Jon Mifsud
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jonathonmifsud.bsky.social
Jon Mifsud
@jonathonmifsud.bsky.social
Postdoc @ KU Leuven | Virus evolution 🧬👨‍💻
Reposted by Jon Mifsud
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.
The next ProSE Seminar will be given by Joana Pereira @joanampereira.bsky.social (VIB, KU Leuven)
🗓️ November 11th, 5pm CET

Registration is now open: tinyurl.com/prose-seminar2
Please share!
November 10, 2025 at 2:00 PM
Reposted by Jon Mifsud
🧬 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...
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...
www.nature.com
November 6, 2025 at 12:52 PM
Reposted by Jon Mifsud
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
October 31, 2025 at 12:44 PM
Reposted by Jon Mifsud
#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)
October 30, 2025 at 12:55 AM
Reposted by Jon Mifsud
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...
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...
www.biorxiv.org
October 27, 2025 at 9:32 PM
Reposted by Jon Mifsud
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...
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...
www.biorxiv.org
October 28, 2025 at 5:07 AM
Reposted by Jon Mifsud
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
APSPM 2026: Structural Phylogenetics Meeting
A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.
biosig.lab.uq.edu.au
October 22, 2025 at 10:17 AM
Reposted by Jon Mifsud
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
Reposted by Jon Mifsud
ICYMI: New online: Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses
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.
go.nature.com
October 11, 2025 at 10:18 AM
Reposted by Jon Mifsud
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
October 7, 2025 at 10:46 PM
Reposted by Jon Mifsud
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! 😁
I gave a talk last year at TEDxNewEngland aimed at introducing the idea of viral sociality to a general audience, including implications for evolution & virology. Video now available online below.

#socialviruses #evosky #virosky 🧪
The social lives of viruses | Asher Leeks | TEDxNewEngland
YouTube video by TEDx Talks
www.youtube.com
October 8, 2025 at 5:38 AM
Reposted by Jon Mifsud
📢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...
September 29, 2025 at 3:56 PM
Reposted by Jon Mifsud
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 Jon Mifsud
🚨 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 Jon Mifsud
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!
September 22, 2025 at 10:50 AM
Reposted by Jon Mifsud
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...
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...
www.cell.com
September 20, 2025 at 10:37 AM
Reposted by Jon Mifsud
This review highlights how structural phylogenetics and time-dependent rate Bayesian models provide new tools to uncover deep viral evolution beyond outbreak timescales.
September 16, 2025 at 3:42 AM
Reposted by Jon Mifsud
🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024...
September 3, 2025 at 8:39 AM
Reposted by Jon Mifsud
🐢Keeping up the #virology momentum is @lrnlm.bsky.social, exploring the metatranscriptomes of necropsied turtles. Check out the wide range of #parasites, #bacteria, and #viruses identified in these tissues! #MicroSeeq2025
September 3, 2025 at 2:21 AM
Reposted by Jon Mifsud
Some more incredibly valuable advice from Jackie: refine experimental designs, be critical of bioinformatic output, and perhaps most importantly, name your novel viruses something that brings you joy! Like Jackie’s coolest virus name: Lilsebastian narna-like virus.
September 3, 2025 at 4:32 AM
Reposted by Jon Mifsud
#MicroSeq2025 Plenary Highlight! ✨
Dr Jackie Mahar is an evolutionary virologist & bioinformatician based at CSIRO, managing projects on NGS-based phylogenomics of zoonotic & animal viruses for pathogen discovery, surveillance & viral ecology.
Register👇
trybooking.com/events/landing/1424679
September 1, 2025 at 4:42 AM
There’s been a bunch of new approaches looking at deep viral evolutionary history. We’ve put together a mini review highlighting some recent advancements in structural phylogenetics and time-dependent rate models and what they could do for the field 🦠
🔗 journals.asm.org/doi/full/10....
Recent advances in the inference of deep viral evolutionary history | Journal of Virology
Phylogenetic studies examining the origins, emergence, and spread of viruses have arguably been one of the most active and successful areas of evolutionary biology and form the bedrock of the flourishing field of genomic epidemiology. This, in part, reflects the ability of viruses, particularly those with RNA genomes, to evolve at rates much greater than their cellular counterparts (1). The rapid rate at which viruses evolve and accumulate mutations enables evolutionary signals to be identified through comparative genomics at short timescales relevant for outbreak investigation and response. The integration of phylogenetics and epidemiology, known as phylodynamics, has become a vital tool in response to numerous viral outbreaks, epidemics, and pandemics, including Ebola (2), Zika (3), and, more recently, COVID-19 (4) and mpox (5).
journals.asm.org
August 25, 2025 at 8:32 PM
Reposted by Jon Mifsud
(1/7)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)

[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)
Accelerating Biomolecular Modeling with AtomWorks and RF3
Deep learning methods trained on protein structure databases have revolutionized biomolecular structure prediction, but developing and training new models remains a considerable challenge. To facilita...
www.biorxiv.org
August 15, 2025 at 5:17 PM
Reposted by Jon Mifsud
A formal ad will be forthcoming soon, but I will be hiring at all levels! If my work is interesting to you, and you are looking for a staff scientist, postdoc, or lab tech position in lovely Vienna, please send CV/cover letter to jason(dot)nomburg(at)gladstone(dot)ucsf(dot)edu
PhD Program
www.oeaw.ac.at
August 15, 2025 at 7:54 PM
Reposted by Jon Mifsud
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...
Protein Structure Informed Bacteriophage Genome Annotation with Phold
Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...
www.biorxiv.org
August 8, 2025 at 7:11 AM