Theo Sanderson
@theo.io
researching viral pathogen genomics at @lshtm.bsky.social | theo.io / sandersonlab.org
Reposted by Theo Sanderson
On the first day of Christmas (in about 2014), @duckswabber.bsky.social gave to me - a partridge in a pear tree.
Happy Christmas everyone!
Happy Christmas everyone!
December 25, 2025 at 8:03 AM
On the first day of Christmas (in about 2014), @duckswabber.bsky.social gave to me - a partridge in a pear tree.
Happy Christmas everyone!
Happy Christmas everyone!
Bike-couriered by the editor himself. An illustrious publication!
December 24, 2025 at 12:42 PM
Bike-couriered by the editor himself. An illustrious publication!
December 21, 2025 at 2:19 PM
Reposted by Theo Sanderson
This smells distinctly like collider bias and/or selection bias and/or regression to the mean... You simply can't select teen prodigies, and world class athletes rom databases, and go run regressions without serious consideration of the selection process!
"Most top achievers (Nobel laureates and world-class musicians, athletes, chess players) demonstrated lower performance than many peers during their early years. Across the highest adult performance, peak performance is negatively correlated with early performance" www.science.org/doi/10.1126/...
Recent discoveries on the acquisition of the highest levels of human performance
Scientists have long debated the origins of exceptional human achievements. This literature review summarizes recent evidence from multiple domains on the acquisition of world-class performance. We re...
www.science.org
December 20, 2025 at 3:48 PM
This smells distinctly like collider bias and/or selection bias and/or regression to the mean... You simply can't select teen prodigies, and world class athletes rom databases, and go run regressions without serious consideration of the selection process!
Reposted by Theo Sanderson
NEW: Housing Minister Matthew Pennycook has just announced the BIGGEST EVER reforms to national policy to deliver more homes! Here are the five biggest: 🧵
December 16, 2025 at 2:56 PM
NEW: Housing Minister Matthew Pennycook has just announced the BIGGEST EVER reforms to national policy to deliver more homes! Here are the five biggest: 🧵
Reposted by Theo Sanderson
To Opus 4.5: "Artifact, no react, with an interactive explainer of how octaves work - should include buttons to press to make sounds and frequency visualizations, make the design minimal, but have a lot of subtle puns" tools.simonwillison.net/octave-expla...
The Octave — A Sound Relationship
tools.simonwillison.net
December 1, 2025 at 4:17 PM
To Opus 4.5: "Artifact, no react, with an interactive explainer of how octaves work - should include buttons to press to make sounds and frequency visualizations, make the design minimal, but have a lot of subtle puns" tools.simonwillison.net/octave-expla...
Reposted by Theo Sanderson
3/ Jean Pierre Musabyimana (Rwanda Biomedical Centre) welcomed the addition, saying: “Having Pathoplexus support the inclusion of the Marburg virus will tremendously benefit our work in Rwanda and the region.”
November 28, 2025 at 12:37 PM
3/ Jean Pierre Musabyimana (Rwanda Biomedical Centre) welcomed the addition, saying: “Having Pathoplexus support the inclusion of the Marburg virus will tremendously benefit our work in Rwanda and the region.”
Reposted by Theo Sanderson
In light of record submission rates and a large volume of AI-generated slop, SocArXiv recently implemented a policy requiring ORCIDs linked in the OSF profile of submitting authors, and narrowing our focus to social science subjects. Today we are taking two more steps:
/1
/1
November 27, 2025 at 2:54 PM
In light of record submission rates and a large volume of AI-generated slop, SocArXiv recently implemented a policy requiring ORCIDs linked in the OSF profile of submitting authors, and narrowing our focus to social science subjects. Today we are taking two more steps:
/1
/1
Supreme confidence that someone else isn't finding something genuinely useful does get my goat
I'm sorry, but the response to this is plainly delusional
I don't begrudge you for disliking AI! there are plenty of reasons to do so! but to claim that it has no use, or has no users, is not a thought based in reality. it's simply not.
are you really, personally, smarter than Terence Tao?
I don't begrudge you for disliking AI! there are plenty of reasons to do so! but to claim that it has no use, or has no users, is not a thought based in reality. it's simply not.
are you really, personally, smarter than Terence Tao?
Is this platform still massively against AI or has it moved more towards acceptance?
November 26, 2025 at 6:46 PM
Supreme confidence that someone else isn't finding something genuinely useful does get my goat
Reposted by Theo Sanderson
Imagine you lived in the 18th century.
Smallpox kills 1 in 3 cases. Yet you can’t culture pathogens, don’t know germ theory, and have no idea what a virus is. How would you invent a vaccine?
In a new episode of HARD DRUGS, we trace the history of vaccines!
Smallpox kills 1 in 3 cases. Yet you can’t culture pathogens, don’t know germ theory, and have no idea what a virus is. How would you invent a vaccine?
In a new episode of HARD DRUGS, we trace the history of vaccines!
The history of vaccines
open.spotify.com
November 26, 2025 at 5:16 PM
Imagine you lived in the 18th century.
Smallpox kills 1 in 3 cases. Yet you can’t culture pathogens, don’t know germ theory, and have no idea what a virus is. How would you invent a vaccine?
In a new episode of HARD DRUGS, we trace the history of vaccines!
Smallpox kills 1 in 3 cases. Yet you can’t culture pathogens, don’t know germ theory, and have no idea what a virus is. How would you invent a vaccine?
In a new episode of HARD DRUGS, we trace the history of vaccines!
Reposted by Theo Sanderson
Hinkley Point C is set to be the most expensive nuclear plant ever built.
The numbers below reveal they spent £700m on fish protection.
Based on the latest estimates that’s £280,000 per fish.
The numbers below reveal they spent £700m on fish protection.
Based on the latest estimates that’s £280,000 per fish.
November 24, 2025 at 12:23 PM
Hinkley Point C is set to be the most expensive nuclear plant ever built.
The numbers below reveal they spent £700m on fish protection.
Based on the latest estimates that’s £280,000 per fish.
The numbers below reveal they spent £700m on fish protection.
Based on the latest estimates that’s £280,000 per fish.
Reposted by Theo Sanderson
Nano banana Pro: “i need a flowchart for how to toast bread, make it as wacky and over the top and complicated as possible.“
Not absolutely perfect, but I can’t believe how much there is a coherent through-line, how clear the text is, and also parts of it are actually funny?
Not absolutely perfect, but I can’t believe how much there is a coherent through-line, how clear the text is, and also parts of it are actually funny?
November 20, 2025 at 7:19 PM
Nano banana Pro: “i need a flowchart for how to toast bread, make it as wacky and over the top and complicated as possible.“
Not absolutely perfect, but I can’t believe how much there is a coherent through-line, how clear the text is, and also parts of it are actually funny?
Not absolutely perfect, but I can’t believe how much there is a coherent through-line, how clear the text is, and also parts of it are actually funny?
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...