Jon Mifsud

Very 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

Scaling down protein language modeling with MSA Pairformer Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...

Excited 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🧵

Excited 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

We (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

Today 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/...

**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.**👇

Are you a trainee interested in giving a flash talk at the Computational Structural Virology symposium? Abstracts are due in three days, on July 10!

Structural motif search across the protein-universe with Folddisco https://www.biorxiv.org/content/10.1101/2025.07.06.663357v1

Hendra virus has caused fatal disease in a horse in QLD, the first case in three years

Got 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...

A call to save the date for MicroSeq2025, returning September 3-4. MicroSeq is an online meeting where microbiology meets sequencing, including bacteria, viruses, and fungi.

🦋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

Interested 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...

Quick 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.

I’m so excited to finally have this work published. Fantastic work from @julienmelade.bsky.social culturing a virus identified through metagenomic virus discovery methods

Our new AI approach for deciphering the virosphere. Led by Mang Shi and Zhao-Rong Li: www.biorxiv.org/content/10.1...

Thanks 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!

We have a new 3-year postdoc position in our group at the @hifmb.de to study plasmids and plasmids systems of the marine environment to survey their utility in microbial responses to environmental change.

Please see the official job ad here, and spread the word:

jobs.awi.de/Vacancies/20...

We've updated our AFESM website to now include biome filtering, allowing exploration of protein structures adapted to specific environments.
🌐 afesm.foldseek.com
Read more about the work in the skeetorial
🦋 bsky.app/profile/mart...
or our preprint
📄 www.biorxiv.org/content/10.1...

The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2 Recombination-aware evolutionary analyses of the entire genomes of SARS-CoV-1-like and SARS-CoV-2-like viruses indicate that SARS-CoV-1 and SARS-CoV-2 descend from bat coronaviruses that circulated as...

Sooo happy to finally have this one published!! (3 years in the making… 👀) A comprehensive investigation into the recency and geographical origins of both SARS-CoVs that spilled to humans in the past few decades, now in @cp-cell.bsky.social www.cell.com/cell/fulltex...

Visit our posters at #RECOMB2025 for:

Structural: MSAs, Virus DB, Core Genes, Motif Discovery, Multimer Clustering & Search, pLM Foldseek, Environmental analysis

Metagenomics: Classification & Metabuli App

GPU-based & RNA search, Proteome clustering, Novel Ribozyme discovery

& get Marv stickers!

InterPro 105.0 24th April 2025

Databases updates Pfam 37.3 PROSITE patterns 2025_01 PROSITE profiles 2025_01 HAMAP 2025_01

New entries 342 new entries with: 318 Pfam 40 NCBIfam 12 Prosite profiles 6 PANTHER 5 CDD

New features InterPro-N annotations BFVD structure predictions Simplified structure pages

📢InterPro release 105.0 is live!
✨Update to Pfam 37.3, PROSITE patterns 2025_01
PROSITE profiles 2025_01 and HAMAP 2025_01
✨342 new entries
✨Addition of InterPro-N annotations
✨Addition of BFVD structure predictions from @martinsteinegger.bsky.social's lab
Have a look: ebi.ac.uk/interpro/htt...
💻🧪🆕

Three recent papers uncovered the intricate interactions between bat merbecoviruses and the ACE2 receptor. In
@cp-cellhostmicrobe.bsky.social
we summarise these findings and lay out the plausible evolutionary scenarios they may imply! 🦇🦇

doi.org/10.1016/j.ch...

EXCITING NEWS🥳! @isme-microbes.bsky.social is now sponsoring 3 travels grants worth EUR 500 each to support early career researchers presenting at the #RdRpSummit2025.
Abstract submissions & registrations are still open!✍️
More info at RdRp.io

A database of structures for ecologically relevant microbial traits - Looks cool - here's the github: github.com/timghaly/Eco...

Just out "Making sense of the virome in light of evolution and ecology" doi.org/10.1098/rspb... from super ⭐ team @meganawallace.bsky.social @duckswabber.bsky.social @jemmageoghegan.bsky.social @ryanmimrie.bsky.social @eddieholmes.bsky.social @xavh.bsky.social in Proc B @royalsocietypublishing.org

Big Fantastic Virus Database (BFVD) version 2 improves 31% of predictions through 12 ColabFold recycles. PAEs and MSAs now also available for download and in the webserver.
🌐https://bfvd.foldseek.com
💾https://bfvd.steineggerlab.workers.dev/
1/3

A Metagenomic Investigation into Apteryx rowi Dermatosis Identifies Multiple Novel Viruses and a Highly Abundant Nematode Abstract. Sporadic cases of dermatosis have been reported in wild Ōkārito Rowi (Apteryx rowi), a species of brown kiwi, for over a decade. The disease exhibits distinctive features, including lesions,...

One for the hepaci fans. We found a cool new hepacivirus (along with some other things) in kiwi with dermatitis meridian.allenpress.com/jwd/article/...

Metabuli App preprint is out!
💻Taxonomic classification & interactive visualization—right on your laptop
🛠️Create new databases or update existing ones with new sequences. 🧵1/5
github.com/steineggerla...
www.biorxiv.org/content/10.1101/2025.03.10.642298v1

Four ways COVID changed virology: lessons from the most sequenced virus of all time After 150,000 articles and 17 million genome sequences, what has science taught us about SARS-CoV-2?

After 5 years, 150k papers and 17 million genomes, here's what we learned about SARS-CoV-2 and viruses in general.

It holds lessons for future pandemics - only if we listen. "We’re in a worse place in terms of pandemic prevention" @eddieholmes.bsky.social told me.

www.nature.com/articles/d41...