Nick Loman

MetaPointFinder:
A new approach for detecting mutation-driven antimicrobial resistance directly from metagenomic reads.
Fills a major gap in current resistome profiling by capturing chromosomal AMR mutations that metagenome tools miss.

github.com/aldertzomer/...

I think this has to be in an individual as both of the lineages cluster with recent human-associated chains

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...

Amazing novel mpox recombination between epidemic clade 1 and 2 in returning traveller detected in UK: virological.org/t/inter-clad...

The Story of Francis Crick, a new masterpiece biography by Matthew Cobb His legendary contributions and remarkable flaws

His legendary work spawned two life science fields: molecular biology and neuroscience. But that's only part of a much bigger story. An enthralling Ground Truths conversation with @matthewcobb.bsky.social on his new book CRICK
erictopol.substack.com/p/the-story-...

Legend!

Hamilton O. Smith, Who Made a Biotech Breakthrough, Is Dead at 94

www.nytimes.com/2025/12/05/s...

Artificial intelligence research has a slop problem, academics say: ‘It’s a mess’ AI research in question as author claims to have written over 100 papers on AI that one expert calls a ‘disaster’

Artificial intelligence research has a slop problem, academics say: ‘It’s a mess’
AI research in question as author claims to have written over 100 papers on AI that one expert calls a ‘disaster’
@aishadown.bsky.social for @theguardian.com
www.theguardian.com/technology/2...

My @politicshome.bsky.social story from the summer about the AI-generated "I rise to speak" phenomenon in Parliament has made it into @nytimes.com 🇺🇸

(sadly, without credit)

the FIFA peace prize that was awarded to trump which shows a bunch of decaying disembodied hands grasping futilely at earth from below, as if in hell

extremely normal peace trophy

Have to say, if the FIFA Chemistry Prize doesn’t go to these guys, they were robbed

illustration image, made of a map of Antarctica (NASA svg) and SARS-CoV-2 virus (NIH BioArt)

Are you familiar with the story of the Antarctica sequences?

If not, good for you: you didn't clutter your brain with yet another Covid-origin damp squib, where innocuous data were made to look suspicious by misrepresenting a date.

For the curious, here's the story. ▫️1/9 🧵 #CovidOrigin

Desk reject for Xmas day!

That thing is happening again when everyone tries to do everything before Xmas. Leave it!!

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.

1/n

The #Ebola outbreak in central DRC that was first reported in September has been declared over. The outbreak, the country's 16th (I think), involved 64 cases (53 confirmed, 11 probable), of which 45 were fatal. It occurred in Bulape health zone in Kasai province. www.who.int/emergencies/...

Major AI conference flooded with peer reviews written fully by AI Controversy has erupted after 21% of manuscript reviews for an international AI conference were found to be generated by artificial intelligence.

The enshitification of scientific publishing marches on. First arXiv had to clamp down on submissions thanks to a flood of AI-written papers.

Now ICLR authors say their peer reviews were churned out by AI. Reviews full of hallucinated content that didn’t exist and offering useless, vague feedback.

Three years on, ChatGPT still isn't what it was cracked up to be – and it probably never will be A skeptic’s pre-mortem

“The results are disappointing because the underlying tech is unreliable, And that’s been obvious from the start.”

open.substack.com/pub/garymarc...

I can't wait to be able to run RT-qPCR in my lab!!!

Eagerly awaiting my Pocket qPCR to arrive. I can finally use my 50k units of reverse transcriptase I got from Gene and Cell Technologies a few years ago.

gaudi.ch/PocketPCR/in...

To reform universities, first tackle global rankings Universities are in thrall to a rankings system that prioritizes narrow aspects of academic life. Three changes would give institutions the freedom to explore fresh ways of working.

University reputations and finances often hinge on their position in global ranking tables that prioritize narrow aspects of academic life. Elizabeth Gadd writes about three changes that would give institutions the freedom to explore fresh ways of working. #Academicsky 🧪

A screenshot of the front page of Pathoplexus' website, showing the addition of a tile for Marburg Virus.

1/ 🚀 Pathoplexus now supports Marburg virus (MARV) and Ravn virus (RAVN) (sister viruses in the same genus). MARV has two main clades and causes severe disease with reported fatality rates of 24–88%.

You can read more detail about adding Marburg here: pathoplexus.org/news/2025-11...

A trillion dollars is a terrible thing to waste The machine learning community is finally waking up to the madness, but the detour of the last few years has been costly.

"An old saying about such follies is that “six months in the lab can you save you an afternoon in the library”; here we may have wasted a trillion dollars and several years to rediscover what cognitive science already knew."

garymarcus.substack.com/p/a-trillion...

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...

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/...

Infographic with AI slop published in Nature Scientific Reports

"Runctitiononal features"? "Medical fymblal"? "1 Tol Line storee"? This gets worse the longer you look at it. But it's got to be good, because it was published in Nature Scientific Reports last week: www.nature.com/articles/s41... h/t @asa.tsbalans.se

Hi Bluesky! I’m a molecular virologist studying how innate immune defences restrict cross-species transmission and shape disease severity.

I just joined, so reposts appreciated to help me reconnect with virology, immunology, and host–pathogen interaction folks.

(whiteboard art from Zhuonan Li)

Wotcha!👋

High frequency body site translocation of nosocomial Pseudomonas aeruginosa - Nature Communications Here, the authors report within-host diversity and body site translocation dynamics in hospital samples of Pseudomonas aeruginosa and reveal that body site sharing was likely due to within-patient tra...

Really pleased to share the first paper to come out of the lab.
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut

www.nature.com/articles/s41...

This is a pretty useful page en.wikipedia.org/wiki/Wikiped...

Google at its peak was basically the best information retrieval system in human history and they and every competitor decided going from there to “you didn’t want answers you wanted half-assed auto-complete 80%-wrong hallucinations” in a few years was the right idea

One of the big tidal forces of the coming years is that the baseline reliability of things you see on a screen is going to decline.

I think this has not been adequately metabolized.

This is one version, but there are a bunch of them.