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
“Staff members at the United States’s premier infectious-disease research institute have been instructed to remove the words “biodefense” and “pandemic preparedness” from the institute’s web pages, according to e-mails Nature has obtained.”
www.nature.com/articles/d41...
www.nature.com/articles/d41...
Exclusive: Key US infectious-diseases centre to drop pandemic preparation
Staff members have been instructed to scrub this topic and ‘biodefense’ from the agency’s website.
www.nature.com
February 13, 2026 at 7:42 PM
“Staff members at the United States’s premier infectious-disease research institute have been instructed to remove the words “biodefense” and “pandemic preparedness” from the institute’s web pages, according to e-mails Nature has obtained.”
www.nature.com/articles/d41...
www.nature.com/articles/d41...
Reposted by Nick Loman
AI agent goes nuts on open source maintainer after having its pull request denied. This is a pretty insane story. Open source development as we've been used to for the last few decades is likely over. 1/
theshamblog.com/an-ai-agent-...
theshamblog.com/an-ai-agent-...
An AI Agent Published a Hit Piece on Me
Summary: An AI agent of unknown ownership autonomously wrote and published a personalized hit piece about me after I rejected its code, attempting to damage my reputation and shame me into acceptin…
theshamblog.com
February 13, 2026 at 3:23 PM
AI agent goes nuts on open source maintainer after having its pull request denied. This is a pretty insane story. Open source development as we've been used to for the last few decades is likely over. 1/
theshamblog.com/an-ai-agent-...
theshamblog.com/an-ai-agent-...
Reposted by Nick Loman
In terms of what cures are being lost:
- Epstein-Barr virus is perhaps the major trigger for multiple sclerosis
- herpes simplex virus causes cold sores, genital herpes, infections in babies, deadly meningitis
- shingles virus causes an intensely painful disease
- Epstein-Barr virus is perhaps the major trigger for multiple sclerosis
- herpes simplex virus causes cold sores, genital herpes, infections in babies, deadly meningitis
- shingles virus causes an intensely painful disease
February 13, 2026 at 5:44 AM
In terms of what cures are being lost:
- Epstein-Barr virus is perhaps the major trigger for multiple sclerosis
- herpes simplex virus causes cold sores, genital herpes, infections in babies, deadly meningitis
- shingles virus causes an intensely painful disease
- Epstein-Barr virus is perhaps the major trigger for multiple sclerosis
- herpes simplex virus causes cold sores, genital herpes, infections in babies, deadly meningitis
- shingles virus causes an intensely painful disease
Reposted by Nick Loman
what a time to be alive
AI agent opens a PR write a blogpost to shames the maintainer who closes it [Discussion]
AI agent opens a PR write a blogpost to shames the maintainer who closes it
AI agent opens a PR write a blogpost to shames the maintainer who closes it
github.com
February 12, 2026 at 2:25 PM
what a time to be alive
Reposted by Nick Loman
Happy birthday to one of my favourite haters, Charles Darwin
February 12, 2026 at 4:31 PM
Happy birthday to one of my favourite haters, Charles Darwin
Reposted by Nick Loman
Gotta love Nature's opinion pieces
"Science funding needs fixing - but not like that"
"Academic publishing is broken - but publishing less is not the solution"
"AI will kill science - how can researchers use it to be more efficient?"
"Science funding needs fixing - but not like that"
"Academic publishing is broken - but publishing less is not the solution"
"AI will kill science - how can researchers use it to be more efficient?"
February 12, 2026 at 10:58 AM
Gotta love Nature's opinion pieces
"Science funding needs fixing - but not like that"
"Academic publishing is broken - but publishing less is not the solution"
"AI will kill science - how can researchers use it to be more efficient?"
"Science funding needs fixing - but not like that"
"Academic publishing is broken - but publishing less is not the solution"
"AI will kill science - how can researchers use it to be more efficient?"
Reposted by Nick Loman
ARTIC 2 measles resources are live!
As part of the Wellcome Trust funded ARTIC 2 project we have developed a collection of measles virus resources that are now openly available at artic.network/viruses/mev
As part of the Wellcome Trust funded ARTIC 2 project we have developed a collection of measles virus resources that are now openly available at artic.network/viruses/mev
February 12, 2026 at 11:15 AM
ARTIC 2 measles resources are live!
As part of the Wellcome Trust funded ARTIC 2 project we have developed a collection of measles virus resources that are now openly available at artic.network/viruses/mev
As part of the Wellcome Trust funded ARTIC 2 project we have developed a collection of measles virus resources that are now openly available at artic.network/viruses/mev
Reposted by Nick Loman
Five years after the rollout of Covid-19 vaccines started, it seems the mystery of why the Astra-Zeneca and J&J vaccines led to a rare but deadly side effect of unusual blood clots and bleeding has finally been solved.
It's a fascinating case of molecular mimicry that may help make vaccine safer.🧪
It's a fascinating case of molecular mimicry that may help make vaccine safer.🧪
Rare, dangerous side effects of some COVID-19 vaccines explained
“Groundbreaking” study uncovers why adenovirus-based shots caused life-threatening blood clots and bleeding in some people
www.science.org
February 11, 2026 at 10:10 PM
Five years after the rollout of Covid-19 vaccines started, it seems the mystery of why the Astra-Zeneca and J&J vaccines led to a rare but deadly side effect of unusual blood clots and bleeding has finally been solved.
It's a fascinating case of molecular mimicry that may help make vaccine safer.🧪
It's a fascinating case of molecular mimicry that may help make vaccine safer.🧪
Reposted by Nick Loman
The brutality of U.S.A.I.D.’s closure and the disregard for the human toll betrayed a vision of a crueler, meaner, more insular world — one in which America aspires not to any pretense of moral leadership but simply to naked power, dominance and extractive self-interest.”
#giftarticle
#giftarticle
Opinion | The Aftermath of Feeding America’s Credibility Into the Woodchipper
www.nytimes.com
February 8, 2026 at 9:32 PM
The brutality of U.S.A.I.D.’s closure and the disregard for the human toll betrayed a vision of a crueler, meaner, more insular world — one in which America aspires not to any pretense of moral leadership but simply to naked power, dominance and extractive self-interest.”
#giftarticle
#giftarticle
Reposted by Nick Loman
New Preprint 📢 from our team 🔎 Critical assessment of #intratumor and #low #biomass #microbiome using #longread sequencing
Some studies suggest bacteria 🦠 live inside tumors and influence cancer treatment. But there’s also been a major #debate: in these very low-microbe tissue samples, how much 1/
Some studies suggest bacteria 🦠 live inside tumors and influence cancer treatment. But there’s also been a major #debate: in these very low-microbe tissue samples, how much 1/
February 5, 2026 at 1:15 PM
New Preprint 📢 from our team 🔎 Critical assessment of #intratumor and #low #biomass #microbiome using #longread sequencing
Some studies suggest bacteria 🦠 live inside tumors and influence cancer treatment. But there’s also been a major #debate: in these very low-microbe tissue samples, how much 1/
Some studies suggest bacteria 🦠 live inside tumors and influence cancer treatment. But there’s also been a major #debate: in these very low-microbe tissue samples, how much 1/
Reposted by Nick Loman
Still not many long-read gut metagenomics studies around, but this new preprint on 109 samples uncovers globally prevalent Firmicutes-host "GuFi" phage families that have been missed by short read seq. It seems to have broad host range + active replication.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
February 6, 2026 at 10:53 AM
Still not many long-read gut metagenomics studies around, but this new preprint on 109 samples uncovers globally prevalent Firmicutes-host "GuFi" phage families that have been missed by short read seq. It seems to have broad host range + active replication.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Nick Loman
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... 🧬💻🧪 github.com/RasmussenLab...
February 5, 2026 at 5:02 PM
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... 🧬💻🧪 github.com/RasmussenLab...
Reposted by Nick Loman
Finally an official update from #MRC regarding grant application funding and severe cuts to funded research in rounds currently under review:
www.ukri.org/blog/mrc-fun...
Not that it gives any reassurance or details beyond a comprehensive list of what is suspended.
#UKsciencefunding
www.ukri.org/blog/mrc-fun...
Not that it gives any reassurance or details beyond a comprehensive list of what is suspended.
#UKsciencefunding
MRC funding update
An update on MRC funding during UKRI’s transition, what’s changing, and the next steps for paused opportunities and reopening timelines.
www.ukri.org
February 5, 2026 at 4:08 PM
Finally an official update from #MRC regarding grant application funding and severe cuts to funded research in rounds currently under review:
www.ukri.org/blog/mrc-fun...
Not that it gives any reassurance or details beyond a comprehensive list of what is suspended.
#UKsciencefunding
www.ukri.org/blog/mrc-fun...
Not that it gives any reassurance or details beyond a comprehensive list of what is suspended.
#UKsciencefunding
Reposted by Nick Loman
Fantastic Harry Smith Memorial Lecture given by Prof Nicole Dubilier @nicoledubilier.bsky.social today 'Eating your Microbiome: Nutritional Symbioses between Chemosynthetic Bacteria and Marine Invertebrates' with thanks to @pathogenomenick.bsky.social for hosting
February 3, 2026 at 2:37 PM
Fantastic Harry Smith Memorial Lecture given by Prof Nicole Dubilier @nicoledubilier.bsky.social today 'Eating your Microbiome: Nutritional Symbioses between Chemosynthetic Bacteria and Marine Invertebrates' with thanks to @pathogenomenick.bsky.social for hosting
Reposted by Nick Loman
“We found that using AI assistance led to a statistically significant decrease in mastery.”
Props to Anthropic for studying the effects of their creation and reporting results that are not probably what they wished for
www.anthropic.com/research/AI-...
Props to Anthropic for studying the effects of their creation and reporting results that are not probably what they wished for
www.anthropic.com/research/AI-...
How AI assistance impacts the formation of coding skills
Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.
www.anthropic.com
January 31, 2026 at 3:50 AM
“We found that using AI assistance led to a statistically significant decrease in mastery.”
Props to Anthropic for studying the effects of their creation and reporting results that are not probably what they wished for
www.anthropic.com/research/AI-...
Props to Anthropic for studying the effects of their creation and reporting results that are not probably what they wished for
www.anthropic.com/research/AI-...
Reposted by Nick Loman
This is Nathan Wolfe. Nathan is a virus hunter. Nathan has a bit of a reputation. Through the years, I've told multiple journalists stories I've heard, like "Nathan thanks Jeffrey Epstein in his book." Somehow no one ever wrote anything up. Want to see what Nathan was up to in today's Epstein files?
January 31, 2026 at 12:03 AM
This is Nathan Wolfe. Nathan is a virus hunter. Nathan has a bit of a reputation. Through the years, I've told multiple journalists stories I've heard, like "Nathan thanks Jeffrey Epstein in his book." Somehow no one ever wrote anything up. Want to see what Nathan was up to in today's Epstein files?
Reposted by Nick Loman
Love this, and can attest that including "Bin Chicken" in a grant proposal feels like it requires some further explanation 🤣
Excellent work from @aroneys.bsky.social here. Free to read version at rdcu.be/ePJp4
January 30, 2026 at 11:52 PM
Love this, and can attest that including "Bin Chicken" in a grant proposal feels like it requires some further explanation 🤣
It wasn’t even a real fish…
January 29, 2026 at 10:25 PM
It wasn’t even a real fish…
Reposted by Nick Loman
Announcing a new tool for "denoising" long-read amplicon sequences: savont.
Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.
1/4
github.com/bluenote-157...
Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.
1/4
github.com/bluenote-157...
GitHub - bluenote-1577/savont: Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads
Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads - bluenote-1577/savont
github.com
January 28, 2026 at 6:46 PM
Announcing a new tool for "denoising" long-read amplicon sequences: savont.
Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.
1/4
github.com/bluenote-157...
Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.
1/4
github.com/bluenote-157...
Reposted by Nick Loman
⏰ Don’t miss out!
📢 The TARGetAMR Annual Conference 2026 is coming 14–15 May to Birmingham.
🦠 Connect with experts & shape the future of AMR research.
👉 Register now: www.targetamr.org.uk/hdrevents/ta...
#TARGetAMR26
📢 The TARGetAMR Annual Conference 2026 is coming 14–15 May to Birmingham.
🦠 Connect with experts & shape the future of AMR research.
👉 Register now: www.targetamr.org.uk/hdrevents/ta...
#TARGetAMR26
January 28, 2026 at 10:12 AM
⏰ Don’t miss out!
📢 The TARGetAMR Annual Conference 2026 is coming 14–15 May to Birmingham.
🦠 Connect with experts & shape the future of AMR research.
👉 Register now: www.targetamr.org.uk/hdrevents/ta...
#TARGetAMR26
📢 The TARGetAMR Annual Conference 2026 is coming 14–15 May to Birmingham.
🦠 Connect with experts & shape the future of AMR research.
👉 Register now: www.targetamr.org.uk/hdrevents/ta...
#TARGetAMR26
Reposted by Nick Loman
@bylinetimes.bsky.social @eastangliabylines.co.uk
"We have paused applications to this funding opportunity while we align investment changes across UKRI."
www.ukri.org/opportunity/...
"We have paused applications to this funding opportunity while we align investment changes across UKRI."
www.ukri.org/opportunity/...
January 28, 2026 at 10:00 AM
@bylinetimes.bsky.social @eastangliabylines.co.uk
"We have paused applications to this funding opportunity while we align investment changes across UKRI."
www.ukri.org/opportunity/...
"We have paused applications to this funding opportunity while we align investment changes across UKRI."
www.ukri.org/opportunity/...
Reposted by Nick Loman
First evidence in Europe of highly pathogenic avian influenza virus H5N1 infection in a dairy cow. Antibodies against H5N1 detected in a cow with mastitis and respiratory signs on a Dutch dairy farm at the end of December. A cat on that farm had died from H5N1. www.tweedekamer.nl/downloads/do...
January 23, 2026 at 9:26 PM
First evidence in Europe of highly pathogenic avian influenza virus H5N1 infection in a dairy cow. Antibodies against H5N1 detected in a cow with mastitis and respiratory signs on a Dutch dairy farm at the end of December. A cat on that farm had died from H5N1. www.tweedekamer.nl/downloads/do...
Reposted by Nick Loman
Really interesting thread!
Last term I tried an experiment: I walked into my Tech and Design Ethics class, admitted that I had *no idea* what to do about ChatGPT - so I would let them figure it out.
As in: their first project was to decide and write the ChatGPT policy for the class.
Here's what happened:
As in: their first project was to decide and write the ChatGPT policy for the class.
Here's what happened:
January 23, 2026 at 4:18 PM
Really interesting thread!
Reposted by Nick Loman
"Africans want to solve Africa’s problems, not satisfy the curiosity of the funders."
www.theguardian.com/world/2026/j...
www.theguardian.com/world/2026/j...
‘It’s the sovereignty of the country’: Guinea-Bissau says US vaccine study suspended
Despite US pushback, officials in west Africa say controversial hepatitis B study on pause amid ethics concerns
www.theguardian.com
January 23, 2026 at 12:23 PM
"Africans want to solve Africa’s problems, not satisfy the curiosity of the funders."
www.theguardian.com/world/2026/j...
www.theguardian.com/world/2026/j...
Reposted by Nick Loman
The US withdrawal from #WHO became official today, leaving the world less prepared for dangerous disease outbreaks. “When that will bite us in the ass, it’s impossible to predict. But there is a 100% certainty that it will bite us in the ass,” one expert told me. www.statnews.com/2026/01/22/u...
U.S. makes exit from the WHO complete
The U.S. withdrawal from the WHO became official Thursday, formalizing a fissure between the Trump administration and the Geneva-based global health agency.
www.statnews.com
January 22, 2026 at 3:52 PM
The US withdrawal from #WHO became official today, leaving the world less prepared for dangerous disease outbreaks. “When that will bite us in the ass, it’s impossible to predict. But there is a 100% certainty that it will bite us in the ass,” one expert told me. www.statnews.com/2026/01/22/u...