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Jason Nomburg

@jnoms.bsky.social
386 followers 309 following 70 posts

Principal Investigator at @aithyra.bsky.social | Structural bioinformatics, virology, and innate immunity | jasonnomburg.com

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Reposted by Jason Nomburg
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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Jason Nomburg @jnoms.bsky.social · 24/09/2026
Congratulations Martin et al! Very nice resource :)
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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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Doris Kaltenecker @dorie00.bsky.social · 21/09/2026
🎓 I am recruiting PhD students through the current Vienna BioCenter PhD Programme call. If you are interested in inter-organ communication, whole-body imaging or systemic disease biology, apply here: training.vbc.ac.at/phd-program/
training.vbc.ac.at
PhD Program
Empowering Curious Researchers at the Vienna BioCenter PhD Program Are you a curious and motivated student looking to launch a successful scientific career? Look no further than the Vienna BioCenter P...
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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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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 19/09/2026
BFVD v3 contains 5.8M viral protein structures, 16× more than v2; 75% high quality, filling a major gap in AFDB coverage. It fully covers 72.6% of reference proteomes and spans 72.7% of ICTV species. Great work by @eunbelivable.bsky.social et al. 📄 www.biorxiv.org/content/10.6... 🌐 bfvd.foldseek.com
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Zach Marin @zacsimile.bsky.social · 17/09/2026
Happy to share our publication on MicroClaw, an AI agent that turns natural language requests into operations on any microscope controlled by Micro-Manager: www.biorxiv.org/content/10.6.... The software is single-click installable (download and click install.bat) at github.com/Micro-Claw/m....
biorxiv.org
Microscope control with a natural language agent
Microscopy underpins modern biology, but acquiring high-quality data from complex experiments at scale remains challenging. Smart microscopy can standardize and automate data collection, but each expe...
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Jason Nomburg @jnoms.bsky.social · 10/09/2026
This application closes on Sept 15! If you're interested in a computational postdoc position in my lab, please apply here! Lots of fun science :)
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François Rousset @francoisrousset.bsky.social · 08/09/2026
🚨 We are excited to share the first preprint of our lab ! We discovered an NADase enzymatic domain in bacterial immunity and in the human protein TEP1. www.biorxiv.org/content/10.6...
biorxiv.org
A widespread NADase domain links bacterial immunity with human TEP1
Recent discoveries on bacterial immunity have revealed that several protein domains involved in anti-phage defense are conserved in eukaryotes, such as SIRim, TIR, PNP and gasdermin. Bacterial immune ...
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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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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 26/08/2026
Foldseek-Interface enables fast search/clustering of the protein interface universe! We clustered 3.1M PDB dimers into 77,167 groups and found new interfaces keep appearing even as fold discovery plateaus. 🧵 📄 www.biorxiv.org/content/10.6... 🔎 search.foldseek.com/interface 🌐 interface.foldseek.com
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Mart Krupovic @mkrupovic.bsky.social · 26/08/2026
Check out our paper on ESCRTs in large DNA viruses. Most enveloped viruses use the host #ESCRT for envelopment, but only mirusviruses and nucleocytoviricots encode it! Congrats @sonaida.bsky.social, @tomdelmont.bsky.social, Ulysse Guyet & Eugene Koonin. @pasteur.fr www.nature.com/articles/s41...
nature.com
Large eukaryotic DNA viruses encode ESCRT machinery for membrane remodelling - Nature Microbiology
A genomic screen reveals homologues of ESCRT components in mirusviruses that infect unicellular aquatic eukaryotes.
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Irma Querques @irmaquerques.bsky.social · 25/08/2026
🎉 Our first paper from the Querques lab is out! We uncover the molecular checkpoints controlling cut-and-paste transposition by CRISPR-associated transposons. Congrats to Mateusz & the whole team! 🧬 www.nature.com/articles/s41... @univie.ac.at @meduniwien.ac.at
nature.com
Transposon end recognition and excision mechanisms of type I-F CRISPR-associated transposases - Nature Communications
CRISPR-associated transposons mediate RNA-guided DNA integration, but the molecular basis of transposase function remains poorly understood. Here, the authors uncover the mechanism of a highly active ...
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Ben Morehouse @benmorehouse.bsky.social · 12/08/2026
Today we are excited to introduce you to PanDA 🐼🐼🐼, a newly uncovered antiphage system!! Attendees at @SISB2026 would have heard a little about this from graduate student Ali Nabhani back in May, but we are now out here in preprint form and delighted to share more of the details. (Thread below)
biorxiv.org
Minimal diadenylate cyclases have been co-opted to detect phage immune evasion
Many bacterial immune defenses transmit recognition of phage infection via the generation of diverse cyclic nucleotide second messengers. Phage have evolved to subvert this kind of immunity by sequest...
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Kranzusch Lab @kranzuschlab.bsky.social · 12/08/2026
The shared principles of human and bacterial antiviral immunity An honor to highlight remarkable discoveries from many labs over the past 12 years that unite previously disparate fields of how animal cells and prokaryotes defend against viruses. www.nature.com/articles/s41... rdcu.be/fzwyB
nature.com
Shared principles of human and bacterial antiviral immunity - Nature
The Review describes shared ancient, conserved mechanisms between human antiviral immunity and bacterial anti-phage systems, outlining universal principles of pathogen sensing, signalling and effector...
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Cornelia Schwayer @cschwayer.bsky.social · 03/08/2026
I will be opening my research group at the Max Delbrück Center later this year to unravel the principles governing the unique context sensing capacity of the liver www.mdc-berlin.de/schwayer and am looking for enthusiastic PhD applicants.
mdc-berlin.de
Schwayer Lab
The mammalian liver possesses a regenerative capacity that is unmatched by any other organ. Following injury, liver epithelial cells can proliferate or even change their identity, enabling the organ t...
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AITHYRA Research Institute of the Austrian Academy of Sciences @aithyra.bsky.social · 04/08/2026
The Nomburg Lab at #AITHYRA is seeking a motivated POSTDOCTORAL FELLOW or BIOINFORMATICS SCIENTIST (all genders) to join the interdisciplinary team that combines AI, structural biol, & high-throughput molecular virology to decode the virus-host conflict. aithyra.at/about/open-p... until 15.9.2026
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Ben Lehner @benlehner.bsky.social · 03/08/2026
1st genome sequenced (Sanger 1977), 1st genome synthesised (Venter 2003), 1st genome + proteome fully mutated (Huijin Xiangua 2026!) @crg.eu @sangerinstitute.bsky.social Complete Mutagenesis of the Genome and Proteome of ΦX174 www.biorxiv.org/content/10.6...
biorxiv.org
Complete Mutagenesis of the Genome and Proteome of ΦX174
The bacteriophage ΦX174 was the first genome to be sequenced and the first to be chemically synthesised. Here we present a complete map of the consequences of changing every nucleotide in the ΦX174 ge...
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Katja Luck @katjaluck.bsky.social · 31/07/2026
Check out our new article if you are interested in disorder-mediated protein interactions, AlphaFold-based structural modeling and variant characterization: rdcu.be/fw2oz Dx.doi.org/10.1038/s41594-026-01846-z
dx.doi.org
Variant characterization in the intrinsically disordered human proteome - Nature Structural & Molecular Biology
Proteome-wide prediction and structural modeling of disordered protein interaction interfaces advance characterization of disease-associated variants in disordered protein regions.
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Jason Nomburg @jnoms.bsky.social · 31/07/2026
I am hiring a computational postdoctoral fellow or bioinformatics scientist! Please apply here if interested, or share with anyone who may be. This position will be following up on our work studying the virus-host conflict. Reposts appreciated! aithyra.onlyfy.jobs/en/job/v2gwu...
aithyra.onlyfy.jobs
Postdoctoral Fellow or Bioinformatics Scientist, Nomburg Lab (all genders)
About AITHYRAAITHYRA is a pioneering biomedical research institute in Vienna, Austria, where artificial intelligence meets life sciences to drive the next biological revolution. AITHYRA is an institut
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Nature @nature.com · 29/07/2026
Nature research paper: Diverse bacterial pattern recognition receptors sense the core phage proteome go.nature.com/45fpXCZ
go.nature.com
Diverse bacterial pattern recognition receptors sense the core phage proteome - Nature
Systematic analysis of prokaryotic STAND NTPases — relatives of animal and plant immune receptors — uncovers diverse antiviral sensors that detect most of the core structural and replicative proteins of bacteriophages.
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Spyros Lytras @spyroslytras.bsky.social · 23/07/2026
Come work on exciting AI for biology projects in Paris!! 🇫🇷 Details and application below, deadline sept 1st!
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
Thanks Alex!
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
Thanks for your efforts, Erin!
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
Thanks so much, Aude!
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
Thank you, Tera! I have quite enjoyed your work on the cell immunity side
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
thanks!
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
Thanks so much!
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
Ad forthcoming, but I am hiring for a postdoc or staff scientist to advance related investigations of the virus-host conflict. This position is ~80-100% computational, but with opportunities for experimental work if desired. If interested, shoot me an email with your CV! Reposts appreciated! 15/15
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
All of this work is thanks to my wonderful co-authors. A big thanks and congratulations to Lorenzo Profeta, who led the domain work, @erinedoherty.bsky.social who led the biochemistry, and the many other bluesky-less colleagues and collaborators who made this work possible :) 14/15
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
TVC is under development, and we welcome feedback! The goal is for it to serve as a unified source of viral protein information - no more "wait, what is this domain anyway?". 13/15
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
Finally, a note on TVC. We've released tvc.apps.aithyra.at to enable exploration by the community. Here, for most viral proteins you can see domain-level annotations at the sequence and structure level. You can also chat with an AI about the database, and do seq/struc searches against TVC 12/15
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
Collectively, we argue that pathogen immune antagonism uses a conserved structural language, and that deciphering this language can allow us to anticipate and identify emerging mechanisms of pathogenesis throughout the tree of life. Read the manuscript for more! 11/15
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
We found that dsRBDs are widespread in the viral proteome, and that diverse eukaryotic viral and phage dsRBDs can restrict dsRNA-sensing in human cells! So, the dsRBD fold is another recurrently-adapted structural feature involved in pan-viral immune antagonism. 10/15
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
Next, we looked at the double-stranded RNA binding domain (dsRBD) fold, which is used by some eukaryotic RNA viruses to evade human dsRNA-sensing pathways. Curiously, the phage protein Acb4, which inhibits cGAS-like enzymes by sequestering cGAMP, is also an adapted dsRBD. So, we dug in. 9/15
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
We found that viral DHH and HD-GYP PDEs can degrade 3'3' cGAMP, and can suppress cGAMP-mediated STING activation in human cells. This suggests that PDE folds capable of immune antagonism are widespread, and shows a fascinating connection between cGAMP regulation by bacterial and viral pathogens 8/15
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
Protein structure searches revealed several viral HD-GYP and a large number of viral DHH PDEs. Phylogenetic analyses revealed evidence of pervasive horizontal gene transfer of DHH PDEs, often from bacteria to bacterial viruses. DHH PDEs are also present in some mimiviruses that infect amoeba 7/15
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
Next, we investigated folds capable of immune antagonism. To start, we took inspiration from bacterial pathogens. M. tuberculosis encodes the DHH-family PDE CdnP to degrade human 2'3' cGAMP, while V. cholerae encodes the HD-GYP family PDEs called v-cGAPs to regulate bacterial 3'3'-cGAMP levels 6/15
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
With this domain-level information, we also could systematically assess how domains co-occur. Using this method, we identified a diverse and widespread family of multi-domain viral proteins reconstituting the Mre11-Rad50 multiprotein complex involved in cellular DNA repair 5/15
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
We separated these proteins into 790K distinct protein domains and systematically mapped their relationships and potential annotations. We found that protein structure alignments give putative annotations for 88% of well-folded domains (compared to 12% with sequence methods!) 4/15
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
We first needed to ask which structures are conserved throughout viruses. To do this, we established The Viral Compendium (TVC, more on this later!), including predicted protein structures from more than 17,000 species of bacterial, archaeal, and eukaryotic viruses 3/15
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
We previously found that viral 2H phosphodiesterases (PDEs) are used by both animal and bacterial viruses to degrade cGAMP, a messenger made by cGAS-like enzymes in bacterial and animal immunity. Here, we asked the question: Are other folds recurrently reused by pathogens for immune antagonism? 2/15
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
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
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Rafael Pinilla-Redondo (Rafa) @rafomics.bsky.social · 21/07/2026
1/4 Every good defence needs a backup! 🛡️⚔ Out now in @natrevmicro.nature.com our Comment on "𝗶𝗺𝗺𝘂𝗻𝗲 𝘀𝗮𝗳𝗲𝗴𝘂𝗮𝗿𝗱𝗶𝗻𝗴"! 🎉 🔗 www.nature.com/articles/s41...
nature.com
Immune safeguarding as a conserved principle of antiviral defence - Nature Reviews Microbiology
All organisms defend against viral infections through active immunity mechanisms that clear the virus or population-level mechanisms that cause regulated cell death. Recent research increasingly shows...
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Aude Bernheim @audeber.bsky.social · 21/07/2026
Out @cp-cellhostmicrobe.bsky.social, natural products meet bacterial immunity! We used genomics to identify lanthivirins: a family of >2,000 lanthipeptide BGCs that protect Actinobacteria against phages. Led by @hshomar.bsky.social & @mariegllm.bsky.social www.sciencedirect.com/science/arti...
sciencedirect.com
A family of lanthipeptides with anti-phage function
Bacteria produce natural products to adapt to their environments, with phage interactions as major ecological and evolutionary drivers. While some nat…
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Jonathan Kagan @jkagan1.bsky.social · 17/07/2026
A new PAMP, a new innate immunity principle and a new preclinical application. I am so pleased to share our study on STING activation mechanisms in health and disease. Led by the fantastic Stephanie Ragland, follow the link below for a summary of all we learned. www.cell.com/immunity/ful...
cell.com
Purine and pyrimidine-based bacterial cyclic dinucleotides egress the phagosome and activate the innate immune sensor STING
Innate immune recognition of bacteria is thought to center on cell-surface or endosomal pattern recognition receptors such as TLRs. Ragland et al. identify an intraphagosomal cyclic dinucleotide (CDN)...
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Antigen Evolution & Design Lab @antigenevo.bsky.social · 14/07/2026
First paper with the lab's affiliation!! ✨✨ summarising some of the cool concepts that the Antigen Evolution & Design Lab will be working on! Together with amazing collaborators @mghafari.bsky.social and @grovearmada.bsky.social www.annualreviews.org/content/jour...
annualreviews.org
Studying the Deep Evolution of Viruses in the Era of Artificial Intelligence Structure Prediction
High mutation rates erode viral sequence similarity, obscuring deep evolutionary history. While protein structure is far more conserved than sequence, its use in evolutionary studies has historically ...
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Burstein lab @bursteinlab.bsky.social · 12/07/2026
It annoyed us that annotation tools aren't great at saying "I just don't know". That's a real problem for metagenomes and non-model organisms, where it usually means picking some threshold and hoping for the best. We built FAMUS to try and fix this. doi.org/10.64898/202... 1/8
doi.org
FAMUS: A Few-Shot Learning Framework for Large-Scale Protein Annotation
Predicting gene function is a pivotal and challenging step in genomic and metagenomic data analysis. Current automatic annotation tools typically rely on the single most similar sequence from the quer...
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Cell - a Cell Press journal @cp-cell.bsky.social · 03/07/2026
Now online! A viral ORFeome library for systems-level genetic dissection of host-pathogen interactions
dlvr.it
A viral ORFeome library for systems-level genetic dissection of host-pathogen interactions
A scalable library of ∼13,000 barcoded viral open reading frames from >500 viral species enables functional genomic screens across the virome. Applying this platform identified viral regulators of cellular proliferation, antigen presentation, and interferon signaling. This platform enables systematic exploration of viral protein function.
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Kevin Forsberg @kvnforsberg.bsky.social · 02/07/2026
Humans and bacteria share strategies to defend against viruses. We wondered: could they use each other's genes? Yes, both can! Bacteria can use human immune genes to defend against phages AND Human cells can use bacterial genes for viral defense. www.biorxiv.org/content/10.6...
biorxiv.org
Bacterial and human exonucleases mediate interkingdom antiviral immunity
All kingdoms of life have developed strategies to limit viral infection. In humans, interferons induce a suite of antiviral factors that collectively provide immunity. Some human immune genes are homo...
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