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 🧪

Had an absolutely wonderful few days at #JSV72 in Hamamatsu & IMSUT in Tokyo. Huge thanks to @shusukekawakubo.bsky.social, @shigeru0701.bsky.social, @spyroslytras.bsky.social & everyone in the @systemsvirology.bsky.social lab for being such brilliant hosts. Japan has been an amazing experience 🇯🇵✨

🚨 DPhil opportunity at Pandemic Sciences Institute🚨 Excited to be co-supervising a new DPhil theme with Christophe Fraser and Yvonne Jones on Developing methods for accurate reconstruction of viral histories to guide pandemic preparedness & targeted interventions. Read more here: lnkd.in/eJXSXkia

We are thrilled to welcome the members of our new Early Career Researcher Advisory Panel! Discover more about the researchers who are helping shape the future of scientific communication: buff.ly/5abtNWQ #ECR 🧪

“Fast change, little spread” The University of Oxford’s Prof Katrina Lythgoe and Dr. Mahan Ghafari unpack ONS-CIS data on 576 persistent infections, rapid within-host evolution, and rare transmission after 1 month. #IDsky #MEDsky Read our Q&A: www.contagionlive.com/view/persist...

🚨Our study on characterising the within-host SARS-CoV-2 evolution during persistent infections is now out in @lancetmicrobe.bsky.social! 👉 www.sciencedirect.com/science/arti...

Looking forward to welcoming you tomorrow, @spyroslytras.bsky.social! Spyros will be giving a seminar in Biology (Mansfield Road) at 11am on ‘AI-enabled structural comparisons uncover the deep evolutionary histories of viral glycoproteins’ — come along if you’re around!

Very grateful to the @biology.ox.ac.uk for the kind spotlight — and for the opportunity to do meaningful work alongside such brilliant and thoughtful colleagues across Biology, Pandemic Sciences Institute, and Lincoln College. #GlobalHealth #VirusEvolution #PandemicPreparedness

I don’t have the words to describe what it feels like to watch my home city of Tehran and the neighbourhoods I haven’t seen in almost a decade, now burning on the news. Then getting messages from family and friends asking where it’s safest to flee, with empty pockets and no fuel to escape.

When I abruptly left my PhD in the US in 2017 and moved to the UK — ‘mastered out,’ as they say — many told me I shouldn’t have. That it was all just temporary. That it would pass soon enough…

I'm super proud to share this piece of work, led by @nrascovan.bsky.social, @avanzich.bsky.social and @marialopopolo.bsky.social. See details in Maria's post here:

Only 10 days left to apply! 👇 my.corehr.com/pls/uoxrecru...

Looking forward to tomorrow’s @smtpb.bsky.social event (5:30–7:00pm UK time)! If you’re interested, you can register here: stanford.zoom.us/meeting/regi...

Great thread by Spyros on this long-in-the-making paper which I also contributed to — a deep dive into the timing and origins of both SARS-CoVs👇

🚨We’re hiring a Postdoc to join our group at Oxford! We’re developing methods to understand how pathogens evolve—across hosts, over time, & through molecular & structural change. Keen or know someone who is? Please share! 🕒 3-year post 📅 Deadline: 30 May 🔗 Apply: www.jobs.ox.ac.uk/vacancy/179640

Really looking forward to this event @oxmartinschool.bsky.social on what turns spillovers into epidemics/pandemics in human populations: www.oxfordmartin.ox.ac.uk/events/what-... with exciting speakers. Hosted by the Pandemic Genomics program and moderated by @jessmetcalf.bsky.social

Now online! The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2

A really nice analysis by Katia Koelle and David Rasmussen on the impact of purifying selection on evolutionary rate estimates, tree topology, and phylodynamic parameters. royalsocietypublishing.org/doi/10.1098/...

Two weeks to go until the application deadline for ILESLA. If you or anyone you know would benefit from full funding to carry out a PhD in Life and/or Environmental Science please visit/refer to our website page iles.web.ox.ac.uk/how-apply where you can see open day videos and get full guidance.

Optimal disease surveillance with graph-based active learning. New work led by Joseph Tsui (DPhil student in our group: www.oxfordmartin.ox.ac.uk/people/josep...). Many potential applications to emerging infectious diseases and routine surveillance of IDs. www.pnas.org/doi/10.1073/...

3 new @nejm.org papers on #H5N1 today "highlight the urgent need for vigilant surveillance of emerging mutations and assessment of the threat of human-to-human transmission" (from overview, text below) www.nejm.org/doi/full/10.... www.nejm.org/doi/full/10.... www.nejm.org/doi/full/10....

Looking at academia in 2024, much of the debate feels like a spectrum of contradictions: Some obsess over top-tier journal publications, dismissing almost anything in technical journals. Others claim that publishing solely in technical journals won’t hurt careers (spoiler: it does).

Fantastic review on chronic SARS-CoV-2 infections by virological superstars @neher.io & Alex Sigal in Nature Microbiology. I’ll do a short overview, outline a couple minor quibbles, & defend the honor of ORF9b w/some stats & 3 striking sequences from the past week. 1/64

🎁 Early Xmas present from your friends at the MRC-University of Glasgow Centre for Virus Research @cvrinfo.bsky.social We're thrilled to unwrap Viro3D - a comprehensive database of virus protein structures: >85,000 predicted structures from 4,400 human & animal viruses! 🦠 viro3d.cvr.gla.ac.uk

🚨Just one month left to apply for this exciting project led by me and @ariskatzourakis.bsky.social, exploring sources of evolutionary rate variation in viruses with pandemic potential. Don’t forget to register your interest! 👇

Excellent study by my Penn-CEIRR colleagues showing that a single HA substitution in H5 (at same exact residue that changed in the British Columbia case!) enables efficient H5N1 binding to receptors in the human upper airway. www.science.org/doi/10.1126/...

A thread🧵 on application systems for postdoc jobs in the UK (applies to my university, but I've seen others and they're similar). I have seen (too many times) good applicants who don't seem to understand how recruitment is done on our side - not their fault! it's a privilege! - so here's how

How fast are viruses spreading in the wild? Check out our latest study now published in @plosbiology.bsky.social: doi.org/10.1371/jour.... A study performed with Paul Bastide, Pauline Rocu, Denis Fargette, Olivier Hardy, @msuchard.bsky.social, @stephaneguindon.bsky.social, and Philippe Lemey (1/7)

📢 New preprint! Ancestral sequence reconstruction 🤝 Alphafold 🤝 Crystallography We combined ancestral sequence reconstruction, protein crystallography and deep learning based structural prediction and resurrected 3 billion years of an enzyme's structural history! ➡️ www.biorxiv.org/content/10.1...

I'm trying put together a list of interesting papers (not exhaustive) broadly related to SARS-CoV-2 evolution. Add your favourites in the comments! SARS-CoV-2 variant biology: www.nature.com/articles/s41... Hypotheses on VoC emergence and SARS-CoV-2 evolution: www.nature.com/articles/s41...

Huge pleasure to be hosting Jonathan Stoye FRS for a seminar today at 3.30 in @oxfordbiology.bsky.social. Please do come along if you are around in Oxford! Details in inboxes.

Hello to everyone on Bluesky 👋 We’re a global charitable foundation. We believe science and research are essential to solving the world’s health challenges – and everyone should benefit from them. Find out more about us ⤵️ wellcome.org/what-we-do?u...

“Pandemics and epidemics continue to be a global threat, further amplified by climate change. There is urgent need for equitable access to these tools and capabilities to protect lives in vulnerable communities.” www.who.int/news/item/26...

Last week, a teenager in British Columbia contracted H5N1, the first human case acquired in Canada. The BC CDC and and Canadian Food Inspection Agency have released sequences from this infected person and domestic and wild birds sampled in BC, which we've just added to Nextstrain. A thread:

inaugural post on the new blue app I'll be wasting my time on! I was conferencing last week and spent a lot of time talking about #H5N1 with colleagues. Particularly the curious human case from BC, Canada 🍁. This week the sequence is out and I'm back in Tokyo, so I made some trees! 🧵

Just posting this to #popgen Here's a link to my notes on population & quantitative genetics: github.com/cooplab/popg... Hoping to extend it more after the winter holidays, as I'm just finishing up teaching the undergrad version of class.

Perfect paper for #EvolMed classes and probably best overview of covid/viruses evolution for undergrads. I am just back to it before my tommorow's lecture. What a gem by @ariskatzourakis.bsky.social et al! www.nature.com/articles/s41...

Here's a starter pack for early career researchers in evolutionary biology. I prioritized the most-junior folks, and this list quickly filled up with undergrads, grad students, and postdocs. Might do another list later, but I'm tired. Have fun everyone! 🐒 #evobio go.bsky.app/MzND7nX

I made a starter pack for researchers who study various aspects of viral sociality. It's woefully incomplete and has lots of room to grow, so do message me if I've missed you! go.bsky.app/3PfgjkP #SocialViruses 🦠 🧪

A new Doctoral Training Programme - the Interdisciplinary Life and Environmental Science Landscape Award - has been launched! It will cultivate researchers able to innovate solutions to challenges in and across biological and environmental sciences 👇 bit.ly/3AGjBRk

Here is a list of labs in #ecology and #evolution who are recruiting graduate students for next year: docs.google.com/spreadsheets... PIs looking to recruit can enter information here: t.co/Fn1LRAA5Ip I believe this list is thanks to @drcarl.bsky.social #evosky #ecoevo #evolbio #AcademicJobs

Hello to new people! If you are watching this account-I generally post about virus evolution, higher education, trade unions and 'things like that' i.e., who knows, could be anything. Not posting on behalf of anyone else, just whatever I happen to be interested in or thinking about.

1/ Hello, BSky community! 👋 I’m an incoming Wellcome Trust Early Career Fellow & Group Leader at the University of Oxford. My research focuses on the molecular evolution of pathogens, especially viruses with pandemic potential. You can find out more about our work here: users.ox.ac.uk/~univ4613

Just spotted that the timeline chart I created, of pandemic death tolls over history, is the cover image of Wikipedia's page "List of epidemics and pandemics". Wow! en.wikipedia.org/wiki/List_of...

Fantastic resource for bio icons: NIH Bioart Source Build figures, presentations, and illustrations with 2,000+ science and medical art visuals. This collection of high-quality, scientifically accurate vectors, #icons, and brushes is freely available within the public domain. bioart.niaid.nih.gov

🚨Exciting DPhil project!🚨 Join us in a new project led by me and @ariskatzourakis.bsky.social to explore “Sources of evolutionary rate variation in viruses with pandemic potential”, offered as part of the @oxfordbiology.bsky.social 🦠🧬 Learn more & apply 👉 www.findaphd.com/phds/project...

Extremely excited that @mghafari.bsky.social will be joining the @oxfordbiology.bsky.social department as a Wellcome Trust Early Career Fellow and independent group leader. Very well deserved and an asset to our department.

Really excited to be starting my new role as a Wellcome Trust Early Career Research Fellow in @oxfordbiology.bsky.social soon! Our group will focus on the molecular evolution of emerging human pathogens 🦠🧬🕗 Looking forward to all that lies ahead!

“The discovery of otherwise animal infecting viruses in plants indicated that we may need to survey plants more extensively to understand the origins of animal viruses as well” great work by Jose Gabriel and @ariskatzourakis.bsky.social! @oxfordbiology.bsky.social

What can cloud computing bring to the discovery of novel EVEs in vertebrate genomes? Rather a lot, really happy to share this work with Jose Gabriel: rdcu.be/dXF4A