Jon Mifsud

APSPM brought together researchers from around the world to explore protein evolution from different angles. Structural approaches are reshaping evolutionary inference and the community is growing. Huge thanks to participants and @official-smbe.bsky.social for making this meeting a success.
#StryPhy

Plus got to do some advertising for the new lab 👀 👀

#strphy26

What a great conference!! Leaving Brisbane inspired about the future of structural phylogenetics!

Thanks again to the organisers @cpuentelelievre.bsky.social @proteinmechanic.bsky.social and Jordan Douglas for an amazing work putting it all together!

Our discovery of novel viruses in invasive camelids in Australia leads us to propose a simple idea: RNA viruses may repeatedly evolve functional modules at the 5′ end of their genomes.

#Virology #RNAvirus #VirusEvolution
#Picornavirus #VirusDiscovery

doi.org/10.64898/202...

Inferring context-specific site variation with evotuned protein language models Abstract. Multiple sequence alignments (MSAs) have been traditionally used for making inferences about site-specific diversity in proteins. Recent advancem

Our paper on inferring context dependent entropy using protein language models is officially out in NAR Genomics & Bioinformatics! 🧬🤖

with Adam Strange, Jumpei Ito, and @systemsvirology.bsky.social

academic.oup.com/nargab/artic...

details below...

#NARGAB

Multiple protein structure alignment at scale with FoldMason Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...

APSPM 2026: Structural Phylogenetics Meeting A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.

The program for the SMBE Australasian Protein Structural Phylogenetics Meeting 2026 is now out! Abstract book coming soon.

@official-smbe.bsky.social @proteinmechanic.bsky.social

biosig.lab.uq.edu.au/strphy26/pro...

Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning Mirdita Lab builds scalable bioinformatics methods.

My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring!
mirdita.org

Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments Abstract. Protein structure-based comparison provides a framework for uncovering deep evolutionary relationships that can escape conventional sequence-base

An interesting way to look at encoded structural characters to build alignments and trees downstream. This takes structural phylogenetics one step further in the post-AlphaFold era.

#Evolution #Science #StrPhy

On Confidence Assessment in Structure-Aware Alignments

doi.org/10.1093/gbe/...

Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...

Foraging ecology drives viral community structure in New Zealand's aquatic birds Wild migratory birds play a major role in the global spread of viruses, yet the diversity, host range and transmission patterns of viruses harboured by migratory species in Aotearoa/New Zealand remain...

Foraging ecology drives viral community structure in New Zealand's aquatic birds www.biorxiv.org/content/10.6...

Huge congrats Spyros!!

Guess the news is officially out! Extremely excited to announce that I will be starting my own laboratory at Institut Pasteur @pasteur.fr this coming spring!

Slight change to my office window view from Tokyo Tower🗼 to the Tour Eiffel. 🇫🇷

HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements AbstractSummary. Endogenous viral elements (EVEs) offer valuable insights into virus and host evolution, but their detection remains computationally and bi

I'm excited to introduce our new workflow for detecting endogenous viral elements - HI-FEVER. 🖥️🧬

academic.oup.com/bioinformati...

🧵

Big thanks to @ariskatzourakis.bsky.social, @humanceae.bsky.social, José Gabriel and Cormac for bringing this from conception to fruition!

Join us tomorrow! Joana Pereira is talking about AI-powered classification and discovery across the protein universe. @joanampereira.bsky.social

5PM CET, link in the post and in our bio.

Taxonomic expansion and reorganization of Flaviviridae - Nature Microbiology Analysis of RNA polymerase hallmark gene phylogenies supported by protein structure relationships of flaviviruses and ‘flavi-like’ viruses underpins the taxonomic expansion and reorganization of Flavi...

🧬 Thrilled to share our latest paper in @natmicrobiol.nature.com 📄

A collaboration to give the Flaviviridae (home to Zika, Dengue & HCV) a much-needed taxonomic re-think.

Our at-scale AI structure prediction gave a complementary perspective on viral evolution.

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

Monumental effort led by Peter Simmonds and Jens Kuhn to reorganize the Family Flaviviridae based on analysis of RNA-directed RNA polymerase (RdRP) hallmark gene sequences is finally out. Enjoy reading. #ICTV @utmbhealth.bsky.social @astmh.bsky.social @sbvirologia.bsky.social

#APSPM2026 is open to anyone curious about combining protein structure and evolution. Learn where to start in our workshops and discover how structure meets phylogenetics.

Feb 15 - 18, 2026
Brisbane, Australia
Register here: biosig.lab.uq.edu.au/strphy26/reg...
(in-person only)

A divergent betacoronavirus with a functional furin cleavage site in South American bats Bats are natural reservoirs for a wide range of RNA viruses. Members of the genus Betacoronavirus, including Severe Acute Respiratory Syndrome virus 2 (SARS-CoV-2) and Middle East Respiratory Syndrome...

We’ve identified a highly divergent betacoronavirus from South American bat that encodes a functional furin cleavage site.
Another fascinating reminder of how diverse coronavirus evolution is in wildlife reservoirs.
#Virology #VirusEvolution #Bats #Coronavirus

www.biorxiv.org/content/10.1...

Structural and phenotypic plasticity of the RBD loop2 region is a key determinant for HKU5r-CoVs’ emergence in mink The emergence of novel coronaviruses from animal reservoirs continues to pose a significant zoonotic threat. Here, we investigate the evolutionary origins and virological properties of a recently repo...

New preprint alert!! 🚨🚨🚨in collaboration with the Letko @fviromics.bsky.social and Baric labs!

Just in case you're tired of sarbecoviruses, this time we looked at ACE2-using merbecoviruses! specifically the first HKU5r-CoVs detected in mink a couple of years ago.

www.biorxiv.org/content/10.1...

APSPM 2026: Structural Phylogenetics Meeting A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.

We are excited to announce APSPM 2026 - the SMBE Australasian Protein Structural Phylogenetics Meeting!

🗓️ 15-18 Feb. 2026
🌏 Brisbane, Australia

🔗 biosig.lab.uq.edu.au/strphy26/

📄 Abstract submission: 28.11.2025
✈️ Travel grant application: 28.11.2025
✏️ Registration: 15.01.2026

#StrPhy26

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

Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses Nature Structural & Molecular Biology, Published online: 10 October 2025; doi:10.1038/s41594-025-01649-8Using a new method called FoldTree, the authors compare proteins on the basis of their shape to construct more accurate family trees over long evolutionary timescales and capture distant relationships where sequence information becomes less reliable.

ICYMI: New online: Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses

Save the date! the SMBE Australasian Protein Structural Phylogenetics Meeting #APSPM will take place on 15 - 18 February, 2026 at the University of Queensland in Brisbane, Australia. More details coming up soon. Registration will be free thanks to the generous support of @official-smbe.bsky.social

what a fantastic ted talk!! for those of you who haven't heard of "sociovirology" before or still wonder why it might be important this is the video to watch! 😁

📢Join us for the next ECR #Viromics Webinar:
"Characterising novel viral proteins using protein language models (PLMs)"
‍🎙️ Kieran Lamb (@kieranlamb.bsky.social) | University of Glasgow/UK
🗓️ 8 October 2025, 4 PM CEST
📍 Online | Zoom (register for login details)
👉 coms.osu.edu/webinars/ecr...

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...

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

🚨 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 🧪 🦠

Check out this new BBC documentary on Disease X and pandemic preparedness, broadcast tonight (22/09) and on BBC iPlayer.

It features @cvrinfo.bsky.social's work using #AI to investigate #virology and much, much more. 🧪🦠🤖

It was a real pleasure working with Chris VT and the team. Thank you!

Molecular basis of sarbecovirus evolution and receptor tropism in natural hosts, potential intermediate hosts, and humans Kosugi et al. elucidate sarbecovirus evolution and ACE2 receptor tropism in natural hosts (12 Rhinolophus bat species), potential intermediate hosts (civets and raccoon dogs), and humans using a pseud...

Great to have this one published @cp-cellreports.bsky.social !! Some sarbecoviruses can use more ACE2 orthologs than others. The reason? A few sites in the RBD modulating the receptor usage of these viruses throughout their evolution! Worth a read 👇👇👇

www.cell.com/cell-reports...