Jason Nomburg
jnoms.bsky.social
Jason Nomburg
@jnoms.bsky.social
Principal Investigator at @aithyra.bsky.social | Structural bioinformatics, virology, and innate immunity | jasonnomburg.com
Pinned
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
The Starting Principal Investigators at #AITHYRA the Research Institute for Biomedical Artificial Intelligence of the OeAW in Vienna invite outstanding candidates to apply for postdoctoral positions in the field of AI/ML & Life Sciences.
www.oeaw.ac.at/aithyra/post...
Please apply by 20 Nov 2025!
Huge congrats to Owen, Jason, and team! Such a fun story
November 14, 2025 at 7:27 AM
Reposted by Jason Nomburg
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/🧵
October 23, 2025 at 1:08 PM
Reposted by Jason Nomburg
#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
October 20, 2025 at 3:46 PM
Reposted by Jason Nomburg
🚨 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... 🔬✨
October 20, 2025 at 2:55 PM
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
The Starting Principal Investigators at #AITHYRA the Research Institute for Biomedical Artificial Intelligence of the OeAW in Vienna invite outstanding candidates to apply for postdoctoral positions in the field of AI/ML & Life Sciences.
www.oeaw.ac.at/aithyra/post...
Please apply by 20 Nov 2025!
October 20, 2025 at 1:03 PM
Highly recommend this position for anyone looking for a technician job! Erin is a wonderful mentor to junior scientists, and her work is awesome!
I'm hiring a lab technician to help me explore some exciting new questions about virus-host interactions! Biochemistry and/or mammalian cell culture experience is desired.
October 17, 2025 at 10:06 PM
Reposted by Jason Nomburg
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...
Antiviral reverse transcriptases reveal the evolutionary origin of telomerase
Defense-associated reverse transcriptases (DRTs) employ diverse and distinctive mechanisms of cDNA synthesis to protect bacteria against viral infection. However, much of DRT family diversity remains ...
www.biorxiv.org
October 17, 2025 at 5:22 PM
Reposted by Jason Nomburg
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/...
The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes
VAD is a Viral AlphaFold Database of protein monomers and homodimers from viruses infecting hosts across the tree of life.
www.science.org
October 2, 2025 at 8:48 AM
Reposted by Jason Nomburg
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...
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 humans. In response, viruses use phosphodiesterase...
www.biorxiv.org
October 2, 2025 at 3:06 AM
Reposted by Jason Nomburg
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...
A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature
Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.
www.nature.com
October 2, 2025 at 3:01 AM
Huge congrats for such an amazing story, @benadler.bsky.social and @erinedoherty.bsky.social!!
October 1, 2025 at 6:01 PM
Reposted by Jason Nomburg
Our story describing the Panoptes bacterial immune defense system is now finally peer-reviewed and published today! www.nature.com/articles/s41...
The Panoptes system uses decoy cyclic nucleotides to defend against phage - Nature
The Panoptes antiphage system defends bacteria by detecting phage-encoded counter-defences that sequester cyclic nucleotide signals, triggering membrane disruption and highlighting a broader strategy of sensing immune evasion through second-messenger surveillance.
www.nature.com
October 1, 2025 at 4:05 PM
Reposted by Jason Nomburg
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...
PhD-positie Bacteriële Verdedigingssystemen tegen Virussen | LUMC
Wij zoeken een getalenteerde en gemotiveerde PhD-kandidaat om het onderzoeksteam van Luuk Loeff te versterken. In dit project maak je gebruik van geavanceerde technologieën om te ontrafelen hoe bacter...
www.lumc.nl
September 29, 2025 at 11:36 AM
Reposted by Jason Nomburg
🚨 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
viro3d.cvr.gla.ac.uk
September 26, 2025 at 11:36 AM
Reposted by Jason Nomburg
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
Viro3D: a comprehensive database of virus protein structure predictions | Molecular Systems Biology
imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for >4,400 viruses, allowing mapping of form and function across the human and animal virosphere. Viro3D i...
doi.org
September 26, 2025 at 2:06 PM
Reposted by Jason Nomburg
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/...
September 25, 2025 at 7:16 PM
Reposted by Jason Nomburg
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/...
Replication-competent adenovirus reporters utilizing endogenous viral expression architecture | Journal of Virology
This research provides powerful new tools to rapidly study adenovirus gene expression and replication. By integrating fluorescent and secreted luciferase reporters into native viral regulatory element...
journals.asm.org
September 16, 2025 at 6:12 PM
Reposted by Jason Nomburg
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...
September 5, 2025 at 10:13 AM
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
September 4, 2025 at 9:03 PM
Reposted by Jason Nomburg
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
Our study from the Steckelberg lab is out now in @narjournal.bsky.social !! We dove into a new nuclease-blocking viral #RNA structure important for viral infection, which provided evidence of similar structure-based strategies across diverse viral families. academic.oup.com/nar/article/...
A conserved viral RNA fold enables nuclease resistance across kingdoms of life
Abstract. Viral exoribonuclease-resistant RNA (xrRNA) structures block cellular nucleases to produce subgenomic viral RNAs during infection. High sequence
academic.oup.com
September 4, 2025 at 8:54 PM
Reposted by Jason Nomburg
📢 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...
Synthetically designed anti-defense proteins overcome barriers to bacterial transformation and phage infection
Bacterial defense systems present considerable barriers to both phage infection and plasmid transformation. These systems target mobile genetic elements, limiting the efficacy of bacteriophage-based t...
www.biorxiv.org
September 2, 2025 at 7:36 AM
Reposted by Jason Nomburg
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
🧵
Synthetically designed anti-defense proteins overcome barriers to bacterial transformation and phage infection
Bacterial defense systems present considerable barriers to both phage infection and plasmid transformation. These systems target mobile genetic elements, limiting the efficacy of bacteriophage-based t...
www.biorxiv.org
September 2, 2025 at 10:48 AM
Reposted by Jason Nomburg
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
August 29, 2025 at 10:50 AM
Reposted by Jason Nomburg
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...
August 27, 2025 at 4:14 PM