Nick Loman

“ResearchFish isn’t a fish”

Asked lots about this piece on Chronic Lyme disease, and disappointed in the @guardian (a publication I both subscribe and contribute to) for running it. Short thread explaining the multitude of problems with it, and why I consider it irresponsible to run as is..🧵

OOOPS! UPDATE: Two HHS officials tell me that disease detectives, measles response officers, global health officials and the MMWR staff were laid off by mistake and will be reinstated. But Washington office is still RIFed

For more information about the Friday night massacre at CDC, I wrote up an analysis of who got terminated and what that means for public health.

Grateful to @saveamericamvmt.bsky.social for supporting and amplifying. We are in really terrible trouble.

rasmussenretorts.substack.com/p/the-death-...

The Death of Public Health Another Friday night massacre, but this time it's not just an essential federal public health agency that will die

“CDC experts actively responding to an Ebola outbreak in the Democratic Republic of Congo that has killed 43 people were RIFed in the middle of their deployment.” rasmussenretorts.substack.com/p/the-death-...

BREAKING: Friday night massacre underway at CDC. Doznes of "disease detectives," high-level scientists, entire Washington staff and editors of the MMWR (Morbidity and Mortality Weekly Report) have all been RIFed and received the following notice:

They trained a specialized model on existing bacterial viruses and had it spit out genomes and some of them worked. And they probably could have done the same thing manually.

This was not "put in an English prompt to GPT and get a custom virus out with desired properties" and never will be.

Lancelot Microbe?

Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt

It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.

Efficient and accurate search in petabase-scale sequence repositories www.nature.com/articles/s41... 🧬🖥️🧪
MetaGraph: metagraph.ethz.ch
Code: github.com/ratschlab/me...

Graph showing COVID-19 positive tests rising steadily from spring 2025 after a low in early 2025. Data from October 2024 to October 2025, England only.

Graph showing flu-positive tests peaking sharply in winter 2024–25 before declining and then beginning to rise again in autumn 2025. Data from October 2024 to October 2025, England only.

Graph showing flu-positive tests peaking sharply in winter 2024–25 before declining and then beginning to rise again in autumn 2025. Data from October 2024 to October 2025.

#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.

Keeping phone off secret to winning Nobel

New respiratory 🫁 infection and microbiomes conference in Hinxton with stellar line up of speakers.

🚨 Submit your abstracts now! 🚨

Please RT

coursesandconferences.wellcomeconnectingscience.org/event/air-20...

Love this!

After being with the journal since its very inception, the time has come for me to step back from Microbial Genomics. This is a wonderful opportunity to have a leadership role in one of the leading journals for microbial genomics research

microbiologysociety.org/news/society...

I just saw someone use the abbreviation “AI;DR” and I’ll be laughing for a while.

Was curious about JFK’s health so I asked google. TIL he was pregnant in 1960 but only put on 15-20lbs

Have we passed peak social media? As platforms degrade into outrage and slop, users are turning away

Please let this be true.

Have we passed peak social media? - on.ft.com/4pTb1Di via @FT

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplas...

New pre-print from the Banfield lab, highlighting an interesting case of 1.5Mb megaplasmids found in human gut.

Plasmid genomes were resolved using #PacBio HiFi sequencing with hifiasm-meta for #metagenome assembly. Host association was detected using epigenetic signals.

doi.org/10.1101/2025...

As the @royalsociety.org council meets on 01 Oct to discuss the repudiation of its core values by one of its fellows, Elon Musk, I respectfully remind them of my proposals for actions that should help the RS recover its standing in the scientific community. occamstypewriter.org/scurry/2025/...

As a survivor of the last AI winter, I endorse Cory's take: "Plan for a future where you can buy GPUs for ten cents on the dollar...[and] there's a ton of extremely promising open source models that have barely been optimized and have vast potential for improvement." pluralistic.net/2025/09/27/e...

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission events, and identifying antimicrobial resistance mutati...

Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise.

Until now, using AccuSNV.

Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...

Phages with a broad host range are common across ecosystems - Nature Microbiology Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.

In this great new paper, the authors use metagenomic Hi-C to show that #phage with broad host range are fairly common, contrary to the prevailing view on their biology. Cutting edge methods like Hi-C are shedding light on our blind spots in the microbial world.

And the CDC has officially decided to switch back from Mpox to Monkeypox. A reminder, the world still uses Mpox, this disease does not come from monkeys, Mpox is less stigmatizing and racist. Switching back is just meaningless, unnecessary, racist, and homophobic.

We worry about Very Online Kids much more than their Very Online Parents, and I'm not sure that's wise

In 2016 Geoffrey Hinton said “we should stop training radiologists now" since AI would soon be better at their jobs.

He was right: models have outperformed radiologists on benchmarks for ~a decade.

Yet radiology jobs are at record highs, with an average salary of $520k.

Why?

The science is, in fact, clear. Good studies [1] consistently show a weak association between tylenol & autism. Those studies are very careful to say they can't establish whether this is causal. A huge Swedish study used a clever sibling design to address this, and showed zero causal effect [2].

JA Westenberg @Daojoan@mastodon.social My 9 year old and his classmates have started using “that’s AI” to mean “I don’t believe you.” Me: we’re having dinosaur meat for dinner Kiddo: that’s AI Sep 24, 2025, 07:36 AM

They've lost the 9yos

How many shopping days til Xmas

Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort Pet dogs are considered part of the family, and understanding their gut microbiomes can provide insights into both animal and household health. Most comprehensive studies, however, relied on short-rea...

Finally, the results of my postdoc at the
@bigdatabiology.bsky.social lab in Shanghai see the light! The work includes my three favorite things research-wise: 🦠 microbiome, 🧬 long-reads, and 🐶 dogs.

See our new preprint:
www.biorxiv.org/content/10.1...