Martin Steinegger 🇺🇦

I’ve never performed gene-targeted assembly myself, so I can’t speak from direct experience. I do remember that SPAdes had a gene-reference-based assembly mode that used HMMER.

Can we simulate realistic evolutionary trajectories and “replay the tape of life”? In this work, we propose a flexible, generalizable deep learning framework for modeling how the entire protein sequence evolves over time while capturing complex interactions across sites. 1/n
doi.org/10.64898/202...

I am happy Marv finally made it!

Congratulations! But how did you get the Marv logo into figure 1? We needed to remove the logos 🥲

AlphaFold Database welcomes community datasets Latest AlphaFold Database update adds high-value datasets for microbial and viral proteins, generated by specialist communities

The AlphaFold Database, jointly developed with Google DeepMind, now contains datasets from specialist communities.

This includes rich datasets for microbes, viruses & parasites associated with tropical diseases.

Explore the new datasets in the AlphaFold Database.

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

Introducing The Structural History of Eukarya (SHE): The first proteome-scale phylogeny constructed entirely from 3D structure.
We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)

:D

Multiple protein structure alignment at scale with FoldMason Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...

Can ever-increasing sequence databases improve phylogenetic reconstruction of a gene family? Our new preprint introduces AmpliPhy, a pipeline that automates homolog enrichment to improve gene tree inference, built on a robust phylogenomic benchmark scheme. 🧵1/n
📃 doi.org/10.64898/2026.01.26.701724

Sorry to hear that :( looks like such a cool paper.

Very good point. We do not show these values in the front end. I flagged this. We will add them.

In the complex report, results are sorted first by TM-score normalized to the query complex length, then by the target complex TM-score. So their should be a visibile ordering.

We don’t combine per-chain bit scores into a single complex score. A proper bit score would need to account for the full complex superposition. However, we consider the per chain e-values. For now, use pair-chain E-values + complex TM-score for filtering is what we do.

Milot’s venture into establishing his own lab is incredibly excitinge. I highly recommend to join Milot on his mission to advance molecular biology through open-source bioinformatics.

Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning Mirdita Lab builds scalable bioinformatics methods.

My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring!
mirdita.org

The 2026 Nucleic Acids Research database issue and the online molecular biology database collection Abstract. The 2026 Nucleic Acids Research database issue has 182 papers from across biology and neighbouring fields. Eighty-four of these papers describe n

The new 2026 NAR Nucleic Acids Research Database Issue is now out! 🎉

Take a look at the Editorial here academic.oup.com/nar/article/...
and browse the whole Issue here
academic.oup.com/nar/issue/54...

I am deeply saddened by this news. Peer was a brilliant scientist, and his passing is a tremendous loss, not only for our field, but for science as a whole.

Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments Abstract. Protein structure-based comparison provides a framework for uncovering deep evolutionary relationships that can escape conventional sequence-base

An interesting way to look at encoded structural characters to build alignments and trees downstream. This takes structural phylogenetics one step further in the post-AlphaFold era.

#Evolution #Science #StrPhy

On Confidence Assessment in Structure-Aware Alignments

doi.org/10.1093/gbe/...

Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...

Did you write them?

A Vtuber is explaining the ProteinTTT paper. I’ve wondered when this trend would hit science.

YouTube video by Miono Yui ch. | 澪乃ゆい 【論文簡単解説】One protein is all you need簡単解説💨 #shorts #vtuber準備中 #澪乃ゆい

Amazing summary of our recent ProteinTTT paper youtube.com/shorts/XWueh...

Looking to start your lab in generative biology / AI?
Come join us at the @sangerinstitute.bsky.social
Sanger is core-funded so you can generate data at scale to train the next generation of models and understanding. Design/Engineering/Chemistry/Proteins/Pathways!
pls RT
tinyurl.com/GenGenFaculty

I hope they fix the system soon. For now, I won’t review for them.

Got three emails on Dec 24th, 25th, and Saturday the 27th asking me to review a manuscript… only to be removed as reviewer today. When I complained, the response was: “Our offices are closed December 24-January 1.”
Thank you @plos.org Computational Biology.

Hey you just broke too many grant proposals.

"..based on a common wavefront design that can be adapted to support a variety of dynamic programming algorithms: local, global, and semi-global alignment of genomic and protein sequences with a variety of commonly used scoring schemes" from
@martinsteinegger.bsky.social andco

New preprint🚨
Imagine (re)designing a protein via inverse folding. AF2 predicts the designed sequence to a structure with pLDDT 94 & you get 1.8 Å RMSD to the input. Perfect design?
What if I told u that the structure has 4 solvent-exposed Trp and 3 Pro where a Gly should be?

Why to be wary🧵👇

💾 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...

Congratulations, Julia Mahamid!

Julia Mahamid receives the @dfg.de Leibniz Prize for her work on structural cell biology!

#LeibnizPreis