Theo Sanderson
@theo.io
researching viral pathogen genomics at @lshtm.bsky.social | theo.io / sandersonlab.org
Reposted by Theo Sanderson
#AMR #Klebsiella cause >100,000 neonatal deaths globally each year.
Our new preprint shows more than half of #Klebsiella pneumoniae neonatal sepsis cases in African and South Asian are nosocomial, acquired through transmission in neonatal units. #WAAW
doi.org/10.1101/2025...
Our new preprint shows more than half of #Klebsiella pneumoniae neonatal sepsis cases in African and South Asian are nosocomial, acquired through transmission in neonatal units. #WAAW
doi.org/10.1101/2025...
![figure showing estimated proportion of cases in clusters, for each site. range from 0.04 to 0.93, mean estimate in random effects model is 0.57 [0.46,0.68]](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:q5nky4heg5sfix4get4zh2pw/bafkreibshmuvkuafxwd2uk3r42ss6ma2dhmaidbysgvufnbkbv5cn4guai@jpeg)
November 19, 2025 at 3:43 PM
#AMR #Klebsiella cause >100,000 neonatal deaths globally each year.
Our new preprint shows more than half of #Klebsiella pneumoniae neonatal sepsis cases in African and South Asian are nosocomial, acquired through transmission in neonatal units. #WAAW
doi.org/10.1101/2025...
Our new preprint shows more than half of #Klebsiella pneumoniae neonatal sepsis cases in African and South Asian are nosocomial, acquired through transmission in neonatal units. #WAAW
doi.org/10.1101/2025...
Reposted by Theo Sanderson
I read the caption first and thought the illusion might be because the y-axis was on a log scale, but it's not!
My brain was bamboozled regardless.
My brain was bamboozled regardless.
November 19, 2025 at 12:15 PM
I read the caption first and thought the illusion might be because the y-axis was on a log scale, but it's not!
My brain was bamboozled regardless.
My brain was bamboozled regardless.
Reposted by Theo Sanderson
A new tab on Google Scholar???
scholar.google.com/scholar_labs...
scholar.google.com/scholar_labs...
November 18, 2025 at 5:48 PM
A new tab on Google Scholar???
scholar.google.com/scholar_labs...
scholar.google.com/scholar_labs...
Reposted by Theo Sanderson
Pathoplexus is growing not only in terms of new sequences, but also integrating into the larger ecosystem of pathogen surveillance by joining WHO's IPSN and expanding membership. This is the way a pathogen sequence database should work! (Lessons learned from GISAID/SARS-CoV-2...)
1/ 🚀 Big thanks to our community - since August we’ve added thousands of new sequences, rolled out major new features, and welcomed fresh faces into the #Pathoplexus world. Let’s dive into what’s new.👇🏻
Read the full update: pathoplexus.org/news/2025-11...
Read the full update: pathoplexus.org/news/2025-11...
November 18, 2025 at 7:32 PM
Pathoplexus is growing not only in terms of new sequences, but also integrating into the larger ecosystem of pathogen surveillance by joining WHO's IPSN and expanding membership. This is the way a pathogen sequence database should work! (Lessons learned from GISAID/SARS-CoV-2...)
gemini 3 living up to the hype for me
November 18, 2025 at 5:59 PM
gemini 3 living up to the hype for me
Another plug for the excellent ourbike.co.uk, which just helped me finish up a move. Cargo bikes across London for £5 per hour.
November 15, 2025 at 4:53 PM
Another plug for the excellent ourbike.co.uk, which just helped me finish up a move. Cargo bikes across London for £5 per hour.
Reposted by Theo Sanderson
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.
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.
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
November 7, 2025 at 2:41 PM
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.
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.
Reposted by Theo Sanderson
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. 🧵👇
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
November 7, 2025 at 5:03 AM
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. 🧵👇
Reposted by Theo Sanderson
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.
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.
November 4, 2025 at 11:14 AM
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.
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.
Reposted by Theo Sanderson
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
November 6, 2025 at 9:46 PM
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
Reposted by Theo Sanderson
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
November 6, 2025 at 9:46 PM
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."
🙃
🙃
Nextstrain: Interruption to GISAID-based SARS-CoV-2 sequence analyses
Nextstrain blog post from 2025-11-06; author(s): Trevor Bedford, Richard Neher and the Nextstrain team
next.nextstrain.org
November 6, 2025 at 9:51 PM
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."
🙃
🙃
Reposted by Theo Sanderson
@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...
Please consider filling out this VERY SHORT survey about your interest and/or concerns.
docs.google.com/forms/d/e/1F...
Community survey on the addition of Dengue, Chikungunya, Oropouche, Zika and Yellow fever virus to Pathoplexus
Pathoplexus is a new platform for sharing pathogen sequence data, launched in August 2024 [1], with the primary aim of making sharing and accessing pathogen genomic data easier, faster, and more effic...
docs.google.com
October 30, 2025 at 8:11 PM
@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...
Please consider filling out this VERY SHORT survey about your interest and/or concerns.
docs.google.com/forms/d/e/1F...
Reposted by Theo Sanderson
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...
www.lshtm.ac.uk/newsevents/e...
How certain is certain enough? | LSHTM
When faced with a new health threat, there are three crucial questions we must consider. What is going on? What can we do about it? And how can we communicate these things effectively? This talk will
www.lshtm.ac.uk
October 24, 2025 at 6:28 PM
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...
www.lshtm.ac.uk/newsevents/e...
Reposted by Theo Sanderson
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
- 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
New episode of Hard Drugs!
What if you could design a protein never seen in nature?
Scientists are using new AI tools like RFDiffusion, AlphaFold & ProteinMPNN to hallucinate novel proteins to solve problems nature hasn't.
@jacobtref.bsky.social & I talk about the art of protein design 🧑🎨
What if you could design a protein never seen in nature?
Scientists are using new AI tools like RFDiffusion, AlphaFold & ProteinMPNN to hallucinate novel proteins to solve problems nature hasn't.
@jacobtref.bsky.social & I talk about the art of protein design 🧑🎨
The art of protein design with AI
YouTube video by Works in Progress
www.youtube.com
October 17, 2025 at 10:30 PM
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
- 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
Reposted by Theo Sanderson
I built a free tool to try to embarrass British police into doing their job cctv.numpad.io. More info here: onodi.co/bisect/
October 17, 2025 at 10:19 AM
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 <a href="https://poll.blue/p/BxInEF/1" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">2026-2027
2️⃣ <a href="https://poll.blue/p/BxInEF/2" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">2028-2029
3️⃣ <a href="https://poll.blue/p/BxInEF/3" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">2030-2035
4️⃣ <a href="https://poll.blue/p/BxInEF/4" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">2036+
📊 Show results
1️⃣ <a href="https://poll.blue/p/BxInEF/1" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">2026-2027
2️⃣ <a href="https://poll.blue/p/BxInEF/2" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">2028-2029
3️⃣ <a href="https://poll.blue/p/BxInEF/3" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">2030-2035
4️⃣ <a href="https://poll.blue/p/BxInEF/4" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">2036+
📊 Show results
October 10, 2025 at 12:10 AM
The first mostly-AI-rendered film to gross >$100m worldwide will be released in
1️⃣ <a href="https://poll.blue/p/BxInEF/1" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">2026-2027
2️⃣ <a href="https://poll.blue/p/BxInEF/2" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">2028-2029
3️⃣ <a href="https://poll.blue/p/BxInEF/3" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">2030-2035
4️⃣ <a href="https://poll.blue/p/BxInEF/4" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">2036+
📊 Show results
1️⃣ <a href="https://poll.blue/p/BxInEF/1" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">2026-2027
2️⃣ <a href="https://poll.blue/p/BxInEF/2" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">2028-2029
3️⃣ <a href="https://poll.blue/p/BxInEF/3" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">2030-2035
4️⃣ <a href="https://poll.blue/p/BxInEF/4" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">2036+
📊 Show results
Reposted by Theo Sanderson
The Mercator projection if it weren’t cropped
(click to view full size)
(click to view full size)
October 9, 2025 at 4:10 PM
The Mercator projection if it weren’t cropped
(click to view full size)
(click to view full size)
Reposted by Theo Sanderson
#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.
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.
October 9, 2025 at 3:18 PM
#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.
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.
Reposted by Theo Sanderson
“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...
Some cautious good news from @who.int
#IDSky
hq_who_departmentofcommunications.cmail19.com/t/d-l-ggllll...
October 8, 2025 at 5:25 PM
“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...
Some cautious good news from @who.int
#IDSky
hq_who_departmentofcommunications.cmail19.com/t/d-l-ggllll...
this is real fiasco
GPT5 switches to hidden output in its chain of thought:
‘However illusions: In Redwood Redwood "embedding ".
D …………………….’
‘However illusions: In Redwood Redwood "embedding ".
D …………………….’
October 7, 2025 at 9:20 PM
this is real fiasco
