Nick Loman
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pathogenomenick.bsky.social
Nick Loman
@pathogenomenick.bsky.social
5.8K followers 680 following 580 posts
Public health (meta)genomics & bioinformatics, Prof @unibirmingham.bsky.social, Director @imibirmingham.bsky.social & @climb.ac.uk
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Reposted by Nick Loman
carlbergstrom.com
I am by no means a prominent public intellectual, but my inbox is increasingly filled with messages from people who have been convinced by sycophantic chatbots that they have discovered revolutionary theories that entirely upend our scientific understanding of the universe.
November 21, 2025 at 2:49 AM
Reposted by Nick Loman
pathoplexus.org
1/ 🚀 Big thanks to our community - since August we’ve added thousands of new sequences, rolled out major new features, and welcomed fresh faces into the #Pathoplexus world. Let’s dive into what’s new.👇🏻

Read the full update: pathoplexus.org/news/2025-11...
Graph showing the change in number of directly submitted sequences to Pathoplexus since August 2024. 0 in Aug 2024 to almost 9000 today.
November 18, 2025 at 7:01 PM
Reposted by Nick Loman
chrystalok.bsky.social
Twitter and chat gpt are down. Bad day for people who suck.
November 18, 2025 at 1:11 PM
Reposted by Nick Loman
jessicamablair.bsky.social
Really excited to say that we have been awarded a BBSRC sLola! Really looking forward to kick off this project with such a fantastic team! @webberma.bsky.social @overtonlab.bsky.social @bugsinblood.bsky.social Sara Jabbari, Dong-Hyun Kim @imibirmingham.bsky.social www.ukri.org/news/powerin...
Powering team science to unlock life’s secrets
Four world-class teams awarded major BBSRC sLoLa grants to push the frontiers of discovery in microbiology, photosynthesis, gene regulation and quantum biology.
www.ukri.org
November 18, 2025 at 9:48 AM
Reposted by Nick Loman
kgandersen.bsky.social
This is an interesting case of a patient from Chad infected with a novel arenavirus species/variant/strain, presenting with meningoencephalitis.

IMO, could be classified as a highly divergent Lassa virus strain in a new country (similar to what Togo has observed).

www.nejm.org/doi/10.1056/...
A Mammarenavirus Close to Lassa Virus in a Patient with Meningoencephalitis | NEJM
A 37-year-old man in Chad presented with a fever and a headache. An extensive evaluation identified a mammarenavirus, close to Lassa virus, in samples of cerebrospinal fluid.
www.nejm.org
November 17, 2025 at 4:47 PM
Reposted by Nick Loman
acritschristoph.bsky.social
so...personally I think this is a very poor work which is really deeply confused about what metagenomics is, why we do it, and what the key biologically relevant biases actually are.

But, hey, I know there are deep divisions in the field which can't be overcome through micro-posts.

Key table:
November 16, 2025 at 5:30 PM
Reposted by Nick Loman
theonion.com
DNA Sequencing Reveals Hitler Was Type Of Fern
DNA Sequencing Reveals Hitler Was Type Of Fern
BATH, ENGLAND—Saying the discovery shed new light on the infamous German dictator’s life, University of Bath researchers revealed DNA sequencing Friday showing that Adolf Hitler was a type of fern. “A...
theonion.com
November 14, 2025 at 11:00 PM
Reposted by Nick Loman
hswapnil.medsky.social
Whoah

EBV not only causes multiple sclerosis, it also might be the root of SLE

www.science.org/doi/10.1126/...

An EBV vaccine to rid ourselves of these horrible autoimmune conditions (and many cancers)?

#lupus #medsky #RheumSky

@christosargyrop.bsky.social
Epstein-Barr virus reprograms autoreactive B cells as antigen-presenting cells in systemic lupus erythematosus
Epstein-Barr virus reprograms autoreactive B cells as antigen-presenting cells to promote pathogenic antinuclear T and B cell responses in lupus.
www.science.org
November 13, 2025 at 11:05 PM
Reposted by Nick Loman
helenbranswell.bsky.social
The outbreak in Ethiopia is #Marburg virus, the first such outbreak for this country. 9 cases so far, including some health workers. x.com/drtedros/sta...
Tedros Adhanom Ghebreyesus on X: "#Ethiopia has confirmed the outbreak that has infected at least 9 people in the south of the country is of #Marburg virus disease. I commend Ethiopia’s @FMoHealth for its rapid and transparent response to the outbreak, and the work of the Ethiopia Public Health Institute and" / X
#Ethiopia has confirmed the outbreak that has infected at least 9 people in the south of the country is of #Marburg virus disease. I commend Ethiopia’s @FMoHealth for its rapid and transparent response to the outbreak, and the work of the Ethiopia Public Health Institute and
x.com
November 14, 2025 at 4:22 PM
Reposted by Nick Loman
aroneys.bsky.social
“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla.
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
Logo of Bin Chicken (Australian white ibis) on a rubbish bin, pulling out a strand of DNA
November 13, 2025 at 10:09 AM
Reposted by Nick Loman
wiringthebrain.bsky.social
New paper with @statsepi.bsky.social and @deevybee.bsky.social in which we show there's really no evidence for a link between the gut microbiome and autism www.cell.com/neuron/fullt...
Conceptual and methodological flaws undermine claims of a link between the gut microbiome and autism
Claims that the gut microbiome causally contributes to autism regularly appear in the scientific literature and popular press. Mitchell et al. critically examine influential studies underpinning these...
www.cell.com
November 13, 2025 at 4:10 PM
Reposted by Nick Loman
adrianwoolfson.bsky.social
My review of #Crick by @matthewcobb.bsky.social has been published online by @science.org. The book is lucid, beautifully crafted, and compelling. It will instantly become the definitive guide to this extraordinary individual’s life and work.
November 13, 2025 at 8:14 PM
Reposted by Nick Loman
New primer alert! Fantastic insight into how to apply machine learning and AI in microbiology. A must read. @microbiologysociety.org @delafuentelab.bsky.social www.microbiologyresearch.org/content/jour...
Microbial Primer: Artificial intelligence for microbiologists
Artificial intelligence (AI) and machine learning (ML) are reshaping microbiology, enabling rapid antibiotic discovery, resistance prediction and clinical diagnostics. For microbiologists, the goal is...
www.microbiologyresearch.org
November 13, 2025 at 6:07 PM
Reposted by Nick Loman
gcbias.bsky.social
We don't want people to think you can see evil in the genome, but we'll call our Channel 4 documentary "Hitler's DNA: Blueprint of a dictator".
November 12, 2025 at 10:35 PM
Reposted by Nick Loman
hansonmark.bsky.social
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision. A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
November 11, 2025 at 11:52 AM
Reposted by Nick Loman
janrosenow.bsky.social
“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...
November 9, 2025 at 9:05 PM
pathogenomenick.bsky.social
Bluesky feels like it’s had a bit of a bump recently
November 10, 2025 at 5:32 PM
Reposted by Nick Loman
daveyfwright.bsky.social
"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
Reposted by Nick Loman
matthewcobb.bsky.social
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.
November 8, 2025 at 7:32 AM
Reposted by Nick Loman
leahlitman.bsky.social
HAPPY FOUR SEASONS TOTAL LANDSCAPING DAY TO ALL WHO CELEBRATE
Rudy press conference at 4 seasons total landscaping
November 7, 2025 at 6:44 PM
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. 🧵👇
nextstrain.org Nextstrain @nextstrain.org · 14d
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
Reposted by Nick Loman
newyorker.com
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
pathogenomenick.bsky.social
😂😂 need a PR for gyat()
hadley.nz Hadley Wickham @hadley.nz · 14d
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.
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
Reposted by Nick Loman
nextstrain.org
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
Reposted by Nick Loman
grovearmada.bsky.social
🧬 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...
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