Jon Mifsud
Postdoc @ KU Leuven | Virus evolution 🧬👨💻
- Reposted by Jon MifsudFoldMason 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...
- Reposted by Jon MifsudThe 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...
- Reposted by Jon MifsudMy 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
- Reposted by Jon MifsudAn 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/...
- Reposted by Jon MifsudPhold'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/...
- 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...
- Reposted by Jon MifsudForaging ecology drives viral community structure in New Zealand's aquatic birds www.biorxiv.org/content/10.6...
- Reposted by Jon MifsudGuess 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. 🇫🇷
- Reposted by Jon MifsudI'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!
- Reposted by Jon MifsudJoin 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.
- 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...
- Reposted by Jon MifsudMonumental 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
- 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)
- Reposted by Jon MifsudWe’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...
- Reposted by Jon MifsudNew 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...
- Reposted by Jon MifsudWe 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
- Reposted by Jon MifsudMy 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!
- Reposted by Jon MifsudICYMI: New online: Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses
- Reposted by Jon MifsudSave 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
- Reposted by Jon Mifsudwhat 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 🧪
- 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...
- Reposted by Jon MifsudViro3D 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
- 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 🧪 🦠
- Reposted by Jon MifsudCheck 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!
- Reposted by Jon MifsudGreat 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...
- Reposted by Jon MifsudThis review highlights how structural phylogenetics and time-dependent rate Bayesian models provide new tools to uncover deep viral evolution beyond outbreak timescales.
- 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....
- 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...
- 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
- Reposted by Jon MifsudSome 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.
- 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
- 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....
- If you’re after more on structural phylogenetics, you’re in luck. Check out this review that came out the other day. Lots of awesome 3Di work coming from @cpuentelelievre.bsky.social @proteinmechanic.bsky.social @jordandouglas academic.oup.com/gbe/article/...
- 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...)
- Reposted by Jon MifsudA 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
- Reposted by Jon MifsudStoked 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...
- Reposted by Jon MifsudCheck out our latest preprint led by Jumpei Ito and @shusukekawakubo.bsky.social !! PLANT 🌱 a protein language model for predicting antigenic cartography! PLANT takes HAs and predicts antigenic map coordinates, allowing for a deep dive into flu antigenic evolution! www.biorxiv.org/content/10.1...
- Reposted by Jon MifsudVery proud of the work from lab members and collaborators that coincidentally came out today www.pnas.org/doi/10.1073/... and www.nature.com/articles/s41.... A bacterial and viral pathogen associated with mass mortality in seastars and oysters. @kevinzhong2006.bsky.social @rhizalyssa.bsky.social
- Reposted by Jon MifsudExcited to share work with Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org biorxiv.org/content/10.1... TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
- Reposted by Jon MifsudExcited to share our work at the interface of virology and AI at two upcoming events! Will present Viro3D (our virus structure database: viro3d.cvr.gla.ac.uk), recent Nature paper on Flaviviruses (www.nature.com/articles/s41...), plus brand new work. #Virology #AI #Research
- Reposted by Jon MifsudWe (with Clement Coclet, not on Bsky) had the chance to work on a broad "state of viromics" review. We tried to use this to give an overview of how the field changed over the last ~ 15 years, and also what we think are some of the major remaining challenges. Full-text access at -> rdcu.be/excHt
- Reposted by Jon MifsudToday at 5pm, @eunbelivable.bsky.social will present her work on the Big Fantastic Viral Database (BFVD) at #ISMB2025 in BOSC. She also has a poster B-123 (tomorrow, 22nd), so please drop by to have ta chat and grab some stickers! 📄 academic.oup.com/nar/article/...
- Reposted by Jon Mifsud**JOBS ALERT** The Virology Unit at @PasteurCambodia hiring 1 Scientist and 2 Postdocs to join our fast-moving, field-connected, research-driven team on emerging viruses and zoonoses. 🧪🧬🥼🦠🔬🐓💉🦇😷 Limited time to apply — and we need people to start ASAP.**👇
- Reposted by Jon MifsudAre you a trainee interested in giving a flash talk at the Computational Structural Virology symposium? Abstracts are due in three days, on July 10!
- Hello everyone! I am pleased to share information on the first ever Computational Structural Virology Symposium, conducted August 4th on zoom and highlighting work in this emerging field. You can register for this event here: forms.gle/CNiqskMwQEuV.... Please re-post!
- Reposted by Jon MifsudStructural motif search across the protein-universe with Folddisco biorxiv.org/content/10.1101/202…
- Reposted by Jon MifsudHendra virus has caused fatal disease in a horse in QLD, the first case in three years
- Reposted by Jon MifsudGot a great idea for a metagenomic virus discovery project but not sure what to do next? We are running a 5 day hands on workshop in beautiful Stellenbosch, South Africa with experts from around the world. Applications are open until 31st July. climade.health/2025/06/22/m...
- Reposted by Jon Mifsud🦋Hello BlueSky!🦋 Let's get right into it. MicroSeq is back September 3-4, 2025! Stay tuned for more details on registration and abstract submission coming soon here and at www.microseqconference.com. 🌟Save the date!🌟 #MicroSeq2025
- Reposted by Jon MifsudInterested in metagenomic virus discovery but don't know where to start? In collaboration with CERI and a group of virus discovery experts from around the world, we'll be running a 5 day hands-on workshop in virus discovery. Find out more here: climade.health/2025/06/22/m...
- Reposted by Jon MifsudQuick thread on the WHO's SAGO report on the origins of COVID-19, highlighting key points and even *new* data. Their summary is that a zoonotic origin of COVID-19 is best supported by available data. This is consistent with most scientific reviews and statements in the rest of the literature.
- Reposted by Jon MifsudI’m so excited to finally have this work published. Fantastic work from @julienmelade.bsky.social culturing a virus identified through metagenomic virus discovery methods
- First isolation of a mammalian chuvirus, bizarrely from Tasmanian Devil facial tumour cells. Work led by @julienmelade.bsky.social and @erinharvey.bsky.social. www.sciencedirect.com/science/arti...
- Reposted by Jon MifsudOur new AI approach for deciphering the virosphere. Led by Mang Shi and Zhao-Rong Li: www.biorxiv.org/content/10.1...
- Reposted by Jon MifsudThanks to @jnoms.bsky.social for putting this excellent online meeting together. Looking forward to talking about viro3d.cvr.gla.ac.uk and our other adventures in structure prediction!
- Hello everyone! I am pleased to share information on the first ever Computational Structural Virology Symposium, conducted August 4th on zoom and highlighting work in this emerging field. You can register for this event here: forms.gle/CNiqskMwQEuV.... Please re-post!
- Reposted by Jon MifsudHello everyone! I am pleased to share information on the first ever Computational Structural Virology Symposium, conducted August 4th on zoom and highlighting work in this emerging field. You can register for this event here: forms.gle/CNiqskMwQEuV.... Please re-post!
