Programmable kinetic barcoding for multiplexed RNA detection with Cas13a - Nature Biomedical Engineering A multiplexed RNA detection method exploits crRNA-dependent variability in Cas13a activity on RNA targets for kinetic barcoding and can be used to distinguish among SARS-CoV-2 variants in clinical sam...

In our new work published in @natbiomedeng.nature.com in collaboration with @theottlab.bsky.social and @doudna-lab.bsky.social, we introduce "interfering" guide RNAs (igRNA) for CRISPR-Cas13a that regulate enzyme activity after activation. Congrats to all the authors!

www.nature.com/articles/s41...

Gene editing that spreads within the body could cure more diseases The idea of self-amplifying gene editing is to get cells to pass on packages of CRISPR machinery to their neighbours, boosting the effect

A big challenge for CRISPR gene editing 🧬 is altering a high enough proportion of target cells in the body 🧪

So @doudna-lab.bsky.social have developed editors that can amplify themselves by spreading from cell to cell

Comment from @gaetanburgio.bsky.social

www.newscientist.com/article/2514...

Five UC Berkeley faculty elected to National Academy of Engineering - Berkeley News A chemical engineer, an electrical engineer, a biochemist, a roboticist and a laser dynamicist are among the new members.

Congratulations to Jennifer Doudna, 2018 #KavliPrize Nanoscience Laureate and CRISPR pioneer, for her recent election to the National Academy of Engineering! She's now one of a few people elected to all three academies @nationalacademies.org. Learn more: bit.ly/4s4k98m

@doudna-lab.bsky.social

"I believe a strong department is built on a culture where people feel supported and included. These investments help retain talent, foster collaboration, and support the next generation of scientists." Laurent Coscoy

"Supporting basic research — and research training — is more important today than ever. Academic research is the engine of discovery for the world, and by supporting student research opportunities, we are developing the skills and minds that will lead the way for future breakthroughs." Jennifer Doudna

"The MCB Department has played a key role in what are arguably the two most impactful discoveries in biomedicine in the 21st century- checkpoint blockade immunotherapy and CRISPR/Cas9-based gene editing. We want to give our undergraduates the best chance of participating in our next big discoveries.: Iswar Hariharan

Today’s the day to make a BIG impact for the MCB community! 🌟
MCB faculty share—in their own words—why our initiatives matter. @doudna-lab.bsky.social @hariharanlab.bsky.social

✅ Read about our goals bit.ly/BigGiveMCB26goals
✅ Click 🔗 bit.ly/BigGiveMCB26 to donate

🚀 New preprint! @jacobsenucla.bsky.social x @doudna-lab.bsky.social collaboration: High-activity TnpB (Ymu1-WFR) + a multi-gRNA system in TRV enables heritable, tissue-culture-free multiplex editing in plants. Big potential for plant biotech 🧬🌾🌱
doi.org/10.64898/202...

How do the ancestors of CRISPR-Cas unwind DNA and how can this lead to better genome editing? With our collaboration between @doudna-lab.bsky.social x @jacobsenucla.bsky.social x Zev Bryant's lab x @savagecatsonly.bsky.social we've uncovered the secrets behind TnpB's dynamics!

Victoria Gray

Check out the latest episode of Rewriting the Code, featuring Jennifer Doudna and #SickleCell patient pioneer Victoria Gray who was cured with a #CRISPR-based treatment in a groundbreaking clinical trial: https://ow.ly/t6FY50XVNO7

Targeted delivery of genome editors in vivo - @doudna-lab.bsky.social @innovativegenomics.bsky.social go.nature.com/4qKp6Tb

Stepwise DNA unwinding gates TnpB genome-editing activity TnpB is a compact RNA-guided endonuclease and evolutionary ancestor of CRISPR-Cas12 that offers a promising platform for genome engineering. However, the genome-editing activity of TnpBs remains limit...

New preprint 👉Doudna x Bryant x Jacobsen x Savage collaboration!
Work led by @zehanzhou.bsky.social, I. Saffarian-Deemyad, @honglue.bsky.social, T. Weiss
We dissect how stepwise DNA unwinding gates TnpB genome editing, revealing how unwound DNA states enhance cleavage
www.biorxiv.org/content/10.6...

Fig. 5. Phylogenetic distribution of VchCAST activator and inhibitor genes. The phylogenetic distribution of 11 E. coli regulatory genes was mapped across 80,789 representative bacterial genomes from 92 phyla in Genome Taxonomy Database, release 214.0 (GTDB version 214.0) (72, 73), with at least 10 members. Homologs were identified using AnnoTree (60) and confirmed with the eggNOG database (70).

New in Science Magazine Science Advances from the Doudna Lab, Rubin Lab and Cress Lab —Identification of proteins influencing #CRISPR-associated #transposases for enhanced #GenomeEditing. Read here: https://ow.ly/U0s450XS82n

During my postdoc in @therubinlab.bsky.social, @leosong.bsky.social and I aimed to make CRISPR-associated transposons more efficient for editing bacteria.

Couldn’t have done it w/o a CAST of characters at IGI and beyond @innovativegenomics.bsky.social, @cresslab.bsky.social, @doudna-lab.bsky.social

Temporal photoproximity labeling of ligand-activated EGFR neighborhoods using MultiMap - Nature Chemical Biology A multiscale photoproximity labeling proteomics workflow captures dynamic neighborhoods of extracellular and intracellular epidermal growth factor (EGF) receptor interactomes during early, middle and late signaling upon activation by EGF.

🎺New paper alert🎺 Out now in Nature Chemical Biology from IGI's Jennifer Doudna (Doudna Lab) and collaborators: Temporal photoproximity labeling of ligand-activated EGFR neighborhoods using MultiMap

Read here: https://ow.ly/izGo50XAkog

Excited to share our work designing genome editors with machine learning! 🧬💻 Huge thanks to
@petrskopintsev.bsky.social @isabelesain.bsky.social @doudna-lab.bsky.social and all co-authors. Check out the thread for a summary of what we found 👇

Viral enzymes degrade to evade Across all domains of life, immune systems rely on nucleotide-based signaling molecules to activate defense responses. In a recent Cell Host & Microbe study, Doherty, Nomburg, and colleagues identify ...

A very nice Preview of our work in
@cp-cellhostmicrobe.bsky.social
this morning from Chrishan Fernando & Nicole D. Marino! www.cell.com/cell-host-mi...

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Congrats to IGI's Jill Banfield, Jennifer Doudna, Mary Firestone, Patrick Hsu, Alex Marson, Kris Niyogi, Eva Nogales, Dan Nomura, and Jennifer Puck — each is on Clarivate's Highly Cited Researchers 2025 list for ranking in the top 1% in their field by citations!

Excited to share our first work on protein design! Huge thanks to the entire team, and especially to Bel, Evan, to the Doudna, Jacobsen, Cate, Banfield labs, all co-authors, and my D-lab mates! 💫

First co-led work from the Doudna lab 🤜🤛
We designed minimal RNA-guided nucleases with AI, and even did Cryo-EM during an earthquake (!) Huge honor working with @petrskopintsev.bsky.social, @evandeturk.bsky.social, Jennifer Doudna and co-authors, everyone at D-Lab and @innovativegenomics.bsky.social

🧵4/4 We solved the first experimental structure of an AI-designed RNA-guided nuclease, which revealed new protein-nucleic acid contacts across conformational states.

🔗 See our preprint:
www.biorxiv.org/content/10.6...

🧵3/4 We assessed activity using a high-throughput bacterial assay, followed by editing the human and plant genomes 🧫🌱

🧵2/4 By coupling inverse folding with evolutionary information, we generated highly active and diverse variants with a high design success rate ⚙️

✨New preprint!

🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al!
Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬

🔗👇

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 multi-domain proteins with robust enzymatic...

🧵4/4 We solved the first experimental structure of an AI-designed RNA-guided nuclease, which revealed new protein-nucleic acid contacts across conformational states.

🔗 See our preprint at the link below!
www.biorxiv.org/content/10.6...

🧵3/4 We assessed activity using a high-throughput bacterial assay, followed by editing the human and plant genomes! 🧫🌱

🧵2/4 By coupling inverse folding with evolutionary information, we generated highly active and diverse variants with a high design success rate ⚙️

Career update: I'm happy to say that I've accepted a postdoc position at UC Berkeley at @innovativegenomics.bsky.social in Jennifer Doudna's lab! I'm looking forward to this exciting new chapter of my scientific career!

We're excited to share our lab's first lead paper!

We developed OriGen, a language model trained to generate plasmid origins of replication. 🔄🦠

The model generates sequences that are significantly different from wild type origins and, remarkably, they allow for replication in vivo.

Read it here ⬇️

New Method Uncovers How Viruses Evade Immune Responses — and How We Might Fight Back Explore how viruses evade immune responses by developing enzymes that disrupt molecular alarm signals in host cells.

1/2 New from co-first authors @erinedoherty.bsky.social and @jnoms.bsky.social of the @doudna-lab.bsky.social — Bacteria fight off viruses using tiny molecular “alarm signals” made of nucleotides. To survive, viruses must find ways to shut these signals down.

My lab is hiring postdocs! We combine AI, protein structure prediction and comparison, and high-throughput virology to study the virus-host conflict.

You can read more about my lab's research here: jasonnomburg.com/research/

Apply here to join us in lovely Vienna! aithyra.onlyfy.jobs/job/0khkxp82

So happy to see this work out! Was such a pleasure to co-lead this effort with Erin. Do you like viral immune evasion, and using protein structure to study immune antagonists? Give it a read!

Divergent viral phosphodiesterases for immune signaling evasion Cyclic dinucleotides (CDNs) and other short oligonucleotides play fundamental roles in immune system activation in organisms ranging from bacteria to …

Work I co-led with @jnoms.bsky.social is now online at
@cp-cellhostmicrobe.bsky.social ! We revealed a previously unrealized diversity of viral immune-evasion proteins that selectively destroy different cyclic nucleotide signals used in bacterial immunity.

www.sciencedirect.com/science/arti...