I'm recruiting 1-2 grad students through the AITHYRA-CeMM PhD program! Applications are due January 30th. This is a fully-funded PhD program, combining AI and biology to advance biological discovery. Please forward to anyone who may be interested! You can apply here: apply.cemm.at

A systematic analysis of STAND NTPases and their associated sensor domains in bacterial immunity 🤯 Mind-blowing work !

Such a cool story! Can't wait to read!

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...

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...

See below for a really exciting opportunity to join AITHYRA through the global adjunct principal investigator program!

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...

Big congrats to @petrskopintsev.bsky.social and @isabelesain.bsky.social !

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...

📢 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 🦠🧬

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!

Can't wait to read! Seriously awesome stuff

Huge congrats to Owen, Jason, and team! Such a fun story

We train machine learning models on millions of proteins. But when it comes to making predictions, do we need them to understand all proteins at once? Often, we need an accurate model for the specific protein we are studying or designing. We address this with ProteinTTT arxiv.org/abs/2411.02109 1/🧵

#AITHYRA, Vienna's new Biomedical AI institute, is hiring Postdocs! Come work with us. Openings in: 🔹 Generative AI 🔹 Multimodal ML 🔹 Virology 🔹 Enzyme Function Apply by Nov 20: oeaw.ac.at/aithyra/post... #PostDoc #AI #ML #Vienna #ScienceJobs

🚨 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... 🔬✨

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

Highly recommend this position for anyone looking for a technician job! Erin is a wonderful mentor to junior scientists, and her work is awesome!

1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from? Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria. www.biorxiv.org/content/10.1...

Viral AlphaFold Database (VAD) is live in Science Advances ~27,000 predicted viral protein monomers & homodimers Conserved folds across bacteria, archaea & eukaryotic viruses New toxin–antitoxin system KreTA uncovered Vast “functional darkness” remains uncharted www.science.org/doi/10.1126/...

This also leads to a major constraint for the evolution of viral proteins that inhibit immune signaling, which we explored in recent pre-print co-led with @jnoms.bsky.social www.biorxiv.org/content/10.1...

Now online at @nature.com we show how the Panoptes defense system protects against viruses that attempt immune evasion - and expands our understanding of the role of oligonucleotides in immunity. Check out this work co-led with @benadler.bsky.social here: www.nature.com/articles/s41...

Huge congrats for such an amazing story, @benadler.bsky.social and @erinedoherty.bsky.social!!

We are also pleased to be published alongside our friends in the @doudna-lab.bsky.social, @erinedoherty.bsky.social, @benadler.bsky.social www.nature.com/articles/s41...

Our story describing the Panoptes bacterial immune defense system is now finally peer-reviewed and published today! www.nature.com/articles/s41...

Hiring! 🧬🔬 Ever wondered how bacteria fight off viruses? We’re looking for a PhD student to dive into the molecular basis of newly discovered microbial immune systems, an area of biology where much remains to be uncovered. RT/share to help us find our next team member! www.lumc.nl/en/about-lum...

🚨 New Web Resource Alert! 🚨 We're delighted to share Viro3D a database of >85000 viral protein structure predictions from >4400 human & animal viruses. 🔗 viro3d.cvr.gla.ac.uk 📄 www.embopress.org/doi/full/10.... @molsystbiol.org @cvrinfo.bsky.social @uofgmvls.bsky.social #Virology #AlphaFold 🧪 🦠

Viro3D paper is out! We predicted 85,000 protein structures from human & animal viruses. 1/5 🧵 📑 Paper doi.org/10.1038/s443... 🔭 Explore virosphere viro3d.cvr.gla.ac.uk

You’ve heard of ubiquitination, meet deazaguanylation: Doug Wassarman in our lab discovered phage defense pathways have co-opted Q nucleobase biosynthetic enzymes to catalyze a new form of protein conjugation chemistry @science.org www.science.org/doi/10.1126/...

Very excited to share the first publication from the Price Lab, "Replication-competent adenovirus reporters utilizing endogenous viral expression architecture", is now online at Journal of Virology! journals.asm.org/doi/10.1128/...

How can we understand the earliest events in evolution of eukaryotic immunity? @yao-li.bsky.social reports incredible molecular fossils of complete bacterial-like operons in eukaryotes that illuminate how animal immunity was first acquired from anti-phage defense www.biorxiv.org/content/10.1...

Come join the Nomburg Lab in lovely Vienna! As our first listing, we have a research technician position available to help support the research and operations of the lab. If you're passionate about virology and innate immunity, apply here! aithyra.onlyfy.jobs/job/3njyn4ey

So excited to see our newest study out in print! Led by the brilliant @jgezelle.bsky.social and @sophiekorn.bsky.social, we discovered how viruses from highly divergent families converge on a shared RNA structure mechanism to inhibit cellular nucleases. #RNAsky #LoveVirology

📢 New preprint alert! We designed synthetic proteins that can block bacterial immune systems, allowing phages + plasmids to overcome natural defenses. This could transform phage therapy + genetic engineering. Here’s what we found 🧵 Preprint🔗: www.biorxiv.org/content/10.1...

Preprint: De-novo design of proteins that inhibit bacterial defenses Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications Congrats Jeremy Garb! tinyurl.com/Syttt 🧵

With great pleasure we announce that XINYI ZHANG is one of the Starting PIs AI/LS who will join AITHYRA. Xinyi will develop machine learning models for cell and tissue biology: from multimodal integration to biomarkers and function. More info: www.oeaw.ac.at/aithyra/rese... #AITHYRA #StartingPI

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...

📢 Preprint out! Together with @reneechang.bsky.social @kranzuschlab.bsky.social and the amazing @soreklab.bsky.social, we explored viral sponges to map their diversity and function. Discovered huge diversity, including sponges that inhibit Pycsar & Type IV Thoeris! www.biorxiv.org/content/10.1...

The beautiful, ever-expanding universe of viral proteins targeting nucleotide immune signals! Paper by @reneechang.bsky.social in @cp-molcell.bsky.social on a nucleotide sponge www.cell.com/molecular-ce... and preprint by @doudna-lab.bsky.social on viral nucleases www.biorxiv.org/content/10.1...

New pre-print from Doudna lab members @erinedoherty.bsky.social & @jnoms.bsky.social ✨ Here we explore how recurrent adaptation of a single anti-defense protein fold enables evasion of distinct immune systems.

So happy to share this new preprint, co-led by @erinedoherty.bsky.social! We found that 2H PDEs exceptionally widespread across the virome. They are also structurally diverse, which enables them to degrade nucleotide messengers involved in diverse bacterial immune systems.

🚨New paper 🚨 Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇 1/12

Very happy to share that I will be starting my lab at AITHYRA in October! My lab will use structural bioinformatics and functional genomics to understand the function of viral proteins, with a special emphasis on understanding how viruses subvert innate immunity.

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...

This symposium is this coming Monday! There is still time to register: forms.gle/CNiqskMwQEuV...

Big congrats to @owentuck.bsky.social , Jason Hu, and the other authors! Such a fun story!

First preprint from the Nemudryi Lab! 🍾 In this work, we link antiviral immunity in bacteria and humans by showing that homologs of human Schlafen nucleases protect bacteria from phages. www.biorxiv.org/content/10.1...

Really exciting work!

Next up from our lab - a ring nuclease with a novel fold which cleaves all cOA species involved in Type III CRISPR defence. It's also found in plasmid and phage genomes, where it presumably functions as an anti-CRISPR. www.biorxiv.org/content/10.1...