Discovery of chimeric RNAs and thousands of new proteins in mammalian cells – including a new regulator of inflammasome signaling! www.nature.com/articles/s41... www.jacksonimmunology.com

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!

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.

dohertylab.org

It was a privilege to lead the biochemistry efforts for the first preprint from the Nomburg lab! Check this exploration of conserved protein folds adapted to suppress immunity. www.biorxiv.org/content/10.6...

Jason Nomburg@jnoms.bsky.social · 3mo ago

Happy to share the first preprint out of the Nomburg lab! Many aspects of cellular immunity are shared across the tree of life. Here, we show that some of these conserved aspects of cellular immunity are mirrored by conserved effectors of immune antagonism. Thread below! 1/15

Happy to share the first preprint out of the Nomburg lab! Many aspects of cellular immunity are shared across the tree of life. Here, we show that some of these conserved aspects of cellular immunity are mirrored by conserved effectors of immune antagonism. Thread below! 1/15

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 3mo ago

Conserved folds enable immune antagonism across the tree of life https://www.biorxiv.org/content/10.64898/2026.07.21.739742v1

New pre-print 📣 “Undruggable” cancer mutations remain very hard to target with current modalities. What if we could instead sense mutant transcripts and convert that recognition into selective cell killing? Check out this work led by postdoc Jingkun Zeng: www.biorxiv.org/content/10.6...

Interested in microbiology, immunology, and host-pathogen interactions? Come work with us! Our department at OHSU is opening a search for a new tenure-track faculty position. See the job advertisement for details. Please share within your networks! www.nature.com/naturecareer...

Faculty Position in Molecular Microbiology and Immunology - Portland, Oregon job with Oregon Health & Science University (OHSU) - Molecular Microbiology and Immunology | 12858852

The Department of Molecular Microbiology and Immunology at OHSU invites applications for a tenure-track Assistant or Associate Professor position.

nature.com

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.

bioRxiv Synthetic Biology@biorxiv-synthbio.bsky.social · 6mo ago

Bridge recombinase enables versatile rewriting of bacterial genomes https://www.biorxiv.org/content/10.64898/2026.04.29.721476v1

We present VIPR, a phage-encoded RNA-guided system that recognizes DNA with a noncontiguous code unlike CRISPR. Tiny, programmable, possibly ancestral to CRISPR immunity; VIPR is built around a striking RNA-DNA-DNA triplex.

Kenneth Loi@kenjmloi.bsky.social · 6mo ago

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.

Amazing work from my talented lab-mates. Check out this phage-encoded RNA-guided system that recognizes DNA with a noncontiguous code unlike CRISPR.

Kenneth Loi@kenjmloi.bsky.social · 6mo ago

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.

Out today: We discovered new viral proteins that target immune signaling molecules, solely based on their AlphaFold-predicted shapes www.science.org/doi/10.1126/... Congrats Nitzan Tal and coauthors! Thank you Kranzusch lab for the fun collaboration! Linking below previous thread on our findings

Structural modeling reveals phage proteins that manipulate bacterial immune signaling

Immune systems in animals, plants, and bacteria often rely on intracellular nucleotide signaling, which viruses can block by sequestering or degrading these signals. We identified structural and bioph...

science.org

Nitzan Tal@nitzantal.bsky.social · last yr.

📢Preprint out! Excited to share my final work from the @soreklab.bsky.social! We mined phage dark matter using structural features shared by anti-defense proteins (viral tools that help phages bypass bacterial immunity) to guide discovery. Found 3 new families targeting immune signaling!

New preprint: Cyclic tri-adenylate signalling by a Panoptes anti-phage guard system with a CARF-TM effector. Great work led by Sabine Grüschow www.biorxiv.org/content/10.6...

Friends, please help spread the word about our microbiology REU program at Montana State University. www.montana.edu/mbi/reu/ Each student receives a stipend ($7000 for 10 wks). Travel compensation, room, and board are also provided. Details in the attached pic--Feb 14 deadline 🧫🧪🦠#microsky

"What we’re … seeing is the toll of the uncertainty." My latest story for @science.org—part of a package that explores how the U.S. scientific community has changed under Trump—includes new numbers on graduate enrollment and faculty hiring. www.science.org/content/arti...

Hello world! I am excited to announce my lab is open at the University of Utah in the Department of Biochemistry. We are looking for scientists at all levels interested in studying host-virus interactions in both bacteria and animals. Come join us in beautiful Utah! (photo is 10 steps from lab)

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!

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...

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...

biorxiv.org

OSTP has issued a request for information, please share with them your ideas for how to improve government functions related to science funding and policy www.federalregister.gov/documents/20...

Notice of Request for Information; Accelerating the American Scientific Enterprise

The Office of Science and Technology Policy (OSTP) requests input from all interested parties on Federal policy updates that aim to accelerate the American scientific enterprise, enable groundbreaking...

federalregister.gov

Divergent viral phosphodiesterases for immune signaling evasion Structure-based searches reveal exceptional diversity among viral 2H phosphodiesterases across the virome that evade immunity by degrading oligonucleotides www.cell.com/cell-host-mi...

Divergent viral phosphodiesterases for immune signaling evasion

Oligonucleotides play fundamental roles in immune system activation across the tree of life. Viral proteins, 2H phosphodiesterases (PDEs), evade immunity by degrading these signals. Doherty and Nombur...

cell.com

Viral enzymes degrade to evade Preview of work identifying & characterizing diverse families of viral two-histidine phosphodiesterase enzymes that degrade nucleotide-based signaling molecules, each with distinct substrate specificities. www.cell.com/cell-host-mi...

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 ...

cell.com

Round 1 of the 2025 Organic Reaction Championship ends today at midnight! Will the Diels–Alder Reaction maintain its legacy dominance? Can the Grignard Reaction overcome its temperament? Vote for your favorite reaction! #ACSOrganic #amplifyorganic zurl.co/DTEvX

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...

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 ...

cell.com

✨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🧬 🔗👇

Excellent story from @aniloza.bsky.social and colleague at STAT on the MOSAIC program. www.statnews.com/2025/12/08/t... 1/4

NIH shut out hundreds of young scientists from funding to start their own labs

Special Report: The NIH has shut out hundreds of young scientists from funding to start their own labs.

statnews.com

This is a neat paper. Especially liked the use of fluoro nucleotides. The specificity and structure of DNA cross-linking by the gut bacterial genotoxin colibactin | Science www.science.org/doi/10.1126/...

The specificity and structure of DNA cross-linking by the gut bacterial genotoxin colibactin

Accumulating evidence has connected the chemically unstable, DNA-damaging gut bacterial natural product colibactin to colorectal cancer, including the identification of mutational signatures that are ...

science.org

I’m happy to share our new preprint! We uncovered the full diversity of bacterial TIR-based antiviral immune signaling, massively expanded the known diversity of Thoeris systems, and revealed conservation of TIR-derived immune signals across the tree of life. www.biorxiv.org/content/10.6...

Systematic discovery of TIR-based immune signaling systems in bacteria

Toll/interleukin-1 receptor (TIR) domains are important for immune signaling across humans, plants and bacteria. These domains were recently found to produce immune signaling molecules in plant immuni...

biorxiv.org

Tomorrow (Thursday) at the Systems Virology Journal Club, Noor Youssef will present her work with Debbie Marks on developing an AI model that predicts how viruses evolve to evade the immune response. Paper: pubmed.ncbi.nlm.nih.gov/40345199/

Shira Weingarten-Gabbay@shiraweingarten.bsky.social · last yr.

🚨 Systems Virology Journal Club – 8th Series! 🚨 #BillSchneider and I are delighted to announce another round of cutting-edge talks in #SystemsVirology! 🦠💡 Join us and an outstanding lineup of speakers, starting Oct 30. Free registration: shiraweingartengabbay.com/systems-viro... 🔬✨

ADAR1 editing is necessary for only a small subset of cytosolic dsRNAs to evade MDA5-mediated autoimmunity @natgenet.nature.com @stanforduniversity.bsky.social www.nature.com/articles/s41...

📢 We have multiple open PhD positions to study bacterial immune systems using cutting-edge cryo-EM, microbiology, and biochemistry in our group! Join us and uncover how bacterial defenses eliminate predators and engineer next-gen biotech tools. 🔥 Apply by Jan 8, 2026 Details: phd.pages.ista.ac.at

Super cool work by @erinedoherty.bsky.social and @jnoms.bsky.social ! 💪🏼 Viruses hack bacterial immunity by breaking down the nucleotide signals that trigger defence 🦠🧬

Erin Doherty@erinedoherty.bsky.social · 11mo ago

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...

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.

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.

innovativegenomics.org