Dongwook Kim

Planetary microbiome structure and generalist-driven gene flow across disparate habitats Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersion, driven by natural processes and human activities, interconnects mic...

Our new preprint is out!
www.biorxiv.org/content/10.1...
In this study, we present the largest systematic analysis of microbiome structure and function, integrating 85K uniformly processed metagenomes from diverse habitats worldwide.
@podlesny.bsky.social @jonas-bio.bsky.social @borklab.bsky.social

OrthoFinder just dropped a major update

It’s faster, more accurate, and ready for thousands of genomes

Let’s break it down (1/10)

github.com/OrthoFinder/...
www.biorxiv.org/content/10.1...

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

A general substitution matrix for structural phylogenetics. Abstract. Sequence-based maximum likelihood (ML) phylogenetics is a widely used method for inferring evolutionary relationships, which has illuminated the

New paper from the lab from Sriram Garg in my group. We introduce a general substitution matrix for structural phylogenetics. I think this is a big deal, so read on below if you think deep history is important. academic.oup.com/mbe/advance-...

This work was done by talented @sukhwanpark.bsky.social and me, supervised by amazing @martinsteinegger.bsky.social !

Try Unicore now 👉 conda install -c bioconda unicore
Code and tutorial: 🌐 github.com/steineggerlab/unicore
Manuscript: 🌐 doi.org/10.1093/gbe/evaf109

Unicore is fast, accurate, and universal. Unicore reconstructed consistent phylogeny of bacterial/fungal species, while maintaining linear time scale over the input size. Besides, Unicore works with any given taxa, presenting scalable and universal method for structure-based phylogeny. 🧵3/n

With Unicore, we identified 13 structural core genes from 166 species across the Tree of Life, where 8 of them could only be defined using structures. Projected on the Tree of Life reconstructed with Unicore, you can see the universally conserved structure of one of the structural core genes. 🧵2/n

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

AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵
🌐 afesm.foldseek.com
📄 www.biorxiv.org/content/10.1...

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!

Not really my announcement to make--I am but a lesser co-author--but IQ-TREE 3 has just been released!

(Most credit to Minh Bui and @roblanfear.bsky.social and their labs)

ecoevorxiv.org/repository/v...

🚀 #AlphaFold Database update

AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.

www.ebi.ac.uk/about/news/u...

@pdbeurope.bsky.social

The PAN-GO paper is a remarkable milestone. It not only provides the most comprehensive picture of human gene function to date, but also carefully maps this knowledge across the tree of life! Congratulations @marcfeuermann.bsky.social, Pascale Gaudet & collaborators!

www.sib.swiss/news/sib-hel...

In our latest review, we explore 12 deep-learning tools for metagenomic analysis, covering their strengths, limitations, and key applications. We hope it serves as both a resource and inspiration for new ways to analyze metagenomic data. Great work by Eli Levy Karin!
📄 doi.org/10.1093/nsr/...

FastOMA retains OMA’s high precision accuracy and even improves upon it in terms of recall, positioning it on the Pareto frontier of orthology inference methods. FastOMA is not only fast but also accurate. a, QfO benchmar, agreement with SwissTree reference phylogeny covering manually curated gene trees. The error bars indicate 95% confidence intervals comparing FastOMA with EnsemblCompara, Domainoid, OrthoMCL, Ortholnspector, sonicparanoid, PANTHER, OrthoFinder, Hieranoid26 and the OMA family including OMA pairs, OMA groups and OMA GETHOGs (graph-based efficient technique for HOGs). c) A computation time comparison of FastOMA and state-of-the-art alternatives. https://www.nature.com/articles/s41592-024-02552-8

FastOMA is out now in Nature Methods 🎉: nature.com/articles/s41592-024-02552-8 A new orthology inference algorithm that scales linearly and is highly accurate. FastOMA can process all >2000 eukaryotic UniProt ref proteomes <24 hours 🚀. Try it out github.com/DessimozLab/fastoma @dessimoz.bsky.social

Unicore identifies single-copy protein structures across genomes using Foldseek, bypassing slow structure predictions by utilizing 3Di predictions from ProstT5, enabling rapid phylogenetic inference at the tree-of-life scale. 1/n
📄 www.biorxiv.org/content/10.1...
💾 github.com/steineggerla...

Unicore enables scalable and accurate phylogenetic reconstruction with structural core genes https://www.biorxiv.org/content/10.1101/2024.12.22.629535v1

Scientists, academics, researchers: We’re excited to share that @altmetric.com is now tracking mentions of your research on Bluesky! 🧪

South Korean citizens helped lawmakers scale the National Assembly walls so they could bypass military barricades and vote against martial law.

Reminder for newcomers that bioRxiv has Bluesky accounts in every subject category - great way to keep up (please re-skeet) connect.biorxiv.org/news/2023/09...

Interested in bioinformatics method development for proteins, structures or metagenomic analysis? Please check out my lab’s starter pack!
🔗 go.bsky.app/VJhXcSs

Promotional logo for MMseqs2 16 with the MMseqs2 Rocket mascot as a smart phone like App logo

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 🖥️🧬🧶

What did the Last Eukaryotic Common Ancestor (#LECA) look like? Consensus View in #PLOSBiology; massive authorship including @AncestralState, @lauraeme.bsky.social, John Archbald, @andrewjroger.bsky.social, @dackslabecb.bsky.social, Jeremy Wideman. plos.io/4g0alq4

Our Big Fantastic Virus Database (BFVD) is now published NAR! It contains protein structure predictions of major viral clades, enhanced by petabase-scale homology search and it's explorable on the web.
🌐 bfvd.foldseek.com
💾 bfvd.steineggerlab.workers.dev
📄 academic.oup.com/nar/advance-...