025

New tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here: benlangmead.github.io/bwt-svg/. (H/t to @robert.bio for pointing me to pyodide!) Full repo: github.com/benlangmead/....

Illustration of Burrows-Wheeler Transform and many auxiliary structures from the input string how$now$brown$cow$#

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Reposted by Jaebeom Kim

Rachel Seongeun Kim @eunbelivable.bsky.social · 08/08/2025

Finally we got an end-to-end structural annotation tool for phages!

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Reposted by Jaebeom Kim

McSweeney's @mcsweeneys.net · 17/07/2025

"Writers have been using me long before the advent of AI. I am the punctuation equivalent of a cardigan—beloved by MFA grads, used by editors when it’s actually cold, and worn year-round by screenwriters. I am not new here."

buff.ly

The Em Dash Responds to the AI Allegations

“In recent months, a curious fixation has emerged in corners of academia: the em dash. More specifically, the apparent moral panic around how it is...

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Reposted by Jaebeom Kim

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 07/07/2025

Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬 📄 www.biorxiv.org/content/10.1... 🌐 search.foldseek.com/folddisco

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Heng Li @lh3lh3.bsky.social · 17/06/2025

Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment. arxiv.org/abs/2506.12986

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Dongwook Kim @dongwookkim.bsky.social · 03/06/2025

Unicore is now published on GBE 🚀 Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n 📃 doi.org/10.1093/gbe/evaf109

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RdRp Summit @rdrpsummit.bsky.social · 02/05/2025

Introducing our invited speaker for the session on 'Viral Dark Matter' we have Rachel Seongeun Kim from the Seoul National University!!!! The registrations for on-site & remote participation are still open! More info: RdRp.io #RdRpSummit2025

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Jaebeom Kim @jbeom.bsky.social · 25/04/2025

I'm presenting a poster about Metabuli, a metagenomic taxonomic classifier leveraging both DNA and protein sequences, at #RECOMB2025! Please come and share yout thoughts!

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Reposted by Jaebeom Kim

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 25/04/2025

Visit our posters at #RECOMB2025 for: Structural: MSAs, Virus DB, Core Genes, Motif Discovery, Multimer Clustering & Search, pLM Foldseek, Environmental analysis Metagenomics: Classification & Metabuli App GPU-based & RNA search, Proteome clustering, Novel Ribozyme discovery & get Marv stickers!

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Reposted by Jaebeom Kim

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 25/04/2025

@eunbelivable.bsky.social presented our viral protein structure database BFVD, including the new V2 update with improved predictions using 12 recycles for higher quality structures. Check out the paper and data here: 📄 academic.oup.com/nar/article/... 🌐 bfvd.foldseek.com #RECOMB2025

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Milot Mirdita @milot.bsky.social · 21/04/2025

I also updated the main #RECOMB2025 things-to-do map to include more tourist attractions and some of the standout vegan places I have visited myself (except the two places next to Yonsei, which I didn't have a chance to visit yet): www.google.com/maps/d/edit?...

google.com

RECOMB2025 Things to do - Google My Maps

RECOMB2025 Things to do

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Milot Mirdita @milot.bsky.social · 21/04/2025

Finding vegetarian and vegan food in Korea can be tricky. I added a mini-guide to the #RECOMB2025 things-to-do site with some resources. Let me know if you want more recommendations! recomb.org/recomb2025/t...

recomb.org

RECOMB 2025 - Things to do

RECOMB 2025 - Seoul, South Korea

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Reposted by Jaebeom Kim

Rachel Seongeun Kim @eunbelivable.bsky.social · 31/03/2025

Big Fantastic Virus Database (BFVD) version 2 improves 31% of predictions through 12 ColabFold recycles. PAEs and MSAs now also available for download and in the webserver. 🌐https://bfvd.foldseek.com 💾https://bfvd.steineggerlab.workers.dev/ 1/3

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Jaebeom Kim @jbeom.bsky.social · 27/03/2025

🚀 New Metabuli DB is out! It includes quality-filtered GTDB R220, RefSeq viruses, and the human T2T. Prokaryotes follow the GTDB taxonomy; viruses and the human genome use NCBI taxonomy. Download it and expand with genomes of your choice using "updateDB" command. metabuli.steineggerlab.workers.dev

metabuli.steineggerlab.workers.dev

Metabuli Databases

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Reposted by Jaebeom Kim

Ragnar {Groot Koerkamp} @curiouscoding.nl · 14/03/2025

Just published simd-sketch, a crate for fast bucket sketches. It's 7x to 30x faster than BinDash, by using the simd-minimizers crate for fast hashing, and a nearly branch-free implementation. Here's a blogpost with a survey of minhash history & methods, and evals: curiouscoding.nl/posts/simd-s...

Schematic of the mod-bucket algorithm: all k-mer hashes are partitioned into s buckets via their remainder mod s. Then, in each bucket the smallest hash is selected.

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Jaebeom Kim @jbeom.bsky.social · 13/03/2025

Metabuli App preprint is out! 💻Taxonomic classification & interactive visualization—right on your laptop 🛠️Create new databases or update existing ones with new sequences. 🧵1/5 github.com/steineggerla... www.biorxiv.org/content/10.1101/2025.03.10.642298v1

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Milot Mirdita @milot.bsky.social · 27/11/2024

MMseqs2 Release 16 Highlights: GPU-accelerated search📄, ORF or new 6-frame translated search modes, contig taxonomy always keeps the longest ORF, bug fixes (reduced memory and higher sensitivity) and relicensed as MIT 📄 biorxiv.org/content/10.1... 💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶

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Jaebeom Kim @jbeom.bsky.social · 30/09/2024

Easy taxonomic profiling with the Metabuli App! Explore your samples with publication-ready Sankey and Krona plots. We accelerated Metabuli further, classifying 2x22M reads vs. GTDB in just 43 min on a MacBook Pro M2. 🧵1/4 🚀https://github.com/steineggerlab/Metabuli-App

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