GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio
www.nature.com/articles/s41...
www.nature.com/articles/s41...
GPU-accelerated homology search with MMseqs2 - Nature Methods
Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...
www.nature.com
September 18, 2025 at 8:09 PM
GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Eirik Lågeide, Gal Ofir and colleagues discover an antiviral protein in plants based on its homology to a bacterial antiphage defense protein called Tiamat. Cool!
Very excited to share the first preprint from my PhD with the community! This is also the first paper from the Plant Immunogenomics group with @galofir.bsky.social, so stay tuned for more!
www.biorxiv.org/content/10.6...
1/n 🧵
www.biorxiv.org/content/10.6...
1/n 🧵
NO VEIN is an ancestral immunity protein involved in plant-virus interaction
The conservation of immune systems from prokaryotes to eukaryotes can guide discovery of immunity genes across the tree of life. Most studies to date have focused on metazoan systems, while the extent...
www.biorxiv.org
October 2, 2026 at 11:46 AM
Eirik Lågeide, Gal Ofir and colleagues discover an antiviral protein in plants based on its homology to a bacterial antiphage defense protein called Tiamat. Cool!
Photoshopped a new maths pun: A "persistent" homology group.
October 1, 2026 at 11:04 PM
Photoshopped a new maths pun: A "persistent" homology group.
What molecular mechanisms underlie the needle-in-a-haystack search for homology required to fix a DNA break? In this preprint, we reveal multiple controls of homology search in cells: onset, coordination, reach and inactivation. www.biorxiv.org/content/10.6...
September 18, 2026 at 6:01 AM
What molecular mechanisms underlie the needle-in-a-haystack search for homology required to fix a DNA break? In this preprint, we reveal multiple controls of homology search in cells: onset, coordination, reach and inactivation. www.biorxiv.org/content/10.6...
MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com
📄 www.nature.com/articles/s41...
💿 mmseqs.com
GPU-accelerated homology search with MMseqs2 - Nature Methods
Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...
www.nature.com
September 21, 2025 at 8:06 AM
MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com
📄 www.nature.com/articles/s41...
💿 mmseqs.com
New preprint from the @gerlichlab.bsky.social @imbavienna.bsky.social!
How do DNA breaks locate homology sites in the vast space of the human genome? We show how cohesin guides homology search for faithful repair!
Read more 👉 https://doi.org/10.1101/2025.02.10
Follow along for key insights! 🧵
How do DNA breaks locate homology sites in the vast space of the human genome? We show how cohesin guides homology search for faithful repair!
Read more 👉 https://doi.org/10.1101/2025.02.10
Follow along for key insights! 🧵
February 12, 2025 at 5:15 PM
New preprint from the @gerlichlab.bsky.social @imbavienna.bsky.social!
How do DNA breaks locate homology sites in the vast space of the human genome? We show how cohesin guides homology search for faithful repair!
Read more 👉 https://doi.org/10.1101/2025.02.10
Follow along for key insights! 🧵
How do DNA breaks locate homology sites in the vast space of the human genome? We show how cohesin guides homology search for faithful repair!
Read more 👉 https://doi.org/10.1101/2025.02.10
Follow along for key insights! 🧵
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-...
🌐 bfvd.foldseek.com
💾 bfvd.steineggerlab.workers.dev
📄 academic.oup.com/nar/advance-...
November 23, 2024 at 9:12 PM
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-...
🌐 bfvd.foldseek.com
💾 bfvd.steineggerlab.workers.dev
📄 academic.oup.com/nar/advance-...
the average American had three friends: homotopy, homology and cohomology
May 2, 2025 at 4:39 AM
the average American had three friends: homotopy, homology and cohomology
End-to-end differentiable homology search for protein fitness prediction.
@yaringal.bsky.social @deboramarks.bsky.social @pascalnotin.bsky.social
arxiv.org/abs/2506.089...
@yaringal.bsky.social @deboramarks.bsky.social @pascalnotin.bsky.social
arxiv.org/abs/2506.089...
June 11, 2025 at 7:00 PM
End-to-end differentiable homology search for protein fitness prediction.
@yaringal.bsky.social @deboramarks.bsky.social @pascalnotin.bsky.social
arxiv.org/abs/2506.089...
@yaringal.bsky.social @deboramarks.bsky.social @pascalnotin.bsky.social
arxiv.org/abs/2506.089...
Being accused of partying when in reality the dark shadows under my eyes are from staying up too late reading about homology
May 26, 2024 at 4:03 AM
Being accused of partying when in reality the dark shadows under my eyes are from staying up too late reading about homology
Thrilled to share that my postdoc research is published today in @science.org! We found that DNA repair uses cohesin complexes to build new chromatin loops that guide the homology search and boost accurate repair! 1/n
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Cohesin drives chromatin scanning during the RAD51-mediated homology search
Cohesin folds genomes into chromatin loops, the roles of which are under debate. We found that double-strand breaks (DSBs) induce de novo formation of chromatin loops in human cells, with the loop bas...
www.science.org
December 4, 2025 at 9:50 PM
Thrilled to share that my postdoc research is published today in @science.org! We found that DNA repair uses cohesin complexes to build new chromatin loops that guide the homology search and boost accurate repair! 1/n
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
New enzymes that create natural phosphorothioate modifications in RNA share homology with proteins in bacterial DndABCDE anti-phage defense!
www.cell.com/cell/abstrac...
www.cell.com/cell/abstrac...
September 17, 2026 at 5:02 PM
New enzymes that create natural phosphorothioate modifications in RNA share homology with proteins in bacterial DndABCDE anti-phage defense!
www.cell.com/cell/abstrac...
www.cell.com/cell/abstrac...
May 16, 2026 at 2:18 PM
I am happy to share that my postdoctoral work in the @gerlichlab.bsky.social at @imbavienna.bsky.social is finally out 🎉!
Our study reveals how cohesin guides focused and accurate homology search.
Read more 👉 www.science.org/doi/10.1126/...
Follow along for key insights and updates! 🧵
Our study reveals how cohesin guides focused and accurate homology search.
Read more 👉 www.science.org/doi/10.1126/...
Follow along for key insights and updates! 🧵
Cohesin guides homology search during DNA repair using loops and sister chromatid linkages
Accurate repair of DNA double-strand breaks (DSBs) is essential for genome stability, and defective repair underlies diseases such as cancer. Homologous recombination uses an intact homologous sequenc...
www.science.org
December 4, 2025 at 8:18 PM
I am happy to share that my postdoctoral work in the @gerlichlab.bsky.social at @imbavienna.bsky.social is finally out 🎉!
Our study reveals how cohesin guides focused and accurate homology search.
Read more 👉 www.science.org/doi/10.1126/...
Follow along for key insights and updates! 🧵
Our study reveals how cohesin guides focused and accurate homology search.
Read more 👉 www.science.org/doi/10.1126/...
Follow along for key insights and updates! 🧵
Very exciting that our new paper on the forces exerted by the Rad51-Rad54 homology search complex is now online. This was a collaborative effort with the Wang here at Cornell, and this work performed primarily by a graduate student, Mitch Woodhouse
genesdev.cshlp.org/content/earl...
genesdev.cshlp.org/content/earl...
The eukaryotic homology search complex distorts donor DNA structure to probe for homology
A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields
genesdev.cshlp.org
April 8, 2026 at 6:18 PM
Very exciting that our new paper on the forces exerted by the Rad51-Rad54 homology search complex is now online. This was a collaborative effort with the Wang here at Cornell, and this work performed primarily by a graduate student, Mitch Woodhouse
genesdev.cshlp.org/content/earl...
genesdev.cshlp.org/content/earl...
What is your most galaxybrained thought about why (co)homology turns out to be so important in almost everything?
February 25, 2026 at 3:02 PM
What is your most galaxybrained thought about why (co)homology turns out to be so important in almost everything?
Our latest preprint describes methods and tools that enable >99% efficient short homology-dependent genome editing in the human fungal pathogen Cryptococcus neoformans. Congratulations to Matt, Sanjita, and Manning!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Near 100% efficient homology-dependent genome engineering in the human fungal pathogen Cryptococcus neoformans
We recently described CRISPR/Cas9-based short homology-dependent genome engineering in the human fungal pathogen Cryptococcus neoformans , a haploid budding yeast that is the most common cause of fung...
www.biorxiv.org
February 18, 2025 at 10:23 PM
Our latest preprint describes methods and tools that enable >99% efficient short homology-dependent genome editing in the human fungal pathogen Cryptococcus neoformans. Congratulations to Matt, Sanjita, and Manning!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
What you’re saying reminds me of persistent homology
October 1, 2026 at 3:53 AM
What you’re saying reminds me of persistent homology
There is a post going around claiming ai is good for historians for translation purposes and it just seems like madness to me. What an artificial way to study history, don’t you want the context? Like trying to study homology without the language of homology
January 27, 2025 at 6:47 PM
There is a post going around claiming ai is good for historians for translation purposes and it just seems like madness to me. What an artificial way to study history, don’t you want the context? Like trying to study homology without the language of homology
RESULTS
Gel order:
Upstream homology arm, downstream homology arm, full length locus with target gene in middle, a not so great detection primer set. Ladders are NEB 1KB Plus. Arms 1kbp. Full locus 2880bp. All amplified in same conditions.
10/n
Gel order:
Upstream homology arm, downstream homology arm, full length locus with target gene in middle, a not so great detection primer set. Ladders are NEB 1KB Plus. Arms 1kbp. Full locus 2880bp. All amplified in same conditions.
10/n
December 11, 2024 at 10:05 PM
RESULTS
Gel order:
Upstream homology arm, downstream homology arm, full length locus with target gene in middle, a not so great detection primer set. Ladders are NEB 1KB Plus. Arms 1kbp. Full locus 2880bp. All amplified in same conditions.
10/n
Gel order:
Upstream homology arm, downstream homology arm, full length locus with target gene in middle, a not so great detection primer set. Ladders are NEB 1KB Plus. Arms 1kbp. Full locus 2880bp. All amplified in same conditions.
10/n