Burstein lab

Having fun with microbial genomic and machine learning @TelAvivUni

[Burstein lab @BursteinLab]

Fellow microbial immunity, mobile elements, and plasmid enthusiasts: the paper of our wonderful @BruriaSamuel on anti-defense genes in plasmids is now published in @Nature!!!

Check out her thread below for highlights of our new results.
1/2

[Bruria Samuel @BruriaSamuel]

Meet The Shielded Plasmid🛡️🧬

Our new @Nature paper reveals how plasmids outsmart bacterial defenses during conjugation.

It's all about being in the right place at the right time! The positioning of anti-defense genes boosts transfer efficiency🧵(1/7) https://t.co/6n8brUx1PU

[Dor Salomon @DrDorSalomon]

1/New paper🚨 combining #T6SS + #antiphage
We previously identified an antiphage system, GAPS4, but we didn’t know what it targets or what triggers it. Chasing that last question took us somewhere we didn’t expect: GAPS4 is a sentinel of DNA integrity.
https://t.co/m7qoEhPTFH

[Burstein lab @BursteinLab]

@MicahGoldrich @EdanGabay Thanks!! Alas, not yet... It’s all simulated insertions so far: no real edited isolates and no unpolished assemblies, for lack of good enough data. That’s indeed a main limitation. Yeast is appealing, but the embeddings are prokaryotic, so it’d need retraining.

[Burstein lab @BursteinLab]

So many bacterial genomes are being edited… Could we spot them in the wild even without obvious markers??? Worry not! Our @EdanGabay has you covered. In our new preprint, she pinpoints such genes disrupting the natural genomic "grammar": https://t.co/WkoUYqMHzQ 1/4

[Burstein lab @BursteinLab]

@Yehuda_Sam @EdanGabay Sorry for the slow reply! Length doesn’t matter here. We first assign each protein to a family, and each family becomes one token. So a 300-codon gene and a 3,000-codon one are each a single “word”. The model sees only which family, and in what order.

[Dor Salomon @DrDorSalomon]

🧵New paper out in @mSystems! We mapped the pan-genome #T6SS effector arsenal of #Pantoea agglomerans. The surprise: its weapons live in dynamic genomic armories that mix antibacterial attack with anti-phage defense. 1/n https://t.co/wad5i2qDGf

[Garyk Brixi @garykbrixi]

Genome language models learn from DNA shaped by billions of years of evolution, but steering them can be challenging. Designing phages with Evo 2 previously meant fine-tuning on thousands of genomes, but ICL succeeds with just four examples across tasks.

[Karen Zhang @thekarenzhang]

Out now in Molecular Cell! Retrons protect bacteria from phage infection, and this one has one of the craziest mechanisms we’ve ever seen. (1/8) https://t.co/LXIxdKtNC0

[Kenneth Loi @kenjmloi]

Viruses have parasites too. Our new preprint shows how phages use VIPR to silence parasitic satellites, and how the satellites fight back with its own decoy VIPR RNAs that redirect VIPR to DNA REP elements in the host genome!!
https://t.co/ys5Qo7p5c5

[Tim Blower @BlowerLab]

For all phage defence pholks - registration for the Symposium on the Immune Systems of Bacteria 2027 is now open! 20-22nd July, 2027, Churchill College, Cambridge, UK. See you there! https://t.co/hXSTHcDSMV

[Dor Salomon @DrDorSalomon]

Check out recent work:
Artificial genetic augmentation of T6SS activity affects effector repertoire and host toxicity | Microbiology Spectrum https://t.co/RQFKSIWAXO

In collaboration with @GerlicL

[Sternberg Lab @SternbergLab]

1/5 Telomerase has long been linked to chromosome maintenance in eukaryotes. Now, we show that telomerase-like activity is also present in bacteria, shedding new light on its ancient origins.

Excited to share that our work on DRT10 is now out in @Nature!

https://t.co/4CekquyMXX

[Stanford University @Stanford]

The most important briefings of the day.

Karl Deisseroth, professor of bioengineering and of psychiatry and behavioral sciences, shares the news of his Nobel Prize with his kids.

[Burstein lab @BursteinLab]

After fine-tuning on potentially malicious insertions, the model reached 0.95 AUROC and 0.95 AUPRC. This indicates that such edits do leave detectable genomic-context signatures, without relying on marker genes or predefined databases. Congrats @EdanGabay!!! 👏👏👏 4/4

[Burstein lab @BursteinLab]

No unified large dataset of engineered bacterial genomes. So we built scalable simulations of random and potentially harmful gene insertions. We trained a classifier on those, along with natural sequences and natural occurrences of the inserted genes as hard negatives. 3/4

[Garyk Brixi @garykbrixi]

Genomes are full of dark matter of unknown functions.

We present Minerva, a new method for discovery guided by genome language models. Minerva reveals the interactions hidden in non-coding DNA, pointing to hundreds of new putative RNAs and repetitive elements per bacterial genome. Minerva allows us to find and study elements invisible to traditional methods at orders of magnitude greater scale than before.

[David Li @_David_Li]

Excited to share Minerva, our approach using genome language models for biological discovery! Using Minerva, we find that UG27 reverse transcriptase systems encode variable arrays of diverse ncRNAs with a shared structure, each templating a short DNA hairpin. With @garykbrixi.

[Martin Pacesa @MartinPacesa]

ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use.

We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition.
https://t.co/O8pr6jH99t

[Kenneth Loi @kenjmloi]

VIPR is now out in @ScienceMagazine!

What started with a mysterious RNA led us to an unexpected way of recognizing DNA, as well as some clues to CRISPR’s origins.

So happy to share these two papers with an incredible team. Links below; original discovery thread here ↓

[Artem Isaev @Artem_Isaev_]

Chromatin structure controls defense island expression!

Why do some systems defend on plasmids but fail natively? H-NS is key. Removing it boosts defense and beats anti-defense proteins but raises toxicity. Lab strains still hide novel immunity modules!

https://t.co/F4ycJ68ZnU