Lightnews — Scholar-powered news

Dr Liam Brierley @liambrierley.bsky.social · 19d

You can when smartass titles become a tickbox in the CRediT author taxonomy 😁

Dr Liam Brierley @liambrierley.bsky.social · 20d

This is the 2nd preprint to come from collaboration between @thepandemicinst.bsky.social @livuniresearch.bsky.social & CSL Seqirus, supported by @baylism.bsky.social & Joaquin Mould.

We hope this work can help risk assess new bird flu strains and flag key mutations in the wild!

#preprint #avianflu

2 3

Dr Liam Brierley @liambrierley.bsky.social · 20d

This stack is able to correctly predict zoonotic potential of sequences in entirely unseen subtypes with AUC=0.95 and F1=0.90, a level of generalisability that is not often seen for machine learning host predictors.

Interestingly, it flags some duck H4 viruses from Americas as having distinct risk.

$A dotplot showing predicted zoonotic probability for all test sequences, which represent 13 subtypes in total. There are blue bird-only sequences toward the left, which generally cluster below the threshold for zoonotic prediction, and red confirmed zoonotic sequences on the right which show subtype specific patterns. Human zoonotic H5N1 sequences are predicted with consistent confidence, all just over the threshold to be considered zoonotic, while H7N9 shows much more variability with a fraction of sequences being misclassified as not zoonotic, and a fraction being classified correctly with extremely strong confidence. Of note is that most sequences of rare spillover events (<10 sequences available, like H10N8 and H3N8) were correctly classified with middling confidence. Highlighted and annotated are also three bird origin sequences that are distinctly higher in predicted zoonotic risk than all other sequences of their same subtypes. They are: H4N6 A/American black duck/New Brunswick/00499/2010, H4N6 A/yellow-billed teal/Argentina/CIP051-91/2011, and H4N8 A/American black duck/New Brunswick/02375/2007.$

1 4

Dr Liam Brierley @liambrierley.bsky.social · 20d

Training on 12 feature sets over each of 8 segments, we find protein properties are usually best at estimating zoonotic potential from a single segment.

But what about whole genomes? We can combine the best models in a single trained meta-learner (or "stack"), that draws on info from all of them!

A heatmap showing how well each modelled combination of feature set and gene/protein predicted zoonotic potential. Protein features showed slightly higher AUC across the board, while the strongest gene/proteins for zoonotic prediction were PB2, PB1, HA, NP, and NS1. We tried five different algorithms, and each was kept at least once, but the best performing algorithms were usually RF (random forests) or XGB (XGBoost).

1 1

Dr Liam Brierley @liambrierley.bsky.social · 20d

We extracted ~19000 influenza sequences from birds and ~600 zoonotic sequences from humans (only non-seasonal subtypes).

Before training, we remove redundancy by grouping similar sequences into clusters. This is important to reduce bias, as most come from just a few subtypes like H7N9 and H5N1.

Histogram over time of the most common avian flu subtypes in our dataset by sequence frequency. Most zoonotic sequences are from H5N1 and H7N9, and peak around 2005-2015. Avian sequences are more mixed and feature many more subtypes including H9N2, H3N8, H10N7, and H5N1, all at highly variable frequencies over time.

1 1

Dr Liam Brierley @liambrierley.bsky.social · 20d

Lots of ML models can predict human spillover. However for influenza this task is harder because of a) genome segmentation, and b) strong signal within subtype or lineage.

We planned a model training architecture to handle this, ensuring predictions are rooted in virus biology, not shared ancestry.

Model training diagram emphasising we hold out an entire subtype of avian influenza during training in order to make unbiased predictions on it, and that we use multiple algorithms, multiple feature sets, and all eight segments to train models

1 1

Dr Liam Brierley @liambrierley.bsky.social · 20d

🚨📝 New work via @thepandemicinst.bsky.social now preprinted!

We took ~19000 sequences of avian influenza virus and trained machine learning models on >40000 genomic/proteomic features - the resulting ensemble can predict zoonotic potential with AUC=0.95. More below!

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

An AI for an AI: identifying zoonotic potential of avian influenza viruses via genomic machine learning

Avian influenza remains a serious risk to human health via zoonotic transmission, as well as a feasible pandemic threat. Although limited zoonotic cases have resulted from the current epizootic outbre...

www.biorxiv.org

2 8 18

Reposted by Dr Liam Brierley

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Sep 1

Experimental infections reveal unexceptional viral tolerance in bats https://www.biorxiv.org/content/10.1101/2025.08.28.672855v1

4 3

Dr Liam Brierley @liambrierley.bsky.social · Jul 11

That'll be St Elmo - same chap who gives his name to the nautical fire!

1

Reposted by Dr Liam Brierley

Colin Carlson @colincarlson.bsky.social · Jun 17

Virus researchers! Please consider participating in this project - it would be a huge help to our lab, and we think it'll lead to some really exciting synthesis. Plus, you'll get an invitation to participate in a workshop later in the project! 🦠😷

Hailey Robertson @haileyrobertson.bsky.social · Jun 17

🧬🦠🌍 What are the big, cross-scale questions shaping the ecology and evolution of emerging viruses?

@torrelavelle.bsky.social and I are building a list of 100 questions + want your input. Help map the future of EEID — fill out & share our short survey!

🔗 airtable.com/appTW4ZoSFjR...

Airtable | Everyone's app platform

Airtable is a low-code platform for building collaborative apps. Customize your workflow, collaborate, and achieve ambitious outcomes. Get started for free.

airtable.com

1 24 28

Reposted by Dr Liam Brierley

Chris Illingworth @chrisillingworth.bsky.social · May 28

We have a job going for a bioinformatician / computational biologist at the CVR in Glasgow. www.jobs.gla.ac.uk/job/computat...

Computational Biologist/Bioinformatician

Computational Biologist/Bioinformatician COLLEGE OF MVLSSchool of Infection and Immunity Job PurposeThe post holder will join the Bioinformatics group at the School of Infection and Immunity, MRC-U...

www.jobs.gla.ac.uk

2

Dr Liam Brierley @liambrierley.bsky.social · May 16

What is this nightmare of flesh

1

Dr Liam Brierley @liambrierley.bsky.social · May 16

If I had a nickel for every consecutive year we've had janky 3D-rendered big cats, I'd only have two nickels but it's weird it's happened twice.

1 4

Dr Liam Brierley @liambrierley.bsky.social · May 15

I look forward to reading www.nature.com/articles/s41...!

A protein language model for exploring viral fitness landscapes - Nature Communications

Ito et al. present CoVFit, an AI model that predicts variant fitness (transmissibility) from spike protein sequences alone. They further demonstrate its utility in forecasting viral evolution via sing...

www.nature.com

3

Dr Liam Brierley @liambrierley.bsky.social · May 15

I'm only able to join ViBioM virtually (thank you @evbc.bsky.social for making this available!!) but some fantastic talks from the @systemsvirology.bsky.social lab who are innovately retraining protein language models to infer virus evolution, antigenicity, and epi! おめでとうございます

1 2

Dr Liam Brierley @liambrierley.bsky.social · May 13

@uofgpe.bsky.social
@uofglasgow.bsky.social
@unistrathclyde.bsky.social

1

Dr Liam Brierley @liambrierley.bsky.social · May 13

So much #scicomm in Glasgow in the next month!

Talks in a pub? ✔️ - @pintofscience.uk: pintofscience.co.uk/events/glasgow

Family activities? - ✔️ Glasgow Science Festival: www.gla.ac.uk/events/scien...

and my (biased) fave - Science comedy??? - ✔️ Bright Club: www.thestand.co.uk/performance/...

1 1 2

Dr Liam Brierley @liambrierley.bsky.social · May 13

(I know it's the same guy cause the photocopy always caught his shirt cuff in the scan)

2

Dr Liam Brierley @liambrierley.bsky.social · May 13

I was tracing the first human reports of every RNA virus in my PhD and I quickly learned about interlibrary loans!

Any uni library can make a request for a paper for you, usually I'd get pdfs, sometimes hardcopies, sometimes even photocopies from a guy at the British library who wore funky shirts.

2 1

Dr Liam Brierley @liambrierley.bsky.social · May 2

Last day for abstract submission to present your work at the 𝗚𝗹𝗮𝘀𝗴𝗼𝘄 𝗩𝗶𝗿𝗼𝗹𝗼𝗴𝘆 𝗪𝗼𝗿𝗸𝘀𝗵𝗼𝗽 and connect with researchers across all directions of virology! We would love to have more representation and contributions from ECRs and students!

Abstracts info in link below!

Dr Liam Brierley @liambrierley.bsky.social · Feb 4

📅 Glasgow Virology Workshop (5 Sep, c/o @cvrinfo.bsky.social ): www.gla.ac.uk/research/az/...

An informal and friendly workshop in all aspects of virology interactive discussions throughout the day. Undergraduates and Masters students welcome!

University of Glasgow - Research - Research units A-Z - MRC-University of Glasgow Centre for Virus Research - Engage - Events & Seminars - Glasgow Virology WorkshopSearch iconClose menu iconMenu icon ...

www.gla.ac.uk

1 1

Reposted by Dr Liam Brierley

School of Biodiversity One Health and Veterinary Medicine @sbohvm.gla.ac.uk · Apr 29

🎓Big Congratulations to Dr Hollie French for passing her Viva yesterday! 🎉

📄Thesis: ‘Genomic Surveillance and Biogeography of Vampire Bat Rabies in Central America and Mexico.’ 🦇🦠and thank you to her supervisor:
@danielstreicker.bsky.social

1 11

Dr Liam Brierley @liambrierley.bsky.social · Apr 2

Yes please! Great to see!

1 3

Reposted by Dr Liam Brierley

Thijs Kuiken @thijskuiken.bsky.social · Mar 24

The UK’s Chief Veterinary Officer has confirmed a case of highly pathogenic avian influenza (H5N1) in a single sheep in Yorkshire following repeat positive milk testing.

To my knowledge, this is the first time the virus has been detected in sheep.

www.gov.uk/government/n...

Influenza of avian origin confirmed in a sheep in Yorkshire

Influenza of avian origin (H5N1) has been confirmed in a single sheep in Yorkshire.

www.gov.uk

2 26 52

Reposted by Dr Liam Brierley

Max Farrell @maxfarrell.bsky.social · Mar 18

Come do a PhD with me using LLMs and comparative methods to understand the emergence of companion animal viruses! 🧠☠️🕸️🐕🐈🖥️

Fully funded 3.5 year PhD based at @sbohvm.gla.ac.uk and @cvrinfo.bsky.social supervised by myself, Margaret Hosie, and Willie Weir

www.findaphd.com/phds/project...

Comparative study of tropism and emergence of virulent companion animal viruses using AI-powered text mining at University of Glasgow on FindAPhD.com

PhD Project - Comparative study of tropism and emergence of virulent companion animal viruses using AI-powered text mining at University of Glasgow, listed on FindAPhD.com

www.findaphd.com

3 8

Reposted by Dr Liam Brierley

Royal Statistical Society @royalstatsoc.bsky.social · Mar 17

We love to hear about about the amazing work of our William Guy Lecturers in bringing stats to young people!

Want to inspire the next generation with a talk about stats and AI?

There's still time to apply for our 2025/26 lectureship 👉 rss.org.uk/news-publica...

Mary Gregory @marygregory.bsky.social · Mar 15

Had a really enjoyable morning @ri-science.bsky.social doing an extended workshop version of my @royalstatsoc.bsky.social William Guy Lecture. It’s a great way to finish my activities for #BritishScienceWeek!

2 4