Nick Loman
@pathogenomenick.bsky.social
Public health (meta)genomics & bioinformatics, Prof @unibirmingham.bsky.social, Director @imibirmingham.bsky.social & @climb.ac.uk
Reposted by Nick Loman
“Heat pumps are superior in efficiency to condensing boilers, even if the heat pumps are powered by electricity from a power station burning natural gas.”
Not me saying that but the late Prof Sir David MacKay.
More in my @carbonbrief.org article 👇
interactive.carbonbrief.org/factcheck/he...
Not me saying that but the late Prof Sir David MacKay.
More in my @carbonbrief.org article 👇
interactive.carbonbrief.org/factcheck/he...
November 9, 2025 at 9:05 PM
“Heat pumps are superior in efficiency to condensing boilers, even if the heat pumps are powered by electricity from a power station burning natural gas.”
Not me saying that but the late Prof Sir David MacKay.
More in my @carbonbrief.org article 👇
interactive.carbonbrief.org/factcheck/he...
Not me saying that but the late Prof Sir David MacKay.
More in my @carbonbrief.org article 👇
interactive.carbonbrief.org/factcheck/he...
Bluesky feels like it’s had a bit of a bump recently
November 10, 2025 at 5:32 PM
Bluesky feels like it’s had a bit of a bump recently
Reposted by Nick Loman
"i asked grok" "i asked chatgpt" yeah well i asked carl sagan and he said the greatest enemy of knowledge is not ignorance but the illusion of knowledge 🧪
July 18, 2025 at 4:12 AM
"i asked grok" "i asked chatgpt" yeah well i asked carl sagan and he said the greatest enemy of knowledge is not ignorance but the illusion of knowledge 🧪
Reposted by Nick Loman
If you believe either that Franklin discovered the double helix, and / or Watson and Crick stole her data, ask yourself how you know this. Then take a read of this article.
If I see one more stupid Rosalind Franklin take I'm going to lose my mind. Thank god for @matthewcobb.bsky.social and @nccomfort.bsky.social. www.nature.com/articles/d41...
What Rosalind Franklin truly contributed to the discovery of DNA’s structure
Franklin was no victim in how the DNA double helix was solved. An overlooked letter and an unpublished news article, both written in 1953, reveal that she was an equal player.
www.nature.com
November 8, 2025 at 7:32 AM
If you believe either that Franklin discovered the double helix, and / or Watson and Crick stole her data, ask yourself how you know this. Then take a read of this article.
Reposted by Nick Loman
HAPPY FOUR SEASONS TOTAL LANDSCAPING DAY TO ALL WHO CELEBRATE
November 7, 2025 at 6:44 PM
HAPPY FOUR SEASONS TOTAL LANDSCAPING DAY TO ALL WHO CELEBRATE
Reposted by Nick Loman
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 Nick Loman
One analytical model shows that, as of November 5th, the dismantling of U.S.A.I.D. has already caused the deaths of 600,000 people, two-thirds of them children. https://newyorkermag.visitlink.me/jUzNSc
The Shutdown of U.S.A.I.D. Has Already Killed Hundreds of Thousands
The short documentary “Rovina’s Choice” tells the story of what goes when aid goes.
newyorkermag.visitlink.me
November 6, 2025 at 9:00 PM
One analytical model shows that, as of November 5th, the dismantling of U.S.A.I.D. has already caused the deaths of 600,000 people, two-thirds of them children. https://newyorkermag.visitlink.me/jUzNSc
😂😂 need a PR for gyat()
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....
genzplyr is dplyr, but bussin fr fr no cap.
genzplyr is dplyr, but bussin fr fr no cap.
GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap
dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.
github.com
November 7, 2025 at 9:53 AM
😂😂 need a PR for gyat()
Reposted by Nick Loman
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
Reposted by Nick Loman
🧬 Thrilled to share our latest paper in @natmicrobiol.nature.com 📄
A collaboration to give the Flaviviridae (home to Zika, Dengue & HCV) a much-needed taxonomic re-think.
Our at-scale AI structure prediction gave a complementary perspective on viral evolution.
www.nature.com/articles/s41...
A collaboration to give the Flaviviridae (home to Zika, Dengue & HCV) a much-needed taxonomic re-think.
Our at-scale AI structure prediction gave a complementary perspective on viral evolution.
www.nature.com/articles/s41...
Taxonomic expansion and reorganization of Flaviviridae - Nature Microbiology
Analysis of RNA polymerase hallmark gene phylogenies supported by protein structure relationships of flaviviruses and ‘flavi-like’ viruses underpins the taxonomic expansion and reorganization of Flavi...
www.nature.com
November 6, 2025 at 12:52 PM
🧬 Thrilled to share our latest paper in @natmicrobiol.nature.com 📄
A collaboration to give the Flaviviridae (home to Zika, Dengue & HCV) a much-needed taxonomic re-think.
Our at-scale AI structure prediction gave a complementary perspective on viral evolution.
www.nature.com/articles/s41...
A collaboration to give the Flaviviridae (home to Zika, Dengue & HCV) a much-needed taxonomic re-think.
Our at-scale AI structure prediction gave a complementary perspective on viral evolution.
www.nature.com/articles/s41...
Reposted by Nick Loman
Shout out to University of Birmingham folk:
A science-themed play that I co-wrote is coming to you at the Midlands Art Centre on the 17th. A lab-night out? See you there! 🤞
linktr.ee/panaceaplay
@wvschaik.bsky.social @alanmcn1.bsky.social @drjorhodes.com @jkreft.bsky.social
A science-themed play that I co-wrote is coming to you at the Midlands Art Centre on the 17th. A lab-night out? See you there! 🤞
linktr.ee/panaceaplay
@wvschaik.bsky.social @alanmcn1.bsky.social @drjorhodes.com @jkreft.bsky.social
November 6, 2025 at 9:53 AM
Shout out to University of Birmingham folk:
A science-themed play that I co-wrote is coming to you at the Midlands Art Centre on the 17th. A lab-night out? See you there! 🤞
linktr.ee/panaceaplay
@wvschaik.bsky.social @alanmcn1.bsky.social @drjorhodes.com @jkreft.bsky.social
A science-themed play that I co-wrote is coming to you at the Midlands Art Centre on the 17th. A lab-night out? See you there! 🤞
linktr.ee/panaceaplay
@wvschaik.bsky.social @alanmcn1.bsky.social @drjorhodes.com @jkreft.bsky.social
We’re gonna see plenty of this I predict
This is a bit weird. Did the backers have unrealistic expectations?https://www.statnews.com/2025/11/04/arena-bioworks-research-institute-shuts-down/
Arena BioWorks, an ambitious biomedical institute backed by billionaires, abruptly shuts down
Exclusive: Arena Bioworks, the buzzy research institute that launched with $500 million to support a decade of scientific R&D, is abruptly shutting down, STAT has learned.
www.statnews.com
November 4, 2025 at 11:10 PM
We’re gonna see plenty of this I predict
Reposted by Nick Loman
I was one of the Editorial Board Members at @gigascience.bsky.social who resigned from the Editorial Board.
🧪 🔓
⬇️
retractionwatch.com/2025/11/03/d...
🧪 🔓
⬇️
retractionwatch.com/2025/11/03/d...
Dozens of board members resign from big-data journal after mass staff firings
More than three-fifths of the editorial board of a biomedical sciences journal resigned after the publication’s operations moved from Hong Kong to Shenzhen, China, and the editors and software team…
retractionwatch.com
November 4, 2025 at 3:46 PM
I was one of the Editorial Board Members at @gigascience.bsky.social who resigned from the Editorial Board.
🧪 🔓
⬇️
retractionwatch.com/2025/11/03/d...
🧪 🔓
⬇️
retractionwatch.com/2025/11/03/d...
Reposted by Nick Loman
Our new preprint is out 🥳🥳🥳
Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?
👇
Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?
👇
November 3, 2025 at 12:26 PM
Our new preprint is out 🥳🥳🥳
Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?
👇
Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?
👇
Reposted by Nick Loman
Nature suggests you use their "Manuscript Adviser" bot to get advice before submitting
I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
November 3, 2025 at 1:55 PM
Nature suggests you use their "Manuscript Adviser" bot to get advice before submitting
I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
Reposted by Nick Loman
PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification www.biorxiv.org/content/10.1...
Code: github.com/nf-core/path...
Nextflow nf-core pipeline: nf-co.re/pathogensurv...
Code: github.com/nf-core/path...
Nextflow nf-core pipeline: nf-co.re/pathogensurv...
November 2, 2025 at 9:58 PM
PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification www.biorxiv.org/content/10.1...
Code: github.com/nf-core/path...
Nextflow nf-core pipeline: nf-co.re/pathogensurv...
Code: github.com/nf-core/path...
Nextflow nf-core pipeline: nf-co.re/pathogensurv...
Reposted by Nick Loman
My article in tomorrow's @theobserveruk.bsky.social now online. But go and buy a copy!
Francis Crick: The science genius with poetry in his DNA
He is celebrated for co‑discovering the double helix, but it was Crick’s poetic appreciation of the world that was key to how his mind worked
observer.co.uk
November 1, 2025 at 11:37 AM
My article in tomorrow's @theobserveruk.bsky.social now online. But go and buy a copy!
Reposted by Nick Loman
We have progressed from data collection to data analysis.
November 1, 2025 at 12:31 AM
We have progressed from data collection to data analysis.
Reposted by Nick Loman
@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 Nick Loman
I've been asked about this paper (www.nature.com/articles/s41...) enough times that I finally had to read it.
The basic claim is that mRNA vaccines had huge synergistic benefit with checkpoint blockade against lung cancer melanoma.
tl;dr it's glam-slop & everyone involved should be embarrassed
The basic claim is that mRNA vaccines had huge synergistic benefit with checkpoint blockade against lung cancer melanoma.
tl;dr it's glam-slop & everyone involved should be embarrassed
SARS-CoV-2 mRNA vaccines sensitize tumours to immune checkpoint blockade - Nature
mRNA vaccines targeting SARS-CoV-2 also sensitize tumours to immune checkpoint inhibitors.
www.nature.com
October 30, 2025 at 3:35 PM
I've been asked about this paper (www.nature.com/articles/s41...) enough times that I finally had to read it.
The basic claim is that mRNA vaccines had huge synergistic benefit with checkpoint blockade against lung cancer melanoma.
tl;dr it's glam-slop & everyone involved should be embarrassed
The basic claim is that mRNA vaccines had huge synergistic benefit with checkpoint blockade against lung cancer melanoma.
tl;dr it's glam-slop & everyone involved should be embarrassed
Reposted by Nick Loman
October 2025 batch of Kraken 2 indexes, including core_nt and many others, available: benlangmead.github.io/aws-indexes/k2
Coming soon to K2: a feature for querying many K2 indexes as though they're a single index. Highly useful if the index you want to query is too big to build and/or fit in RAM.
Coming soon to K2: a feature for querying many K2 indexes as though they're a single index. Highly useful if the index you want to query is too big to build and/or fit in RAM.
Index zone by BenLangmead
benlangmead.github.io
October 30, 2025 at 6:11 PM
October 2025 batch of Kraken 2 indexes, including core_nt and many others, available: benlangmead.github.io/aws-indexes/k2
Coming soon to K2: a feature for querying many K2 indexes as though they're a single index. Highly useful if the index you want to query is too big to build and/or fit in RAM.
Coming soon to K2: a feature for querying many K2 indexes as though they're a single index. Highly useful if the index you want to query is too big to build and/or fit in RAM.
Reposted by Nick Loman
Genuinely delighted to download a PhD thesis from a university repository where the author has neglected to remove the words "BITCH THIS IS YOUR THESIS" from the filename.
October 30, 2025 at 8:21 AM
Genuinely delighted to download a PhD thesis from a university repository where the author has neglected to remove the words "BITCH THIS IS YOUR THESIS" from the filename.
Reposted by Nick Loman
We’ve identified a highly divergent betacoronavirus from South American bat that encodes a functional furin cleavage site.
Another fascinating reminder of how diverse coronavirus evolution is in wildlife reservoirs.
#Virology #VirusEvolution #Bats #Coronavirus
www.biorxiv.org/content/10.1...
Another fascinating reminder of how diverse coronavirus evolution is in wildlife reservoirs.
#Virology #VirusEvolution #Bats #Coronavirus
www.biorxiv.org/content/10.1...
A divergent betacoronavirus with a functional furin cleavage site in South American bats
Bats are natural reservoirs for a wide range of RNA viruses. Members of the genus Betacoronavirus, including Severe Acute Respiratory Syndrome virus 2 (SARS-CoV-2) and Middle East Respiratory Syndrome...
www.biorxiv.org
October 27, 2025 at 9:32 PM
We’ve identified a highly divergent betacoronavirus from South American bat that encodes a functional furin cleavage site.
Another fascinating reminder of how diverse coronavirus evolution is in wildlife reservoirs.
#Virology #VirusEvolution #Bats #Coronavirus
www.biorxiv.org/content/10.1...
Another fascinating reminder of how diverse coronavirus evolution is in wildlife reservoirs.
#Virology #VirusEvolution #Bats #Coronavirus
www.biorxiv.org/content/10.1...
Reposted by Nick Loman
Nobody makes enemies by finishing their talk early…
October 29, 2025 at 9:55 AM
Nobody makes enemies by finishing their talk early…
Reposted by Nick Loman
Musk calling for civil war in Britain again.
Man’s clearly never met a Brit. You can’t get them out when it’s drizzling, never mind manning the barricades.
Man’s clearly never met a Brit. You can’t get them out when it’s drizzling, never mind manning the barricades.
October 29, 2025 at 9:02 AM
Musk calling for civil war in Britain again.
Man’s clearly never met a Brit. You can’t get them out when it’s drizzling, never mind manning the barricades.
Man’s clearly never met a Brit. You can’t get them out when it’s drizzling, never mind manning the barricades.