Mahan Ghafari

congratulations!

HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements AbstractSummary. Endogenous viral elements (EVEs) offer valuable insights into virus and host evolution, but their detection remains computationally and bi

I'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!

Congratulations to @mghafari.bsky.social who has been selected as one of the New Voices in Virology!

Mahan's research focuses on the evolution of pathogens, particularly those with epidemic or pandemic potential and with implications for human, animal, and plant health 🦠

A poster with branding for the MRC-University of Glasgow Centre fo Virus Research, labelled 'Virus Snowflakes.' The poster shows snowflake-like virus designs and song lyrics reading: On the twelfth day of Christmas, a virus gave to me, Twelve fights worth winning, Eleven Christmas dinners, Ten lunar landers, Nine childhood vaccines, Eight tools for teaching, Seven dogs a-barking, Six wasps a-laying, FIIIIVE TIIINY RIIIIIIINGS, Four vaccine platforms, Three genome segments, Two twinned capsids, and A world that is too small to see

Feeling festive?
Why not deck the halls with @cvrinfo.bsky.social's papercraft #VirusSnowflakes and celebrate the science of viruses and the fight against viral diseases.
Download for free: cvr-engagement.co.uk/virus-snowfl...
#scicomm #sciart #decorations

H3N2 preprint: there are concerns of a severe incoming influenza season due to the drifted H3N2 K clade. We at @psioxford.bsky.social analysed epi data and ran scenario models to see what we could discern about K clade transmission dynamics: zenodo.org/records/1770....

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New Voices in Virology Annual competition for early-career virologists to publish a minireview in JVI. Their minireviews will be peer reviewed & published in a collection.

Excited to be part of this amazing group of virologists!
@asm.org
journals.asm.org/journal/jvi/...

Huge congrats, Spyros! Pasteur is very lucky to have you.

Guess 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. 🇫🇷

Yes, exciting times ahead! :)

YouTube video by TEDx Talks The social lives of viruses | Asher Leeks | TEDxNewEngland

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 🧪

Thanks @tah-sci.com!

Persistent SARS-CoV-2 Infections in the Community Show Fast Within-Host Change but Little Late Transmission Oxford’s Prof Katrina Lythgoe and Mahan Ghafari, DPhil, report ONS-CIS data on 576 persistent UK infections with rapid within-host evolution and rare transmission after one month.

“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...

how is the syn vs nonsyn MOV context score/likelihood calculated in these cases?

Grateful to @ryanhisner.bsky.social for his thoughtful comments on the work. Huge thanks also to the incredible ONS-CIS team—especially Sarah Walker—for making this study possible, and to Katrina Lythgoe for her leadership throughout.

We analysed 576 persistent infections and found:
– More common in men & those >60yrs
– Most variation driven by nonsynonymous mutations, esp. in spike NTD & RBD
– Longer infection → higher viral clock rates
– Onward transmission is rare
– Only ~2% showed viral rates on par with highly divergent VOCs

🚨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.

But I also think that leaving when I did was the right move. And to fellow academics affected by this — you’re not alone. And to colleagues in the US: please speak up, advocate for inclusion, and keep those bridges open however you can. Science doesn’t thrive in isolation. And neither do we.

I’ve been very fortunate in my academic journey and the support I’ve found elsewhere. But it’s disheartening to think how many doors remain closed for reasons far beyond our control. I still carry a deep appreciation for my time in the US — mentors, friends, opportunities.

Well, it didn’t, did it? And now, years later, we’re watching history repeat itself — not just in policy, but in the way it quietly redirects the paths of young researchers who simply want to engage, collaborate, and contribute to global science. A lot has changed in my life since then.

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...

Apologies, the link above was incorrect — this one should work: stanford.zoom.us/meeting/regi...

Sorry, my fault—sent the wrong link! This one should work: stanford.zoom.us/meeting/regi...