Dr Emma Hodcroft
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Dr Emma Hodcroft
@firefoxx66.bsky.social
17K followers 180 following 320 posts
Die Virenjägerin! 🏹🧬!
Using programming & phylogenetics, I study & track viruses. Co-developer of Nextstrain, based at Swiss TPH & Uni Basel.
Founder of the orig SC2 variant-tracking website, CoVariants.org
I like 🐈 & 🛫
@[email protected]
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firefoxx66.bsky.social
5/ 💡 How to use it (cont):

- In the results: you’ll see QC status (red/yellow/white), clade calls, mutation counts, coverage gaps, etc. 🔠🚩💯
- The tree view places your sequences into the global phylogeny alongside curated reference data. 🌳
Screenshot showing the results screen of Nextclade, with example D68 sequences having been run, showing the sequence name, QC status, clade assignment, and mutations relative to the reference Screenshot of the tree view in Nextclade, with the D68 sequences having been run. The sequences provided by the user show up as solid circles and thick lines, highlighting their position in the reference tree, which is shown as thin lines.
November 20, 2025 at 12:49 PM
firefoxx66.bsky.social
4/ 💡 How to use it:

- Go to nextclade.org → choose the EV-D68 dataset or go to clades.nextstrain.org?dataset-name...

- Drag & drop your FASTA (or load example)

- Click Run - alignment, QC & clade assignment happen in your browser (no data leaves your computer)
Screenshot showing the EV-D68 dataset on Nextclade, with some example data loaded, ready to run
November 20, 2025 at 12:49 PM
firefoxx66.bsky.social
1/ 🚀 Exciting news: we’ve just released the first Nextclade dataset for Enterovirus D68 (EV-D68), developed in collaboration with the European Non-Polio Enterovirus Network (ENPEN).

👉🏻 Check out the dataset on Nextclade! clades.nextstrain.org?dataset-name...

#EVD68 #Enterovirus #OpenData
November 20, 2025 at 12:49 PM
firefoxx66.bsky.social
October 28, 2025 at 8:52 AM
firefoxx66.bsky.social
Thrilled & honoured to have run the first @pathoplexus.org workshop with @chaoranchen.de @pagasi.bsky.social @kanyerezi30.bsky.social & Arthur Shem Kasambula at @pha4ge.bsky.social on Saturday! 🎉🤝

A fantastic turnout & wonderful time spent with curious users!
October 27, 2025 at 7:58 AM
firefoxx66.bsky.social
We're looking forward to including more details of our current projects, new tools we're working on, and sharing regular updates and musings from the lab members via the blog!

Please do check it - hope it helps you learn a bit about EVE! 💗
eve-lab.org

4/4
A cartoon version of the EVE lab, generated by ChatGPT from a similar photo, showing Nosihle, Emma, Nadia, and Keno
August 29, 2025 at 9:33 AM
firefoxx66.bsky.social
🔍 On our new site you can:

- Meet the EVE team 👥
- Explore our research on viral evolution & spread 🧬
- Explore our phylogenetic @nextstrain.org builds 🌳
- See the tools we build for analysis 🛠️
- Read about our publications & news 📰

2/4
Screenshot of the Collaborations page of the Eve-lab website, showing some of our collaborations: ARTIC2, Center for Pathogen Bioinformatics, ENPEN, ESCAPE, Pathoplexus, & VIM
August 29, 2025 at 9:33 AM
firefoxx66.bsky.social
Interested to learn about how to run your own Loculus (the database code behind @pathoplexus.org)? 🤔🖥️

Sign up for the Loculus Tutorial on Mon 8 Sept at BC2 Conference (@sib.swiss‬) in Basel, run by @chaoranchen.de & Anya Parker! 🧬

Register: www.bc2.ch/registration...

#bioinformatics #openScience
Image showing information on the BC2 (Basel Computational Biology Conference) from 8-10 Sept 2025. Says: "Tutorial: build a microbial genomic sequence database with Loculus - Register now. 8 Sept 2025 - Biozentrum, Basel. Early bird until 30 June 2025"
August 8, 2025 at 8:46 AM
firefoxx66.bsky.social
Right! I forgot that bit - and the money :)
August 6, 2025 at 2:59 PM
firefoxx66.bsky.social
📢New job posting!📢
Are you excited by the idea of building global infrastructure to make pathogen sequencing more accessible, interpretable, and equitable? 🧑🏻‍💻🧬

My group at @swisstph.ch has an opening working with ARTIC2, @pathoplexus.org, & Loculus - read on!

1/5
An image showing the ARTIC and Pathoplexus logos connected by blue lines, with the text "Hiring: post-doc/software engineer" and "Global open-source pathogen tools" and "Join Swiss TPH, Work on ARTIC2 and Pathoplexus, Basel, Switzerland"
July 25, 2025 at 10:44 AM
firefoxx66.bsky.social
Louder for the people in the back 📢
"The main contradiction of liberal democracy is that it has largely been shaped through a history of various friends of illegal civil disobedience against entrenched power structures. Such civil disobedience is (retrospectively) seen as justified, and the people committing it are (retrospectively) seen as heroes... But each successive generation is asked to believe that any further civil disobedience would be unreasonable."
July 4, 2025 at 6:51 AM
firefoxx66.bsky.social
My American friends: I hope you join me today.
To stand up for our freedom to assemble & our freedom of speech. To reject authoritarianism & dictatorship.
To demand the government be accountable to the people - not the reverse.

#NoKings #NoKingsDay #NoKingsProtest
A picture of Emma, the post author, on a train holding a homemade sign stating "the power of the people is stronger than the people in power"
June 14, 2025 at 12:28 PM
firefoxx66.bsky.social
And from here it was straight on to @who.int IPSN to exchange ideas about how to improve global pathogen genomic surveillance & data sharing! Though in some ways the other end of the spectrum, still the themes of empowering communities, building systems, & decentralisation shine on!!
June 12, 2025 at 9:00 PM
firefoxx66.bsky.social
So many moments from yesterday are still hot in my brain, but in particular: fantastic workshop w Joshuaz Tan "funding is governance" & "public goods funding isn't charity" from @julianzawistowski.bsky.social, changing culture &privacy w @web3privacy.info & the incredible music from Shaka Kaumaka!
June 12, 2025 at 8:52 PM
firefoxx66.bsky.social
What a trip! ✨ Enormous thanks to @vitalik.ca & @octantapp.bsky.social for inviting me to d/acc yesterday - the synergies between pathogen surveillance & d/acc are super exciting. But on top of this - discovering a new, energetic community trying to build a better future! 💫
June 12, 2025 at 8:38 PM
firefoxx66.bsky.social
Diving right in, Julian Zawistowski from @octantapp.bsky.social opens with the fact that we need new funding models - because public good funding increases value to everyone! Something that resonates in science with the many tools & resources we depend on - yet can be so hard to fund! #dacc
June 11, 2025 at 9:14 AM
firefoxx66.bsky.social
Thrilled to be at d/acc #dacc Day in Berlin today, hosted by @octant.bsky.social & @vitalik.ca - to speak about how @pathoplexus.org can play a role in a decentralised, community-forward future for pathogen surveillance & research! 🧬🔎🌏 #openscience #opensource
June 11, 2025 at 9:00 AM
firefoxx66.bsky.social
Let's go #Eurovision!
Congrats #Basel on such a great event! ❤️🧡💛💚💙💜
May 17, 2025 at 4:22 PM
firefoxx66.bsky.social
Wishing myself a happy 10 year Viva-versary! 🎓🎉

I could never have imagined that day what lay in store for me after completing my PhD - and am so incredibly grateful for all those who helped me to get there, and helped me from there to here!

Here's to the next 10 years of scientific adventures! 🥂
A photo of the poster, Emma Hodcroft, on 5 May 2015. She is wearing a dark blue top and orange-and-blue patterned skirt, and looking nervous but smiling. She holds a very thick copy of her thesis (printed one-sided and double-spaced as regulations required) with many coloured page-marking tabs sticking out of the sides & top. She stands before a wooden desk covered in notes, notebooks, post-its, small knick-nacks and toys (and a computer), in Ashworth Building at University of Edinburgh, where she did her PhD.
May 5, 2025 at 7:33 AM
firefoxx66.bsky.social
It's a huge honour to have been named one of In Vivo's 'Rising leaders' of 2025! 🙏

And a huge congratulations to all of the incredible pharma, medical, and health scientists selected this year! 🎉

insights.citeline.com/in-vivo/lead...
A screenshot of the In Vivo website showing 30 selected 'Rising Leaders' for 2020, including Emma Hodcroft.
April 23, 2025 at 11:57 AM
firefoxx66.bsky.social
💠And similarly, on the Shared Mutations page:

In addition, you’ll notice some nice touches in functionality & tidying up across the page - like the much-shorter legends! 📏

And more cool things are to come soon, stay tuned! 👂

3/3
A screenshot of the shared mutations view on CoVariants, showing columns labelled with the Nextstrain names of variants A screenshot of the shared mutations view on CoVariants, showing columns labelled with the Pango lineage names of variants
April 20, 2025 at 11:37 AM
firefoxx66.bsky.social
🎚️ This switch applies to all pages & charts across CoVariants.org, and all elements (except tables where both were already displayed!)

For example, here's the legend on the Per Country 🗺️ view showing Nextclade & Pango lineages:

2/3
A screenshot of the per-country view on CoVariants, with the mouse-hover legend appearing, showing variant names labelled with Nextstrain names A screenshot of the per-country view on CoVariants, with the mouse-hover legend appearing, showing variant names labelled with Pango lineage names
April 20, 2025 at 11:37 AM
firefoxx66.bsky.social
🙏Thanks to support from swissuniversities & help from TNG Tech, particularly Simon - we've got a very exciting update to CoVariants! 📢

🎉You can now switch between Nextstrain & Pango lineages!! 🎚️

1/3
April 20, 2025 at 11:37 AM
firefoxx66.bsky.social
Did you even grow up in the UK if you don't have 'summer' holiday snaps like this? 😆

(In case you can't tell, I'm the one drowning in her parka on the left.)
#summerTimeAndTheLivingsEasy #britishSummer
A photo from the 1990s showing 2 girls, aged roughly 5 and 3, making sandcastles on a UK beach on an overcast summer day. Both are bundled up against the cold - wearing long trousers, shoes, and thick parka-style jackets with faux-fur trimming. The post author (Emma) is the girl on the left, barely visible peeking out cheekily from her huge furry hood.
April 13, 2025 at 4:30 PM
firefoxx66.bsky.social
It's beyond ridiculous that one of TWO BSL4 (highest security) labs in the USA & World Reference Centre for Emerging Viruses and Arboviruses has had funding cut by Trump & DOGE because it had a COVID component.

We are willfully & actively throwing valuable & critical science in the trash.
Photo of the World Reference Centre for Emerging Viruses and Arboviruses University of Texas Medical Branch and some description of their work.
April 9, 2025 at 8:16 AM