I want to spell this out in case the implications aren't clear: This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited. The file allowed this. Cut that - cut off all tools the public & others were using.

Nextstrain's daily-updated tree of SARS-CoV-2 genomes was my gateway into the world of viral phylogenetics in early 2020, and Nextstrain's beautiful interactive tree display is crucial to making usher.bio results usable. GISAID cutting off data harms global surveillance efforts. 🧵👇

If you are looking for a PhD in the UK, please check out the LIDo program - www.lido-dtp.ac.uk/apply. If you are interested in viruses and making genetically edited salmon, please look up my icase project. International students are welcome to apply! Please reach out if you have questions.

Closing these public analyses puts the world more in the dark and concretely harms surveillance as it becomes more difficult for variant spotters to contribute to global situational awareness. 4/5

On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5

GISAID on providing data to @Nextstrain.org: "After consulting with our staff and advisors on the feasibility of keeping your global tree up-to-date, there was a clear consensus that continuing to generate, zip and move big files back and forth is not sustainable and a waste of resources." 🙃

@andersonfbrito.bsky.social and I are seeking input from the community on hosting/sharing arbovirus sequencing data (DENV, CHIKV, OROV, ZIKV, & YFV) on @pathoplexus.org. Please consider filling out this VERY SHORT survey about your interest and/or concerns. docs.google.com/forms/d/e/1F...

How certain is certain enough? This is probably the last public London talk I'll be giving on Proof in 2025 – and it's free – so see you there at 5.30pm on 24th November if you're around! www.lshtm.ac.uk/newsevents/e...

Tune in to find out: - how to go from hallucinated cat pictures to hallucinated proteins - whether @jacobtref.bsky.social can do photosynthesis - whether we can make tiny protein straws for tardigrades to drink from

I built a free tool to try to embarrass British police into doing their job cctv.numpad.io. More info here: onodi.co/bisect/

The first mostly-AI-rendered film to gross >$100m worldwide will be released in 1️⃣ 2026-2027 2️⃣ 2028-2029 3️⃣ 2030-2035 4️⃣ 2036+ 📊 Show results

The Mercator projection if it weren’t cropped (click to view full size)

#UKHSAVirusWatch is back, a summary of our weekly winter surveillance report .🦠🧵 This week's data shows an increase in COVID-19 activity, which is circulating at medium levels. Flu activity has also increased, particularly in those aged 15 to 24, but remains at baseline levels.

“The Ebola virus disease (EVD) outbreak in the Democratic Republic of the Congo (DRC) shows signs of containment, with no new confirmed or probable cases reported since our last update” Some cautious good news from @who.int #IDSky hq_who_departmentofcommunications.cmail19.com/t/d-l-ggllll...

seems like we'll still have a job for a year or two #sora

this is real fiasco

🤫

Do you guys remember when they created a neuron-level model of a fruit fly’s brain and they made it sense something sweet and it stuck out its tongue

enjoyed the bento lab in one battle after another

(not intended as serious analysis!)

No, you are not our product. Our product _is_ the code that we write and distribute for others to use. For others to take and build their communities. Making the users the product is exactly the model that never works and continues to never work.

Amazing breakfast this morning. I love waffles

In 2030 what proportion of the video content the average American watches will be directly AI-generated? (normalised by watch-time) 1️⃣ <10% 2️⃣ 10-30% 3️⃣ 30%-60% 4️⃣ >60% 📊 Show results

WAFFLES

Most graphs of the fertility rate depict the 'period fertility rate', which is based on a single year's data and doesn't necessarily reflect how many children women actually have across their lifetimes. I've used data from the Human Fertility Database to show the cumulative number instead:

I'm giving a free public talk asking 'How certain is certain enough?' at @lshtm.bsky.social on Monday 24th November at 5.30pm, as part of the Global Health Lecture Series. From epidemic response and clinical trials to online misinformation and AI, I'll look at how truth emerges – and why it falters.

HHMI adopts Plan U journals.plos.org/plosbiology/...

The science is, in fact, clear. Good studies [1] consistently show a weak association between tylenol & autism. Those studies are very careful to say they can't establish whether this is causal. A huge Swedish study used a clever sibling design to address this, and showed zero causal effect [2].

Terrific new feature presented by @theo.io on @pathoplexus.org called SeqSets for generating DOIs for sequence subsets used in publications, that can then be tracked for impact via CrossRef that will allow data generators to track impact! #IMMEMXiV

I just learned that John McCallum, who maintained an excellent database of storage costs over time, has died. In his final update, he said "I must pass the work of keeping the data updated to the next generation". Has anyone yet picked up the torch, and if not, any advice on how I might?

What also gets to me is that it's bad in a way that you don't need any training to recognize. Any thinking undergraduate student can tell it's incoherent. In fact, it takes multiple years of training and dedication to that particular subfield to fail to realize how bad it is.

it was lots of fun to have the chance to chat pathoplexus with the microbinfie podcast team!

I definitely thought of this word as pain-staking, which doesn't actually make any sense now that I think about it

Amid the concerning news of a new Ebola Zaire outbreak in DRC, teams on the ground have already managed to sample, sequence, and share data. This rapid turnaround is a testament to their commitment and capacity to respond. Read more: virological.org/t/the-16th-e... 1/7

In under 24h following the newly identified outbreak of #Ebola in the DRC, the virus has been isolated, sequenced and the virus sequence data made publicly available. virological.org/t/the-16th-e...

judge your date by how they treat their agentic assistants

The minutes noted that “everyone was searched, including their vehicles, on the grounds that researchers might be carrying mosquitoes in their pockets.” #IDsky #malaria 🧪 www.science.org/content/arti...

NEW EPISODE of HARD DRUGS! “5 hours is too long!” some of you said after our first episode. So our second episode is 20 minutes 🤭 @jacobtref.bsky.social and I explore the world of proteins: how proteins fold into complex shapes, why complexity matters, how crowded and dynamic a cell really is.

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...

Be interested to know what GWAS folks think of this - a preprint suggesting the DNA of blood cells may often have variants/mutations not present in the rest of the body, which would obviously skew results doi.org/10.1101/2025...

AP live feed of the CDC walkout in Atlanta. www.youtube.com/watch?v=KZ7Q...

Finally, CoV-Spectrum is meeting trees 🌳 – this week, we released a new feature to browse the SARS-CoV-2 UShER tree on CoV-Spectrum. With the new feature, you can see a subtree of your variant of interest. 1/4

🗓 Pathoplexus turns ONE! 🎂🎉 In the past year we’ve grown from 4 pathogens to a truly global, community-driven platform for transparent, equitable & impactful pathogen sequence sharing. 📰 Read the full update: pathoplexus.org/news/2025-08... 1/10

It's our birthday! Super proud of what this little database has become in the past year. Today we launched support for measles and a bunch of new features 👇

By what year will greater than 25% of US households own a humanoid robot? 1️⃣ By 2030 2️⃣ By 2035 3️⃣ By 2040 4️⃣ After 2040 / Never 📊 Show results

I know they're a robot. how do I know? they write poetry of course. -life in 2025