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Nick Loman

@pathogenomenick.bsky.social
6K followers 709 following 718 posts

Public health (meta)genomics & bioinformatics, Prof @unibirmingham.bsky.social, Director @imibirmingham.bsky.social & @climb.ac.uk

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Nick Loman @pathogenomenick.bsky.social · 29/09/2026
It makes no sense to me that Microsoft do Office365 2FA through WhatsApp.
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Amy Maxmen, PhD @amymaxmen.bsky.social · 28/09/2026
While the news & white papers breathlessly cover the idea of a threat of a future AI bioweapon, an Ebola outbreak is escalating, having killed nearly 4,000 people so far. The Trump admin has diminished US support to control it w/travel bans, an eroded CDC & a hobbled WHO www.who.int/emergencies/...
who.int
Ebola disease caused by Bundibugyo virus - Democratic Republic of the Congo
Since the last Disease Outbreak News was published on 11 September 2026, the Bundibugyo virus outbreak in the Democratic Republic of the Congo has expanded further, with two additional health zones af...
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Vaughn Cooper @vscooper.micropopbio.org · 27/09/2026
How do Burkholderia multivorans bacteria adaptively evolve during infections of the cystic fibrosis airway? A longtime collab and intensive study of 8 patients links bacterial adaptations to disease progression. Our findings also unite prior studies. www.biorxiv.org/content/10.6...
biorxiv.org
Convergent genetic evolution within Burkholderia multivorans chronic infections correlates with lung function decline in cystic fibrosis patients
The patterns and pathways of pathogen adaptation during chronic infections can reveal the gateways microbes must unlock to colonize and persist. In chronic lung infections of cystic fibrosis (CF) pati...
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Colin Carlson @colincarlson.bsky.social · 25/09/2026
David Quammen's essay in The New York Times today closes with this paragraph. It's both a scientific falsehood, and an incredibly dangerous narrative. If you're willing to give me five minutes of your time, I'd like to explain why.
The Ebola virus doesn’t need to spill back. It abides in its reservoir host, and awaits its next opportunity. A virus can’t climb out of a bat or a monkey and fly off in search of human prey. It can only spill over. If humans left the reservoir host alone — not hunting it, not capturing it, not eating it, not exporting it live, not disturbing its forest habitat — the virus wouldn’t re-emerge in humans. It would remain where it is, harming no one. But of course that’s not what happens. And when viruses spill, they often spill into us, because the human population is such a big, busy target.
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Evelien Adriaenssens @evelienadri.bsky.social · 25/09/2026
Here are my first thoughts as a phage person about the @anthropic.com announcement about a novel enzyme on a phage: www.linkedin.com/pulse/my-tho...
linkedin.com
My thoughts on the Anthropic phage enzyme discovery
* Disclaimer: This is not a scientific review, just a few thoughts I had while reading..
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Nick Loman @pathogenomenick.bsky.social · 25/09/2026
This is spectacular: kudos to whoever did it meridian-ai.info
meridian-ai.info
Meridian — Pathogen surveillance, reasoned by AI, pandemic ready.
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Carl Zimmer @carlzimmer.com · 25/09/2026
Anthropic's new biology lab released a technical report on using AI to discover new enzymes. Experts I talked to say "discover" is doing a lot of work here. Story: nyti.ms/4xOGWI7
nyti.ms
Anthropic’s A.I. Is Teaching Itself Biology. Now It’s Made Its First Discovery. (Gift Article)
Scientists at the company announced their first finding: a group of enzymes whose function is unknown.
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Colin Carlson @colincarlson.bsky.social · 24/09/2026
Lab leak people on X are demanding that the editor of Nature be fired because we said Covid-19 is zoonotic in the first sentence of our paper
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Willem van Schaik @wvschaik.bsky.social · 24/09/2026
Steve Busby's scientific family. An impressive career achievement.
Group photo of Busby lab alumni
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Nick Loman @pathogenomenick.bsky.social · 24/09/2026
Celebrating 40 years of Steve Busby’s exceptional research career today @imibirmingham.bsky.social
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Gytis Dudas @evogytis.bsky.social · 22/09/2026
baltic v1.0.0 is live! Get it via pip or clone from Github repo. Now with documentation (baltic.readthedocs.io) & a gallery of tutorials & examples (phylo-baltic.github.io/baltic-gallery, still WIP). Huge thanks to @barney-potter.bsky.social for all the initiative & help along the way. #ViroSky
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 22/09/2026
baltic: the Backronymed Adaptable Lightweight Tree vIsualisation Code www.biorxiv.org/content/10.64898/20…
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Nick Loman @pathogenomenick.bsky.social · 22/09/2026
Folks - if you're interested in how machine learning/AI can be used for microbial genomics, microbiome and metagenomics studies - please join us for a workshop in Birmingham on Thursday 8th October organised with CLIMB & NVIDIA. www.climb.ac.uk/blog/2026/09...
climb.ac.uk
Call for Applications: GPU-Accelerated Computing for Microbiome and Metagenomic Research · CLIMB
CLIMB is a cloud computing infrastructure for microbial bioinformatics — notebook servers, shared storage and reproducible workflows for genomics, metagenomics and pathogen surveillance researchers ac...
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Joseph Cox @josephcox.bsky.social · 18/09/2026
OpenAI and Microsoft admitted LLMs are predatory tech built on “an astonishing theft of unprecedented proportions,” and the “largest theft of labor in human history.” An internal Microsoft document said AI has created a “doom loop” that is killing “the entire web.” www.404media.co/doom-loop-op...
404media.co
‘Doom Loop’: OpenAI and Microsoft Admits LLMs Are Destroying the Web and Built on Theft
"Millions of people around the world will soon consider large models ‘hoovering up’ all their work to be an astonishing theft of unprecedented proportions."
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Mark Histed @markhisted.org · 16/09/2026
Scientist here: It is widely known inside science that this—top-down imposition of a research agenda—leads to mostly rote, boring, non-innovative work. Building an institute to do discovery science is hard: you hire young people, put them together, hope synergies arise and ideas fall out.
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Kristian G. Andersen @kgandersen.bsky.social · 10/09/2026
Take a look at the examples Antrophic provides for research that they blocked, and it's immediately clear almost much all of it is just basic research - but research that has gotten scary-sounding names via the media. An example, put Ebola genomes into Claude Science and ask for a TMRCA > blocked!
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LeithMotive @leithmotive.bsky.social · 11/09/2026
I keep saying this. But the value isn't the AI, it's the data it's trained on. You'd be a fool to give access to company data to these AI companies. You should be training your own on top of their base model.
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Zamin Iqbal @zaminiqbal.bsky.social · 11/09/2026
From @wkhuber.bsky.social and colleagues comparing foundation models against simple baselines. www.nature.com/articles/s41...
nature.com
Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines - Nature Methods
The analysis presented in this Brief Communication shows that, despite their complexity, current deep learning models do not outperform linear baselines in predicting gene perturbation effects, thus e...
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Kristian G. Andersen @kgandersen.bsky.social · 10/09/2026
Controversial, not so controversial, take - the dangers posed by AI are real, current, and well-documented. Those do not include human extinction within a decade, nor do they include AI-manufactured-printed-out-in-the-lab bioweapons, yet, those are the ones we chose to focus on. Good lord.
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Nick Loman @pathogenomenick.bsky.social · 09/09/2026
AI acting more like a real academic than we’d like here
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Nick Loman @pathogenomenick.bsky.social · 09/09/2026
Gosh it looks like again we will have a full house for Genome Science in Manchester next week and the now finalised agenda is looking fantastic: genomescience.org.uk/agenda/ - looking forward to meeting up with this friendliest of science communities again. Who knows if Andy Burnham will swing by?!*
genomescience.org.uk
Genome Science UK 2026
Manchester University
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Gabrielle Gozo @gabriellegozo.com · 03/09/2026
CHATGPT AND CLAUDE ARE DOWN!! Teachers, time for an exam
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Nature @nature.com · 03/09/2026
Top artificial-intelligence models failed to predict the biological consequences of rewriting a virus's entire DNA code. go.nature.com/4rbHdmN
go.nature.com
Mutating every DNA letter of a genome shows surprising effects — and the limits of AI
Top artificial-intelligence models failed to predict the biological consequences of rewriting a virus's entire DNA code.
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By Cory Doctorow (GPG 0xBF3D9110957E5F4C) @doctorow.pluralistic.net · 03/09/2026
What if post-Trump America is even *worse*? 1/
A nuclear mushroom cloud wearing a giant Trump wig. A decaying American flag fills the sky behind it.
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Adam Kucharski @adamjkucharski.bsky.social · 02/09/2026
New post, on why your vibe-coded dashboard looks terrible:
kucharski.substack.com
Ten reasons your vibe-coded dashboard looks terrible
Jagged journeys and wasted heroes
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Gerry Tonkin-Hill @gerrythill.bsky.social · 02/09/2026
Glad to share StrainSpy, a new method developed by Sudaraka and co which identifies strain-level associations in metagenomics using ANI estimates from tools like Sylph. www.biorxiv.org/content/10.6...
biorxiv.org
Accurate detection of metagenomic strain-level associations using average nucleotide identity with StrainSpy
Genetic variation among microbial strains of the same species can profoundly influence their phenotypes, ecological functions, and impacts on human health. Traditionally, the relative abundance of a s...
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Jim Shaw @jimshaw.bsky.social · 02/09/2026
Cool preprint about strain-level metagenome association studies using k-mer containment. Mallawaarachchi et al. from @gerrythill.bsky.social's group. I tried tackling this in our original paper for sylph (sylph-docs.github.io), but this seems to be much more sophisticated. Excited to read!
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T. Ryan Gregory 🇨🇦 @tryangregory.bsky.social · 01/09/2026
🎯 "Personally, when I see GenAI images in a talk or paper, I treat the rest of the talk or paper with more scrutiny and skepticism than I would have otherwise."
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Stuart Neil @tetherin.bsky.social · 01/09/2026
Fantastic article about the life and work of Bob Garry that highlights both the personal and scientific costs that the conspiracy theory industry has had on Global public health and the scientists who have dedicated their lives to fighting infectious diseases www.bloomberg.com/news/feature...
bloomberg.com
A Top Virus Scientist Stared Down Covid Lab-Leak Proponents. Now His Life’s Work Is at Stake
The battle over Covid’s origins has come for Bob Garry, who’s faced some of the world’s deadliest viral threats.
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European Conference on Computational Biology @eccb-europe.bsky.social · 01/09/2026
This morning we remembered four computational biology pioneers, who the world sadly lost over the past year. Thank you to all speakers for your moving tributes at ECCB. #ECCB2026 #Bioinformatics
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Helen Branswell 🇨🇦 @helenbranswell.bsky.social · 24/06/2026
Have you ever seen this iconic image of the Ebola virus, from the first known outbreak in DRC in 1976? An electron microscopic image, it was captured by #CDC 's Fred Murphy, a virological giant and a very kind interviewee. He died yesterday. He will be missed, but his scientific legacy lives on.
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Nick Loman @pathogenomenick.bsky.social · 31/08/2026
In Geneva for #ECCB2026 ! Been a long time since I was last at this meeting. Talking tomorrow in morning session about bioinformatics for pathogen surveillance with legends of the field: @angieshinrichs.bsky.social @firefoxx66.bsky.social and @theo.io ! eccb2026.org/schedule/par...
eccb2026.org
Parallel sessions
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Thiago Carvalho @cyrilpedia.bsky.social · 30/08/2026
'Our findings illustrate a curious paradox: despite universities being key producers of evidence and seeking the use of their research to inform public policymaking, they are less adept at using evidence to inform their own decision-making.' blogs.lse.ac.uk/impactofsoci...
blogs.lse.ac.uk
Universities rarely use research evidence in their decision-making, so why do they expect anyone else to? - LSE Impact
Despite universities’ important role as evidence-producing organisations, they rarely draw upon research evidence for internal decision making, why?
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Claus Wilke @clauswilke.com · 30/08/2026
I'm really frustrated by the constant fear-mongering about AI-designed superviruses. Can we focus on the things that should actually worry us, such as measles? blog.genesmindsmachines.com/p/im-sorry-y...
blog.genesmindsmachines.com
I'm sorry, you're not going to die from an AI-engineered supervirus
God save us from economists who think they can competently talk about biology
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Juliet E McKenna @julietemckenna.bsky.social · 29/08/2026
Journalists need to stop describing these incidents in terms implying software has agency and intent. It does not. The people who created a faulty and dangerous product are the ones responsible for whatever happens, and must be held to account, with punitive financial penalties for damage done.
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Nick Loman @pathogenomenick.bsky.social · 29/08/2026
I am sticking with Silo on Apple TV and I quite like the general vibe but wow .. everrrryyy interaction and scene is sooooo slowwwww. No wonder it took hundreds of years to figure out.
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Justin Ling @justinling.ca · 27/08/2026
Today's @xkcd.com
It's a stickman holding a hammer, lifting up his leg, and saying:

"Listen up, leg. I've been sending you rich, oxygenated blood for years, while you send me worthless used-up blood with no oxygen. Time to teach you a lesson about not ripping me off!"

It is captioned: tariffs
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mgualt.bsky.social @mgualt.bsky.social · 25/08/2026
A letter to the math community, to appear in the Notices. In response to what I view as irresponsible messaging and unfortunate decisions from some mathematical leaders influencing many in my department. www.math.toronto.edu/mgualt/math-...
math.toronto.edu
Mathematics and the LLM: 2026 – Coordinate Change
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Nix @nix.wsocial.eu · 26/08/2026
Cory Doctorow lays out a roadmap for Europe and Canada to strike back against enshittification. Roll back the legislation which criminalises jailbreaking enshittified tech, both sticking it to the tech giants and Trump as well as unleashing massive growth in our own economies.
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Amadi Lovelace @amaditalks.bsky.social · 25/08/2026
Remember that if you got the Moderna Covid vaccine, you have Dolly Parton to thank, she gave the largest individual contribution toward their research to make it possible.
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Nick Loman @pathogenomenick.bsky.social · 19/08/2026
The first summer on record where I’ve thought thank fuck summer is over by the end of it
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Kristian G. Andersen @kgandersen.bsky.social · 16/08/2026
It is remarkable to see a, supposedly, serious scientist write an OpEd in @theguardian.com but completely refusing to engage with a large body of scientific evidence. All of that gets throw away, and scientists who have studied the "origin" question, told to "back off" and "display [..] humility" 🤷‍♂️
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Katy Brown @thekatybrown.bsky.social · 07/08/2026
Me, @emma-harding.bsky.social, @rtarlinton.bsky.social and @royalsociety.org are organising a meeting on endogenous viral elements! 8-9 Feb 2027, Birmingham UK. 2 whole days of EVEs! Many amazing researchers already agreed to speak. Invites: shorturl.at/jp9sh Provisional schedule: shorturl.at/8O5KV
royalsociety.org
Endogenous viral elements | Royal Society
Theo Murphy meeting organised by Dr Katy Brown, Dr Emma Harding and Professor Rachael Tarlinton
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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 11/08/2026
Howdy, In my spare time I have been working on a modern web version of BRIG, and it is now in a state fit for public consumption. Please share with your team + students. And If they have feedback they can reach me on email. brigx.genomicx.org BRIGX is a modern implementation of BRIG […]
mstdn.science
Original post on mstdn.science
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Colin Carlson @colincarlson.bsky.social · 10/08/2026
I wrote about a reason not to use generative AI in your writing that I haven't seen anyone talking about. Once I realized this, banning GenAI in our lab's writing became a no-brainer. Feel free to share, I think this is probably useful especially for trainees: www.carlsonlab.bio/thoughts/the...
carlsonlab.bio
The only reason you’ll ever need not to write with AI — The Carlson Lab
Over the last year, our lab has been developing a policy on AI use. To do this, we did three main things: We read a lot of academic publications and tech news. We set up an #ai channel on our la...
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By Cory Doctorow (GPG 0xBF3D9110957E5F4C) @doctorow.pluralistic.net · 08/08/2026
Hardly a day goes by without my getting email from someone looking for ways to do good with tech. From computer science students thinking about post-grad careers to seasoned coders with decades of experience, there's an army of hackers looking for a way to turn their expertise into public goods. 1/
The giant head of the Statue of Liberty. Around it are many medieval machines, tended by little medieval rude mechanicals. In the background is a crosshatched architectural drawing of some classical arches and such.
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Falk Hildebrand @bioinf.bsky.social · 07/08/2026
After a very long time, I'm very proud that we have now Joachim "magnus opum" on www.biorxiv.org/content/10.6... Protal is a ultra fast metagenomic species profiler. More precise than other profiled software, faster than most (not sylph though), but generates strain resolution instead.
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Alex Crits-Christoph @acritschristoph.bsky.social · 06/08/2026
see also this work, which helps provide some helpful framing of how novel these phages are: www.biorxiv.org/content/10.6... tl;dr: I believe this work generates only marginally novel phages, which have only a moderate likelihood of working, that decreases the more novel they get.
biorxiv.org
Quantifying evolutionary novelty and design efficiency in generative genome design
Generative genome design models can now produce previously unobserved genome-length sequences, but assessing their capabilities is complicated by limitations in functional prediction. The ability to e...
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