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Conner Langeberg

@clangeberg.bsky.social
132 followers 189 following 4 posts

RNA, viruses, and everything in between | Postdoc in Doudna and Cate Labs @UCBerkeley

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Reposted by Conner Langeberg
Sorek Lab @soreklab.bsky.social · 20h
Very nice discovery from the Jackson, Bravo and Basel labs. Cleaved tRNA ends, loaded with an amino acid, activate a form of bacterial immunity
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 14/10/2026
LoL-align is out in @natmethods.nature.com! It aligns protein structures without superposition. More sensitive than TM-align and DALI, producing better alignments 5–20× faster. Now available in Foldseek! 📄 www.nature.com/articles/s41... 💾 github.com/steineggerlab/foldseek 🌐 search.foldseek.com
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pilarcossio.bsky.social @pilarcossio.bsky.social · 14/10/2026
1/5 Cryo-EM gives high-resolution RNA structures, but only when high Mg²⁺ freezes out their motion. At physiological conditions, RNAs are dynamic and 3D reconstruction fails. Can we still learn their folding equilibria? New preprint: yes, straight from the raw particle images👇
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Luis E. Valentin-Alvarado @luisvalentin.bsky.social · 09/10/2026
Massive thanks to P. Yoon and, S. Lopez, @kshulgina.bsky.social, @clangeberg.bsky.social, @knottrna.bsky.social , @doudna-lab.bsky.social and to all our collaborators. Now on @biorxivpreprint.bsky.social www.biorxiv.org/content/10.6... 11/11
biorxiv.org
tRNA-derived second messengers confer bacterial immunity
Bacterial small-molecule messengers that function in diverse immune signaling pathways have been thought to derive strictly from biosynthesis using nucleotide and cofactor substrates. Here we report a...
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Marvin Tanenbaum @marvintanenbaum.bsky.social · 08/10/2026
Did you ever want to sequence that one interesting cell you observed in your microscopy experiment? We have a new pre-print out today that describes a genetic barcoding method, Waldo, to perform live-cell imaging and single-cell sequencing on the same single cells. www.biorxiv.org/content/10.6...
biorxiv.org
Linking live-cell imaging to single-cell sequencing using genetic barcoding
Linking cellular phenotype to genotype and gene expression is a central goal in biomedical research. Live-cell imaging captures dynamic cellular phenotypes, whereas single-cell sequencing measures gen...
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Reposted by Conner Langeberg
Karolin Luger @nucleosomepolice.bsky.social · 08/10/2026
a fantastic new paper by lab alumni @codyz.bsky.social and yangliu9.bsky.social. Congratulations - such a cool mechanism! check it out 👇👇👇👇👇👇 www.sciencedirect.com/science/arti...
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Danny IncaRNAto @incarnatolab.bsky.social · 09/10/2026
#RNA Framework 2.9.8 is out! Check the full CHANGELOG: github.com/dincarnato/R.... Get the latest version at: github.com/dincarnato/R... This release features a major renovation of the engine. A few highlights in a short thread (1/n).
github.com
RNAFramework/CHANGELOG.md at master · dincarnato/RNAFramework
RNA structure probing and post-transcriptional modifications mapping high-throughput data analysis - dincarnato/RNAFramework
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bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 09/10/2026
Directed evolution of a thermostable family-A DNA polymerase into a reverse transcriptase for 2'-modified RNA www.biorxiv.org/content/10.64898/20…
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Przemek Dutka @przemekdut.bsky.social · 08/10/2026
Our latest development is now on bioRxiv: cryoSHIELDs — amphipathic peptide additives that make cryo-EM grid prep far more reliable. Tested across 24 protein systems, they enabled the first ABCC6 structure and GPCR–G protein structures at just 0.1–0.5 mg/mL! www.biorxiv.org/content/10.6...
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Nature Microbiology @natmicrobiol.nature.com · 05/10/2026
The October issue is live, featuring... 📈a history of bacterial growth rate 🌥️pollution and pneumococcal diseases 🦔hedgehog merbecovirus receptors 🌡️microbial responses to global change 💦how Mtb survives aerosolization ...and more! 👇 www.nature.com/nmicrobiol/v...
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The EMBO Journal @embojournal.org · 02/10/2026
How about stress-induced ribosome hibernation in archaea? @diorgeps.bsky.social, @archaeon-alex.bsky.social, Joey Davis et al identify conserved archaeal factor AHA with evolutionary link to bacterial hibernation-promoting factor HPF & eukaryotic energy sensor AMPKγ link.springer.com/article/10.1...
link.springer.com
A conserved archaeal protein with evolutionary links to bacterial ribosome hibernation and eukaryotic energy sensing - The EMBO Journal
Ribosome hibernation helps cells survive stress by reversibly silencing translation and preserving ribosomal complexes. Although well characterized in bacteria and eukaryotes, archaeal hibernation rem...
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Kranzusch Lab @kranzuschlab.bsky.social · 01/10/2026
Our story with @hobbslabutah.bsky.social discovering CBASS sensing of phage proteases out now in @science.org New data include CBASS recognition of diverse proteases beyond T4, and verifying CD-NTase activation loop cleavage as the trigger for defense in vivo www.science.org/doi/10.1126/...
science.org
Phage proteases activate CBASS antiphage immunity
Cyclic oligonucleotide–based antiphage signaling systems (CBASS) are bacterial immune pathways evolutionarily related to cGAS-STING (cyclic GMP-AMP synthase–stimulator of interferon genes) in humans. ...
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Nature @nature.com · 28/09/2026
Gene-editing techniques could soon allow researchers to replace entire genes and engineer complex cellular circuits — if the systems can be delivered safely into cells go.nature.com/4z4UP5W
go.nature.com
Bigger than CRISPR? A guide to the latest genome editors
Gene-editing techniques could soon allow researchers to replace entire genes and engineer complex cellular circuits — if the systems can be delivered safely into cells.
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Malcolm White @mfwhite2.bsky.social · 25/09/2026
New from the @multidefence.bsky.social consortium: a deep dive into MANTIS defence. Thanks to @ukri.org for funding. www.biorxiv.org/content/10.6...
biorxiv.org
Dual ATPase-activated DNA hemimethylation and cleavage by the MANTIS defence system
Bacterial defence systems are diverse and form major barriers to horizontal gene transfer and bacteriophage (phage) infection. Though restriction-modification systems were the first such defences disc...
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Craig Kaplan @triggerloop.bsky.social · 25/09/2026
Cryo-EM peeps are living the dream www.science.org/doi/10.1126/...
science.org
In-cell structures visualize human pre-ribosome assembly in the nucleolus
In eukaryotes, ribosome biogenesis initiates within the nucleolus, a hallmark multilayered compartment of the nucleus. Structures of pre-ribosomes have been characterized ex situ, but their assembly p...
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Dorentina Humolli @humollidorentina.bsky.social · 25/09/2026
Very happy to share that HIDEN-SEQ is now out in @natmicrobiol.nature.com! Using this technique, we recapitulated decades of established phage genetics and uncovered new gene functions, including previously unknown anti-defense factors against several defense systems. www.nature.com/articles/s41...
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Alexander Harms @aharms485.bsky.social · 25/09/2026
The final version of our manuscript on TnSeq in bacteriophages (“HIDEN-SEQ”) is out today – if you have an interesting phage phenotype and want to know the underlying genetic basis, this one is for you! 1/4
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Arc Institute @arcinstitute.org · 23/09/2026
Many important bacterial non-coding RNAs and structural elements remain undiscovered. To help, David Li, Garyk Brixi, Michael Fischbach, @brianhie.bsky.social & team introduce Minerva, which uses a genome language model to predict RNA base pairing, repeats, & other interactions from sequence alone.
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 24/09/2026
AlphaFold Database is expanding into pandemic preparedness. Together with NVIDIA, DeepMind, EBI et al. we exhaustively predicted ~1.7 million homo- & heterodimers across 2,812 viral proteomes, resulting in 8,028 high-confidence predictions. 📄 research.nvidia.com/labs/dbr/ass... 🌐 alphafold.ebi.ac.uk
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Innovative Genomics Institute @innovativegenomics.bsky.social · 24/09/2026
Predicting how #RNA folds would be a valuable tool for scientists, but #AI has not been able to crack the problem. A team at the IGI made significant progress on two key hurdles: limited structural data, and the fact that RNA can take on multiple shapes. Read more: ow.ly/Yjgo50ZJcU3
Coauthors Roma Nagle and Conner Langeberg
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George Pearkes @peark.es · 23/09/2026
Technical report here: www-cdn.anthropic.com/22573675ada5...
www-cdn.anthropic.com
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George Pearkes @peark.es · 23/09/2026
Anthropic threw Claude at a DNA database. 21 hours, 950 agents, and 210mm tokens later, it emerged with a novel reverse transcriptase (similar to CRISPR). They're running a non-pathogenic (BSL-1/2) research lab in the Bay Area.
anthropic.com
Claude discovers a novel enzyme system with CRISPR-like repeats
Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.
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Structura Biotechnology @structurabio.bsky.social · 23/09/2026
🔎 A classic #cryoEM particle curation conundrum: 2D or 3D classification? "Decoy Classification" using Heterogeneous Refinement in #CryoSPARC curates particles directly in 3D, helping remove junk particles while preserving valuable views. Read more in the CryoSPARC Blog 👉 bit.ly/3SXfwS0
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RNA Society Journal @rnajournal.bsky.social · 22/09/2026
In Lactobacillus casei, the AUA codon is decoded predominantly by tRNA-Ile(UAU), whereas lysidine-containing tRNA-Ile(LAU) contributes little because of its low aminoacylation level #RNA #tRNA bit.ly/3UmlWua
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Elodie Carmen Leroy @ecleroy.bsky.social · 21/09/2026
How can a single antibiotic halt translation across all domains of life? 🧬 Our new study in Nucleic Acids Research reveals how Sparsomycin traps active ribosomes through a conserved mechanism. academic.oup.com/nar/article/... #Ribosome #Translation #StructuralBiology #Antibiotics #RNA #iTPseq
Graphical representation of the T. thermophilus 70S ribosome showing the 30S and 50S subunits, mRNA, and P-site tRNA. Sparsomycin (yellow) binds in the peptidyl transferase center at the interface between the A and P sites. The enlarged view shows sparsomycin occupying the A-site cleft adjacent to the P-site fMet-tRNA, closely contacting its 3′ CCA end (C74, C75 and A76) and the attached fMet.
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Nature @nature.com · 21/09/2026
Nature research paper: Scalable near-real-time Bayesian phylogenetics for outbreaks with Delphy go.nature.com/4AzKbWq
go.nature.com
Scalable near-real-time Bayesian phylogenetics for outbreaks with Delphy - Nature
Delphy makes near-real-time and scalable Bayesian phylogenetics possible for growing viral outbreaks, enabling public health bodies anywhere to analyse and react to their own data with state-of-the-art accuracy and minimal friction.
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Ben Parker @ben-parker.bsky.social · 21/09/2026
Excited that our new paper with @henrylabsymbio.bsky.social and Kerry Oliver is out @pnas.org! We show that mobile genetic elements can spread adaptive host-benefiting traits across heritable insect symbionts on eco-evolutionary timescales.🧵 www.pnas.org/doi/10.1073/...
pnas.org
Phenotypic divergence is driven by mobile genetic elements in a heritable insect symbiont | PNAS
Heritable microbes profoundly influence insect biology, yet the traits they confer often evolve rapidly and differ among closely related symbiont s...
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Malcolm White @mfwhite2.bsky.social · 21/09/2026
New preprint from PhD student Yu Sun. TSR1 is a TIR effector specialised for CRISPR defence. It is an obligate dimer activated by cA3 and degrades its own activator using a ring nuclease domain. Perhaps the first confirmed dimeric TIR effector? www.biorxiv.org/content/10.6...
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Daniel Hurdiss @danielhurdiss.bsky.social · 21/09/2026
Excited to share that our norovirus NS3 study is now online in Nature Communications! 🎉 These enzymes, found across an entire order of RNA viruses, have long been molecular motors in search of a function. We think we’ve uncovered their role. (🧵) www.nature.com/articles/s41... #virology #cryoEM
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Martin Pacesa @martinpacesa.bsky.social · 21/09/2026
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/Bi...
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 20/09/2026
An RNase Toxin Hijacks Elongation Factor-Tu to Cleave the Ribosomal Sarcin-Ricin Loop www.biorxiv.org/content/10.64898/20…
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Kenneth Loi @kenjmloi.bsky.social · 18/09/2026
VIPR is now out in Science! 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 ↓
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Innovative Genomics Institute @innovativegenomics.bsky.social · 17/09/2026
Before #CRISPR, there was VIPR — a tool viruses used to battle each other with a never-before-seen genetic coding system, uncovered by researchers in the Doudna Lab. Read more here: ow.ly/KblS50ZOxwQ #AI #LanguageModel #RNA
Terry Zhang, Peter Yoon, Kenneth Loi (left to right) wanted to make sure to include Trevor Docter (on the phone from Harvard).
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Carl Zimmer @carlzimmer.com · 17/09/2026
I wrote about what came before CRISPR 4 billion years ago: a war among viruses. Gift link: nyti.ms/3TBq4q0
nyti.ms
The Next Gene-Editing Technology May Also Be the Oldest (Gift Article)
Scientists have discovered a powerful gene-targeting system in viruses. Billions of years old, VIPR seems to predate CRISPR and may be even more powerful.
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Elise White @elisew00.bsky.social · 17/09/2026
🧬Join us today for the next Nucleic Acid CASP webinar! 🧬 #rna #casprnasig @jiricernyjc.bsky.social will show us how DNATCOv5.0 can be used to analyze and validate nucleic acid structures. Zoom: tinyurl.com/4j263z9d Mailing list: tinyurl.com/57dhy8et Schedule: tinyurl.com/rna-sig-sche...
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denoisingthenoise.bsky.social @denoisingthenoise.bsky.social · 15/09/2026
Our September session will feature "De Novo Design of RNA Pseudoknots with Deep Learning." Speakers: Jill Townley @jilltownley.bsky.social, Chaitanya Joshi @chaitjo.bsky.social, and Andrew Kubaney (Baker Lab) Sept. 30th, 2-3 PM PT on Zoom. See you there! Sign up via Luma below.
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Yun S. Song @yun-s-song.bsky.social · 09/09/2026
We are thrilled to share that our GPN-Star manuscript is now published and freely available: doi.org/10.1038/s415... (1/n)
doi.org
Predicting genome-wide functional constraints with GPN-Star - Nature
GPN-Star, a genomic language model with a phylogeny-aware architecture for whole-genome alignment data, is shown to be a scalable and flexible tool for genetic variant effect prediction across species...
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Innovative Genomics Institute @innovativegenomics.bsky.social · 04/09/2026
Predicting how #RNA folds would be a valuable tool for scientists, but #AI has not been able to crack the problem. A team at the IGI made significant progress on two key hurdles: limited structural data, and the fact that RNA can take on multiple shapes. Read more: ow.ly/Yjgo50ZJcU3
Conner Langeberg and coauthor Roma Nagle look at an RNA molecule structure in the Cate Lab at the IGI. (Photo: Glenn Ramit)
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Conner Langeberg @clangeberg.bsky.social · 05/09/2026
RNA structure prediction lags behind proteins for lack of data. RNASSTR, our new dataset, offers millions of RNA sequence-secondary structure pairs, split structurally to avoid train/test leakage. 📄 doi.org/10.1261/rna.... 📰 innovativegenomics.org/news/ai-mode...
doi.org
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Rubin Lab @therubinlab.bsky.social · 31/08/2026
Happy Monday! ☀️ On the last day of August, the Rubin Lab presents a researcher interview. We sat down with @leosong.bsky.social, co-first author of this paper, at @innovativegenomics.bsky.social! 🎥🧬 Hear more about the science directly from one of the researchers behind the study!
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Erin Doherty @erinedoherty.bsky.social · 31/08/2026
I'm very excited to share that this January, I’ll be joining Columbia University’s Department of Biological Sciences as a tenure-track Assistant Professor 🏙️🦁🍎 @columbiauniversity.bsky.social 🧬 Learn more: dohertylab.org Thank you to all those who supported me along the way!
dohertylab.org
Doherty lab at Columbia University | immune signaling | Sherman Fairchild Center, 1212 Amsterdam Ave, New York, NY 10027, USA
We treat viral antagonism as a discovery tool for host biology to reveal fundamental mechanisms of immune signaling and new opportunities for therapeutic intervention.
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Beckmann Lab @beckmannlab.bsky.social · 01/09/2026
Preprint alert: a helicase watching the ribosomal A-site 👀🧬 Our cryo-EM structure reveals how yeast Dhx29 senses mRNA hairpins forming in the A-site and positions its helicase at the mRNA entry channel to resolve them during translation elongation: doi.org/10.64898/202... #cryoEM #ribosome #RNA
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Matthew Taliaferro @jmtali.bsky.social · 12/08/2026
Excited to share our newest work! We asked whether RNA molecules need to be in a specific place in the cell to do their job. We found that a single RNA must reach the midbody, the structure that pinches two dividing cells apart, for cell division to finish efficiently. 🧵⬇️
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Innovative Genomics Institute @innovativegenomics.bsky.social · 11/08/2026
We're excited to officially welcome UC San Diego as an IGI partner campus! We're working to jointly develop cutting-edge genomic tools for addressing large-scale challenges in health and the environment. Read more about our plans: ow.ly/My0h50Zp8Lj
School of Biological Sciences Dean Kit Pogliano (right) will lead the new IGI collaboration for UC San Diego.
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Doudna Lab @doudna-lab.bsky.social · 16/07/2026
Our AI-guided design of RNA-guided nucleases is now out in @science.org 💻🧬 We used structure and evolutionary data to generate minimal, active and divergent gene editors! www.science.org/doi/10.1126/... Congrats to @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social & team!
science.org
Structure and evolution-guided design of minimal RNA-guided nucleases
The design of RNA-guided nucleases with properties not limited by evolution can expand programmable genome-editing capabilities. However, generating diverse multidomain proteins with robust enzymatic ...
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Nilesh Banavali @nilesh-banavali.bsky.social · 13/06/2026
Continuous recording beam image shift speeds up single particle and tomographic data collection. www.nature.com/articles/s41...
nature.com
Ultra-rapid cryo-EM data acquisition method enabled by continuous recording based beam image shift - Nature Communications
The authors report continuous recording beam-image shift (CR-BIS), a continuous recording strategy that overcomes camera delays to markedly accelerate cryo-EM data acquisition, improving throughput fo...
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Matthew Taliaferro @jmtali.bsky.social · 11/06/2026
New paper! How do RNAs "know" where to go inside a cell? We dug into the sequence elements that route RNAs to the right place. It turns out that, in mammals, they're surprisingly massive (>200 nt), multipartite, and wonderfully complicated. 🧵
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Ahmad Jomaa @jomaalab.bsky.social · 13/05/2026
Excited to share our work uncovering SNOR, a ribosome-associated factor that promotes translation restart after dormancy published in Nature!! This was, as usual, a wonderful collaborative effort between our group and the Mattei Lab @simonemattei.bsky.social @embl.org www.nature.com/articles/s41...
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Cress Lab @cresslab.bsky.social · 30/04/2026
Our lab is proud to present our latest work harnessing Bridge Recombinase for genome-scale editing in diverse bacteria, microbiome editing, and programmable horizontal gene transfer.
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Jamie Cate @jhdcate.bsky.social · 27/04/2026
The best thing since *before* sliced bread... VIPRs. www.biorxiv.org/content/10.6... www.biorxiv.org/content/10.6...
biorxiv.org
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