Jaebeom Kim
@jbeom.bsky.social
Developing bioinformatics software in Steinegger lab. at Seoul National Univ.
Pinned
Jaebeom Kim
@jbeom.bsky.social
· Oct 16
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...
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...
Reposted by Jaebeom Kim
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...
🧬💻
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...
🧬💻
A new gateway to global antimicrobial resistance data
New online portal connects bacterial genomes with experimental resistance data to support antimicrobial resistance research.
www.ebi.ac.uk
November 18, 2025 at 9:59 AM
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...
🧬💻
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...
🧬💻
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...
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...
October 16, 2025 at 7:29 AM
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...
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...
Reposted by Jaebeom Kim
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/....
October 14, 2025 at 8:48 PM
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/....
Reposted by Jaebeom Kim
Finally we got an end-to-end structural annotation tool for phages!
Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Protein Structure Informed Bacteriophage Genome Annotation with Phold
Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...
www.biorxiv.org
August 8, 2025 at 8:26 AM
Finally we got an end-to-end structural annotation tool for phages!
Reposted by Jaebeom Kim
Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Protein Structure Informed Bacteriophage Genome Annotation with Phold
Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...
www.biorxiv.org
August 8, 2025 at 7:11 AM
Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Jaebeom Kim
"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."
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...
buff.ly
July 17, 2025 at 6:20 PM
"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."
Reposted by Jaebeom Kim
My colleague asked me to circulate this job posting for Professor / Associate Professor in Computational Biology / Genomics at the University of Tokyo (P.S. I'm not affiliated):
www.k.u-tokyo.ac.jp/en/informati...
www.k.u-tokyo.ac.jp/en/informati...
Call for applications (professor or associate professor), Department of Computational Biology and Medical Sciences (Deadline Sep 30) ｜Job Opportunities｜Information｜Graduate School of Frontier Scienc...
Call for applications (professor or associate professor), Department of Computational Biology and Medical Sciences (Deadline Sep 30) ｜Job Opportunities｜Information｜GSFS offers both master‘s and doct...
www.k.u-tokyo.ac.jp
July 15, 2025 at 3:24 AM
My colleague asked me to circulate this job posting for Professor / Associate Professor in Computational Biology / Genomics at the University of Tokyo (P.S. I'm not affiliated):
www.k.u-tokyo.ac.jp/en/informati...
www.k.u-tokyo.ac.jp/en/informati...
Reposted by Jaebeom Kim
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
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
July 7, 2025 at 8:21 AM
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
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
Reposted by Jaebeom Kim
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
arxiv.org/abs/2506.12986
June 17, 2025 at 1:49 AM
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
arxiv.org/abs/2506.12986
Reposted by Jaebeom Kim
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
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
June 3, 2025 at 6:55 AM
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
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
Reposted by Jaebeom Kim
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
The registrations for on-site & remote participation are still open! More info: RdRp.io
#RdRpSummit2025
May 2, 2025 at 2:54 PM
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
The registrations for on-site & remote participation are still open! More info: RdRp.io
#RdRpSummit2025
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!
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!
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!
April 25, 2025 at 7:52 AM
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!
Reposted by Jaebeom Kim
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!
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!
April 25, 2025 at 7:46 AM
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!
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!
Reposted by Jaebeom Kim
@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
📄 academic.oup.com/nar/article/...
🌐 bfvd.foldseek.com
#RECOMB2025
April 25, 2025 at 5:02 AM
@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
📄 academic.oup.com/nar/article/...
🌐 bfvd.foldseek.com
#RECOMB2025
Reposted by Jaebeom Kim
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?...
www.google.com/maps/d/edit?...
RECOMB2025 Things to do - Google My Maps
RECOMB2025 Things to do
www.google.com
April 21, 2025 at 1:48 PM
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?...
www.google.com/maps/d/edit?...
Reposted by Jaebeom Kim
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/recomb2025/t...
RECOMB 2025 - Things to do
RECOMB 2025 - Seoul, South Korea
recomb.org
April 21, 2025 at 4:42 AM
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/recomb2025/t...
Reposted by Jaebeom Kim
Congratulations to @imartayan.bsky.social and @curiouscoding.nl whose paper on fast minimizer computation with simd has been accepted to SEA 2025 🙌🏻 www.biorxiv.org/content/10.1...
SimdMinimizers: Computing random minimizers, fast
Motivation Because of the rapidly-growing amount of sequencing data, computing sketches of large textual datasets has become an essential preprocessing task. These sketches are typically much smaller ...
www.biorxiv.org
April 1, 2025 at 8:23 AM
Congratulations to @imartayan.bsky.social and @curiouscoding.nl whose paper on fast minimizer computation with simd has been accepted to SEA 2025 🙌🏻 www.biorxiv.org/content/10.1...
Reposted by Jaebeom Kim
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
🌐https://bfvd.foldseek.com
💾https://bfvd.steineggerlab.workers.dev/
1/3
March 31, 2025 at 5:07 AM
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
🌐https://bfvd.foldseek.com
💾https://bfvd.steineggerlab.workers.dev/
1/3
🚀 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
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 Databases
metabuli.steineggerlab.workers.dev
March 27, 2025 at 7:43 AM
🚀 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
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
Reposted by Jaebeom Kim
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...
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...
March 14, 2025 at 12:35 AM
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...
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...
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
💻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
March 13, 2025 at 8:51 AM
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
💻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
Reposted by Jaebeom Kim
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 🖥️🧬🧶
📄 biorxiv.org/content/10.1...
💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶
November 27, 2024 at 9:08 AM
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 🖥️🧬🧶
📄 biorxiv.org/content/10.1...
💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶
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
🚀https://github.com/steineggerlab/Metabuli-App
September 30, 2024 at 1:20 AM
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
🚀https://github.com/steineggerlab/Metabuli-App