Tim Downing
@downingtim.bsky.social
@[email protected] - also downingtim.bsky.social - Head of #Genomics at The #PirbrightInstitute (UK). He/him. All posts (etc) are in a personal capacity. I log in regularly, nearly every month. #Andacyclist #genomics #virus #pathogen #evolution
Pinned
Using pangenome variation graphs to improve mutation detection in a large DNA virus
Accurately quantifying viral genetic diversity is essential for understanding pathogen evolution, transmission, and emergence. However, standard approaches that map sequencing reads to a single linear...
www.biorxiv.org
Our work on mapping read libraries to viral #pangenome variation graphs (PVGs) to reduce reference bias
Using lumpy skin disease virus #lsdv (dsDNA #virus) as an example
"Using pangenome variation graphs to improve mutation detection in a large DNA virus"
www.biorxiv.org/content/10.1...
[1/7]
Using lumpy skin disease virus #lsdv (dsDNA #virus) as an example
"Using pangenome variation graphs to improve mutation detection in a large DNA virus"
www.biorxiv.org/content/10.1...
[1/7]
Reposted by Tim Downing
There are some spectacularly misguided "assumptions" in the Home Office's impact assessment on its changes to immigration rules. More than that though, it confirms not only will these changes cost the country billions, they are also discriminatory. 1/
assets.publishing.service.gov.uk/media/6937e6...
assets.publishing.service.gov.uk/media/6937e6...
December 9, 2025 at 5:12 PM
There are some spectacularly misguided "assumptions" in the Home Office's impact assessment on its changes to immigration rules. More than that though, it confirms not only will these changes cost the country billions, they are also discriminatory. 1/
assets.publishing.service.gov.uk/media/6937e6...
assets.publishing.service.gov.uk/media/6937e6...
Reposted by Tim Downing
Details for people who like phylogenetics: virological.org/t/inter-clad...
Inter-Clade Recombinant Mpox Virus Detected in England in a Traveller Recently Returned from Asia
Inter-Clade Recombinant Mpox Virus Detected in England in a Traveller Recently Returned from Asia Authors: Steven T. Pullan1, Isobel Everall1, Rebecca Doherty1, Lucy Crossman1, Emma Wise1, Hassan Ha...
virological.org
December 8, 2025 at 6:00 PM
Details for people who like phylogenetics: virological.org/t/inter-clad...
Reposted by Tim Downing
1. In Hamburg there is a "fully autonomous train" that for some reason has a human operator to press the ON switch first thing in the morning and the OFF switch at the end of the night. In a recent talk about AI in science, I asked the audience to consider whether they want to be like that operator.
All aboard except the driver? A fully autonomous train takes to the tracks in Germany
YouTube video by euronews
www.youtube.com
December 8, 2025 at 8:12 AM
1. In Hamburg there is a "fully autonomous train" that for some reason has a human operator to press the ON switch first thing in the morning and the OFF switch at the end of the night. In a recent talk about AI in science, I asked the audience to consider whether they want to be like that operator.
Reposted by Tim Downing
WELL NOW, would you look at that? A massive, 24-YEAR-LONG study of MORE THAN 1.2 MILLION people in Denmark found NO LINK between aluminum in childhood vaccines and autism, asthma, OR chronic disorders.
Aluminum is an ADJUVANT.
It ENHANCES your immune response to a vaccine.
That’s it.
Aluminum is an ADJUVANT.
It ENHANCES your immune response to a vaccine.
That’s it.
December 5, 2025 at 5:00 PM
WELL NOW, would you look at that? A massive, 24-YEAR-LONG study of MORE THAN 1.2 MILLION people in Denmark found NO LINK between aluminum in childhood vaccines and autism, asthma, OR chronic disorders.
Aluminum is an ADJUVANT.
It ENHANCES your immune response to a vaccine.
That’s it.
Aluminum is an ADJUVANT.
It ENHANCES your immune response to a vaccine.
That’s it.
Reposted by Tim Downing
I think you just discovered a meme
December 2, 2025 at 6:10 PM
I think you just discovered a meme
Reposted by Tim Downing
The connections between sugar and alcohol in the liver:
Alcohol And Fructose, Tangled (and Untangled?)
www.science.org
December 2, 2025 at 7:36 PM
The connections between sugar and alcohol in the liver:
Reposted by Tim Downing
December 2, 2025 at 8:48 AM
Reposted by Tim Downing
Comparative analysis of commercial Imaging-based #SpatialTranscriptomics methods
Xenium
CosMx 1k
MERSCOPE
Tissue Microarray
17 tumor+16 normal tissue
Transcript count
vs Reference RNAseq
Segmentation accuracy
Cell type annotation
#NatComms 2025
www.nature.com/articles/s41...
Xenium
CosMx 1k
MERSCOPE
Tissue Microarray
17 tumor+16 normal tissue
Transcript count
vs Reference RNAseq
Segmentation accuracy
Cell type annotation
#NatComms 2025
www.nature.com/articles/s41...
December 1, 2025 at 12:52 PM
Comparative analysis of commercial Imaging-based #SpatialTranscriptomics methods
Xenium
CosMx 1k
MERSCOPE
Tissue Microarray
17 tumor+16 normal tissue
Transcript count
vs Reference RNAseq
Segmentation accuracy
Cell type annotation
#NatComms 2025
www.nature.com/articles/s41...
Xenium
CosMx 1k
MERSCOPE
Tissue Microarray
17 tumor+16 normal tissue
Transcript count
vs Reference RNAseq
Segmentation accuracy
Cell type annotation
#NatComms 2025
www.nature.com/articles/s41...
Reposted by Tim Downing
If you run across a gen A.I. slop 🤖💩 diagram in an academic journal, I’d love to know about it! Please fill out this form:
docs.google.com/forms/d/e/1F...
Slop in journals is illuminating about journals’ quality control. And journals would like you to forget their mistakes.
#AcademicChatter
docs.google.com/forms/d/e/1F...
Slop in journals is illuminating about journals’ quality control. And journals would like you to forget their mistakes.
#AcademicChatter
Slop graphics in academic journals
Use this form to share graphics (e.g., figures, covers, graphical abstracts) made using generative A.I. that have appeared in academic journals.
The plan is to compile these slop graphics in an ope...
docs.google.com
December 1, 2025 at 6:36 PM
If you run across a gen A.I. slop 🤖💩 diagram in an academic journal, I’d love to know about it! Please fill out this form:
docs.google.com/forms/d/e/1F...
Slop in journals is illuminating about journals’ quality control. And journals would like you to forget their mistakes.
#AcademicChatter
docs.google.com/forms/d/e/1F...
Slop in journals is illuminating about journals’ quality control. And journals would like you to forget their mistakes.
#AcademicChatter
Reposted by Tim Downing
Using pangenome variation graphs to improve mutation detection in a large DNA virus https://www.biorxiv.org/content/10.1101/2025.11.26.690900v1
November 28, 2025 at 12:32 AM
Using pangenome variation graphs to improve mutation detection in a large DNA virus https://www.biorxiv.org/content/10.1101/2025.11.26.690900v1
Our work on mapping read libraries to viral #pangenome variation graphs (PVGs) to reduce reference bias
Using lumpy skin disease virus #lsdv (dsDNA #virus) as an example
"Using pangenome variation graphs to improve mutation detection in a large DNA virus"
www.biorxiv.org/content/10.1...
[1/7]
Using lumpy skin disease virus #lsdv (dsDNA #virus) as an example
"Using pangenome variation graphs to improve mutation detection in a large DNA virus"
www.biorxiv.org/content/10.1...
[1/7]
Using pangenome variation graphs to improve mutation detection in a large DNA virus
Accurately quantifying viral genetic diversity is essential for understanding pathogen evolution, transmission, and emergence. However, standard approaches that map sequencing reads to a single linear...
www.biorxiv.org
November 28, 2025 at 5:32 AM
Our work on mapping read libraries to viral #pangenome variation graphs (PVGs) to reduce reference bias
Using lumpy skin disease virus #lsdv (dsDNA #virus) as an example
"Using pangenome variation graphs to improve mutation detection in a large DNA virus"
www.biorxiv.org/content/10.1...
[1/7]
Using lumpy skin disease virus #lsdv (dsDNA #virus) as an example
"Using pangenome variation graphs to improve mutation detection in a large DNA virus"
www.biorxiv.org/content/10.1...
[1/7]
Reposted by Tim Downing
I taught (and co-taught) a course on human population genetics from 2000-2024. Having retired, I'm now making all the course materials public: github.com/alanrogers/p... #popgen #evbio
GitHub - alanrogers/popgen: A course on population genetics
A course on population genetics. Contribute to alanrogers/popgen development by creating an account on GitHub.
github.com
November 27, 2025 at 7:10 PM
I taught (and co-taught) a course on human population genetics from 2000-2024. Having retired, I'm now making all the course materials public: github.com/alanrogers/p... #popgen #evbio
Reposted by Tim Downing
How does fever work?
Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence.
This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵
www.science.org/doi/10.1126/...
Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence.
This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵
www.science.org/doi/10.1126/...
Avian-origin influenza A viruses tolerate elevated pyrexic temperatures in mammals
Host body temperature can define a virus’s replicative profile—influenza A viruses (IAVs) adapted to 40° to 42°C in birds are less temperature sensitive in vitro compared with human isolates adapted t...
www.science.org
November 27, 2025 at 7:55 PM
How does fever work?
Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence.
This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵
www.science.org/doi/10.1126/...
Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence.
This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵
www.science.org/doi/10.1126/...
Reposted by Tim Downing
Ireland should be doing this too. There isn’t an alarm bell big enough to wake this government up. We should be in crisis mode, but instead it’s still shaking-developers’-hands-at-the-race-course, business as usual.
Iceland has designated the potential collapse of the Atlantic Meridional Overturning Circulation (AMOC) a national security concern and an existential threat.
Yet still fossil fuel usage continues to grow, and they barely agreed to *name* the problem at #COP30.
www.reuters.com/sustainabili...
Yet still fossil fuel usage continues to grow, and they barely agreed to *name* the problem at #COP30.
www.reuters.com/sustainabili...
Iceland deems possible Atlantic current collapse a security risk
Iceland has designated the potential collapse of a major Atlantic Ocean current system a national security concern and an existential threat, enabling its government to strategize for worst-case scenarios, the country's climate minister told Reuters.
www.reuters.com
November 25, 2025 at 5:04 PM
Ireland should be doing this too. There isn’t an alarm bell big enough to wake this government up. We should be in crisis mode, but instead it’s still shaking-developers’-hands-at-the-race-course, business as usual.
Reposted by Tim Downing
What should we expect this flu season?
Here’s a forecast from a wastewater perspective (because sh*t don’t lie)
1/
Here’s a forecast from a wastewater perspective (because sh*t don’t lie)
1/
November 23, 2025 at 8:07 PM
What should we expect this flu season?
Here’s a forecast from a wastewater perspective (because sh*t don’t lie)
1/
Here’s a forecast from a wastewater perspective (because sh*t don’t lie)
1/
Reposted by Tim Downing
“AI workers said they distrust the models they work on because of a consistent emphasis on rapid turnaround time at the expense of quality.”
Meet the AI workers who tell their friends and family to stay away from AI
When the people making AI seem trustworthy are the ones who trust it the least, it shows that incentives for speed are overtaking safety, experts say
www.theguardian.com
November 22, 2025 at 5:12 PM
“AI workers said they distrust the models they work on because of a consistent emphasis on rapid turnaround time at the expense of quality.”
Reposted by Tim Downing
Published today in @nature.com, @adititm.bsky.social & researchers from the @brianhie.bsky.social lab report that the large-scale genomic model, Evo, is capable of using surrounding genomic context to produce novel, functional genes, enabling an an emergent approach they've termed 'semantic design'.
November 19, 2025 at 6:17 PM
Published today in @nature.com, @adititm.bsky.social & researchers from the @brianhie.bsky.social lab report that the large-scale genomic model, Evo, is capable of using surrounding genomic context to produce novel, functional genes, enabling an an emergent approach they've termed 'semantic design'.
Reposted by Tim Downing
Scientific breakthroughs are rarely unique; someone else would’ve made them soon enough. But when prominent scientists cause harm, that harm isn’t inevitable; the world might simply have been better had the harm not been inflicted.
liorpachter.wordpress.com/2018/05/18/j...
liorpachter.wordpress.com/2018/05/18/j...
James Watson in his own words
“Some anti-Semitism is justified” “Whenever you interview fat people, you feel bad, because you know you’re not going to hire them” “Japan should be bombed for d…
liorpachter.wordpress.com
November 8, 2025 at 4:29 AM
Scientific breakthroughs are rarely unique; someone else would’ve made them soon enough. But when prominent scientists cause harm, that harm isn’t inevitable; the world might simply have been better had the harm not been inflicted.
liorpachter.wordpress.com/2018/05/18/j...
liorpachter.wordpress.com/2018/05/18/j...
Reposted by Tim Downing
So the plan is, we just take their valuable possessions off them, and put them in a camp...
November 17, 2025 at 5:39 PM
So the plan is, we just take their valuable possessions off them, and put them in a camp...
Reposted by Tim Downing
In case you missed it.
www.science.org/content/arti...
www.science.org/content/arti...
The ‘invented persona’ behind a key pandemic database
GISAID offers a safe space to post viral genomes. Peter Bogner, its perplexing creator and overseer, may be jeopardizing its future
www.science.org
November 10, 2025 at 2:46 AM
In case you missed it.
www.science.org/content/arti...
www.science.org/content/arti...
Reposted by Tim Downing
New paper with @statsepi.bsky.social and @deevybee.bsky.social in which we show there's really no evidence for a link between the gut microbiome and autism www.cell.com/neuron/fullt...
Conceptual and methodological flaws undermine claims of a link between the gut microbiome and autism
Claims that the gut microbiome causally contributes to autism regularly appear in
the scientific literature and popular press. Mitchell et al. critically examine influential
studies underpinning these...
www.cell.com
November 13, 2025 at 4:10 PM
New paper with @statsepi.bsky.social and @deevybee.bsky.social in which we show there's really no evidence for a link between the gut microbiome and autism www.cell.com/neuron/fullt...
Reposted by Tim Downing
so I just commented on that paper in Cell Host and Microbe that is cited as evidence that the autism/microbiome link is solid: pubpeer.com/publications...
(not sure what the word “precision” is supposed to mean in the title)
tldr; looks p-hacked 🫤 and I couldn’t find the ethics approval 🤔
(not sure what the word “precision” is supposed to mean in the title)
tldr; looks p-hacked 🫤 and I couldn’t find the ethics approval 🤔
November 15, 2025 at 3:06 PM
so I just commented on that paper in Cell Host and Microbe that is cited as evidence that the autism/microbiome link is solid: pubpeer.com/publications...
(not sure what the word “precision” is supposed to mean in the title)
tldr; looks p-hacked 🫤 and I couldn’t find the ethics approval 🤔
(not sure what the word “precision” is supposed to mean in the title)
tldr; looks p-hacked 🫤 and I couldn’t find the ethics approval 🤔
Reposted by Tim Downing
London interdisciplinary #PhD position now open with myself, @sergemostowylab.bsky.social, & @gmknght.bsky.social on #phage -bacteria-host immune dynamics for WHO priority bacterial pathogens #Klebsiella, #Shigella, and #Staph. Combines cellular microbiology, genomics, & mathematical modelling.
2026-27 Project (Dyson & Mostowy & Knight) - MRC London Intercollegiate Doctoral Training Partnership Studentships
PHACTS: Unravelling PHAge-baCTeria-host immune dynamicS to inform phage therapy SUPERVISORY TEAM Supervisor Dr Zoe Dyson...
mrc-lid.lshtm.ac.uk
November 13, 2025 at 11:11 AM
London interdisciplinary #PhD position now open with myself, @sergemostowylab.bsky.social, & @gmknght.bsky.social on #phage -bacteria-host immune dynamics for WHO priority bacterial pathogens #Klebsiella, #Shigella, and #Staph. Combines cellular microbiology, genomics, & mathematical modelling.
Reposted by Tim Downing
The link between the gut #microbiome and autism is not backed by science, researchers say.
Read the full opinion piece in @cp-neuron.bsky.social: spkl.io/63322AbxpA
@wiringthebrain.bsky.social, @statsepi.bsky.social, & @deevybee.bsky.social
Read the full opinion piece in @cp-neuron.bsky.social: spkl.io/63322AbxpA
@wiringthebrain.bsky.social, @statsepi.bsky.social, & @deevybee.bsky.social
November 13, 2025 at 4:00 PM
The link between the gut #microbiome and autism is not backed by science, researchers say.
Read the full opinion piece in @cp-neuron.bsky.social: spkl.io/63322AbxpA
@wiringthebrain.bsky.social, @statsepi.bsky.social, & @deevybee.bsky.social
Read the full opinion piece in @cp-neuron.bsky.social: spkl.io/63322AbxpA
@wiringthebrain.bsky.social, @statsepi.bsky.social, & @deevybee.bsky.social
Reposted by Tim Downing
“Understanding the Covid-19 pandemic as a catalyst for right-wing backlash is misleading because it’s too passive” www.liberalcurrents.com/propaganda-r...
Propaganda, Rather than Pandemic Policies, Caused the War on Public Health
The backlash narrative ignores basic facts of the case.
www.liberalcurrents.com
November 10, 2025 at 11:04 AM
“Understanding the Covid-19 pandemic as a catalyst for right-wing backlash is misleading because it’s too passive” www.liberalcurrents.com/propaganda-r...