@BursteinLab

Having fun with microbial genomic and machine learning @TelAvivUni

 Israel
burstein-lab.github.io/
Joined September 2022
  • Tweets225
  • Following359
  • Followers644
21Media
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
9 Oct 2024
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) nature.com/articles/s41586-0…
Illustrated by @Irisburstein

ALT Illustrated by @Irisburstein

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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": biorxiv.org/content/10.64898… 1/4
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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
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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
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Garyk Brixi
@garykbrixi
Sep 22
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.
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David Li@_David_Li
Sep 22
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.
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Martin Pacesa@MartinPacesa
Sep 21
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. github.com/PacesaLab/BindCra…
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Kenneth Loi
@kenjmloi
Sep 17
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 ↓
Kenneth Loi
@kenjmloi
Apr 27
Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.
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Artem Isaev@Artem_Isaev_
Sep 11
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! biorxiv.org/content/10.64898…

H-NS silences antiviral immunity through 3D chromatin compaction

Bacterial antiviral immunity systems can be toxic to their hosts and must be tightly regulated. Immunity genes are often encoded by AT-rich mobile genetic elements subjected to silencing by nucleoid...

biorxiv.org
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Sergey Ovchinnikov@sokrypton
Sep 17
Also a highly experimental port of these models into WebGPU, allowing direct prediction on your 💻: localfold.org WARNING: will drain battery🪫, overheat 🔥💻 & eat your data plan 📱 Started by Martin Steinegger as AF2 port to WebGPU martin-steinegger.github.io/… (3/3)
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Sergey Ovchinnikov@sokrypton
Sep 17
ColabFold 1.6.3 is out! 2.5x faster, pip-installable, ipSAE+pDockQ2 scores. Thanks Choonghwan Lee, Marielle Russo, Gyuri Kim, Martin Steinegger, Milot Mirdita 🐍 pip install colabfold[alphafold] (1/3)
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Published now in @Nature - "Long-read sequencing reveals pre-meiotic gene conversion in sperm". We show an unexpected source of new genetic variation in human sperm, occuring earlier in development than previously thought. Check it out here: nature.com/articles/s41586-0… Thread: 1/

Long-read sequencing reveals pre-meiotic gene conversion in sperm

Nature - Single-molecule long-read sequencing of human sperm reveals variation in recombination across donors and that a substantial fraction of non-crossover gene conversions arises before...

nature.com
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The leading region of many plasmids is adapted for translational efficiency doi.org/10.1093/nar/gkag810

The leading region of many plasmids is adapted for translational efficiency

Abstract. To successfully transfer, conjugative plasmids must overcome a recipient cell’s defence mechanisms. The leading region of many plasmids—the first

academic.oup.com
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Avigdor Eldar@AvigdorEldar
Aug 20
Toxin-Antitoxin systems are thought to induce death or dormancy under some stress conditions. Focusing on the well studied MazEF system, we now show that this is not always the case. biorxiv.org/content/10.64898…

Highly specific mRNA cleavage by the MazF endoribonuclease orchestrates stationary transcriptome...

Bacterial toxin-antitoxin (TA) systems are classically viewed as stress-activated toxic switches. Specifically, ribonucleolytic toxins are thought to indiscriminately cleave RNA to halt cellular...

biorxiv.org
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Frederik Schulz
@frederikschu
Aug 8
Riboseek encodes RNA and DNA sequences as overlapping di-mers and detects homologs more sensitively than BLASTN and nhmmer. It produces alignments 250-fold faster than nhmmer and 376-fold faster than rMSA. doi.org/10.64898/2026.07.31.…
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Sternberg Lab@SternbergLab
Aug 3
Out now! In collaboration with Hiroshi Nishimasu's lab, we uncover how a dual reverse transcriptase immune system builds double-stranded DNA from both RNA and protein templates. sciencedirect.com/science/ar… Previous thread for the preprint: nitter.cf/SternbergLab/status/20…
Sternberg Lab@SternbergLab
May 12
1/9 New preprint from the Sternberg Lab in collaboration with the Nishimasu Lab! We uncover how the DRT3 antiphage immune system pairs two reverse transcriptases, one RNA-templated and one protein-templated, to build a double-stranded DNA effector. doi.org/10.64898/2026.05.04.…
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קטע מדהים מיומן ברלין של חסידת אומות העולם רות אנדריאס-פרידריך. בכלל המלצת מעקב חמה על מני אדלר שמביא כל יום קטעים נפלאים מספרי הסטוריה והופך את הפיד למרתק
Meni Adler@meniadler
Jul 23
יום ו, 24 בפברואר 1939 כולם מדברים בברלין על 'ליפטים'. הכוונה איננה למעליות הנוסעים בבתי מלון מפוארים, אלא לארגזי העץ הגדולים שבהם אורזים את מטלטליהם המהגרים ששיחק להם מזלם לעזוב את גרמניה. מזה ששה שבועות מהווה 'הליפט' את הנושא המרכזי לכל שיחה בחוג מכרינו.
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1/4 Every good defence needs a backup 🛡️⚔️ Out now in @NatureRevMicro our Comment on "𝗶𝗺𝗺𝘂𝗻𝗲 𝘀𝗮𝗳𝗲𝗴𝘂𝗮𝗿𝗱𝗶𝗻𝗴"! 🎉 🔗 nature.com/articles/s41579-0…

Immune safeguarding as a conserved principle of antiviral defence

Nature Reviews Microbiology - All organisms defend against viral infections through active immunity mechanisms that clear the virus or population-level mechanisms that cause regulated cell death....

nature.com
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1/10 🚨Preprint! One RING to rule them all (phages)👑💍⚔️ Bacteria build giant DNA-scaffolded RNase rings (larger than the ribosome!) to shut down viral infection🧬🧵👇 🔗biorxiv.org/content/10.64898…
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Ella Rannon@EllaRannon
Jul 12
My paper on reduced amino acid alphabets for protein language models is out in Bioinformatics! I'll be giving a talk on this on Thursday at ISMB, would love to chat there. #ISMB2026 doi.org/10.1093/bioinformati…

Optimizing protein tokenization: reduced amino acid alphabets for efficient and accurate protein...

AbstractMotivation. Protein language models (pLMs) typically tokenize sequences at the single-amino-acid level using a 20-residue alphabet, resulting in lo

academic.oup.com
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