It's going to be even worse the next time they appoint Peter Mandelson

Don’t believe headlines saying that vaccine skepticism is widespread Despite some headlines, a new poll does not show that most Americans no longer trust vaccines.

A badly worded poll is making vaccine skepticism look more common than it is. www.statnews.com/2026/04/17/v...

Unfalsifiable by Design: A Year of Trying and Failing to Reproduce a Human Microbiome and Autism Study The myth of open data, reproducibility, responsibility, and accountability in science, and your role in it

How every layer of science's "self-correcting machinery" failed when Iva Veseli and I simply wanted to reproduce the findings of a high-profile study on gut microbiome and autism:

merenlab.org/2026/04/15/u...

Side-by-side image. Left: the first page of an article in T.E.R.M. (Teaching Educational Research Methods), Volume 1 Issue 1 (Spring 2026), titled ‘The Five Gs for Teaching Statistics: Greek, Graphs, Grammar, Gadgets, and Games’ by Andrew Dean Ho (Harvard Graduate School of Education), with the abstract visible. Right: a photo of a pegboard-style learning "gadget" with colored pins and elastic bands forming a scatterplot, with a best-fit regression line as a dowel and rubber bands representing ordinary least squares residuals.

I wrote about how I teach statistics. As I redesign for the AI era, I won't forget the benefits of multimodal, tangible representations.
The Five Gs: Greek, Graphs, Grammar, Gadgets, and Games.
In the new journal, Teaching Educational Research Methods: doi.org/10.5149/term...

How Ireland's far-right movement got involved in the fuel protests and tried to hijack them While many are protesting fuel costs, far-right actors and international figures are using the movement to push anti-immigrant narratives.

While many protesters in Ireland are complaining about fuel costs, far-right actors and international figures are using the movement to push anti-immigrant narratives.

Insights into goatpox virus and sheeppox virus genomes from pangenome graphs www.biorxiv.org/content/10.64898/2026.03...

A picture of a cat. It says, “4 years ago lived in a bush and hunted my own meals. Now I have 2 passive incomes, my own house, & a personal chef. Follow me for more financial advice.”

#Caturday

High-throughput DNA extraction and cost-effective miniaturized metagenome and amplicon library preparation of soil samples for DNA sequencing Reductions in sequencing costs have enabled widespread use of shotgun metagenomics and amplicon sequencing, which have drastically improved our understanding of the microbial world. However, large seq...

I was reminded of this paper from colleagues at AAU:

"We ... miniaturize Illumina amplicon and metagenomic library preparation volumes by a factor of 5 and 10, respectively, with no significant impact on the observed microbial communities."
journals.plos.org/plosone/arti...

Great assembly, as should be expected from a small genome that doesn't have much repetitive complexity in it.

Repaver plot (k=12 bp) for Lumpy skin disease virus isolate Oman_2009, complete genome. There is a lot of noise in the repeat structure at 12bp density (somewhat typical for viral genomes), but both the inverted repeats at the ends and the 39bp terminal tandem repeat arrays can be seen.

Spiral sequence plot of the first 700bp of the LSDV genome, with a ring size of 39 bases, showing a tandem repeat region in approximately the centre of the range. I'm not sure I'd call this a telomere (due to the fairly long repeat length), but it's at least an end repeat.

This is a challenging genome to get a good density for because you need to go fairly dense to properly capture the end repeats, but then the inverted repeats start to get swamped by the background random noise.

Doesn't seem to display well on semicircular or spiral plots either, unfortunately.

Hi David, yes you are correct about the end repeats being complex (they even have extra-helical base) but pretty homogeneous in the middle. Nice visuals 😀

New #poxvirus #preprint on #pangenomegraphs in #goatpox & #sheeppox virus

"Insights into goatpox virus and sheeppox virus genomes from pangenome graphs"
www.biorxiv.org/content/10.6...

This is either brilliant or scary:

Anthropic accidentally leaked the TS source code of Claude Code (which is closed source). Repos sharing the source are taken down with DMCA.

BUT this repo rewrote the code using Python, and so it violates no copyright & cannot be taken down!

Protein Language Models (PLMs) could transform outbreak response

New research from @kieranlamb.bsky.social & colleagues show that PLMs can identify mutation hotspots and key features of viral proteins - even from a single sequence.

www.gla.ac.uk/research/az/...

"Characterizing novel viral proteins using protein language models (PLMs)" -Kieran Lamb YouTube video by Variant Effects

Listen to Kieran's recent presentation at the AVE Virology Interest Group "Characterizing novel viral proteins using protein language models (PLMs)":

youtu.be/phrIC-J5Je0?...

My main gripe with the alphafold example is how it shows you need decades and decades of high quality data, well structured, open and accessible to train a model -- and yet they always gloss over it and pretend it's just AI and magic. No, we need to continuously invest in real data and FAIR data.

If you use fgbio or UMIs at all, you should start using fgumi. Up to 100x faster, and soon 2x faster sort than samtools, it’s been a labor of love and something we’ve wanted to do for a long time.

New blogpost by @deevybee.bsky.social on Wellcome LEAP's $50 million program on autism and the microbiome deevybee.blogspot.com/2026/03/upda...

Our new work - "A high-quality telomere-to-telomere LSDV genome assembly"

A 151 Kb #t2t #genome #assembly of the Lumpy skin disease #virus #LSDV Oman 2009 using high-accuracy long ONT reads. Illumina reads only made a tiny difference, so probably ONT only in future!
www.biorxiv.org/content/10.6...

Wonderful exposition in this modern classic

"Describing..population structure in terms of ancestry (“your ancestors lived in Ireland”), rather than relatedness (“your relatives live in Ireland”) underestimates the contribution of migration to..demography."
journals.plos.org/plosgenetics...

Matt Ridley gave the inaugural "NIH Scientific Freedom Lecture Series" earlier today and I just wanted to run through some of the main claims he made - you'll be unsurprised to learn that almost all of them are false.

Here's his summary slide - let's start there.

🧵👇

Data Organization in Spreadsheets Karl W. Broman & Kara H. Woo Pages 2-10 | Received 01 Jun 2017, Accepted author version posted online: 29 Sep 2017, Published online: 24 Apr 2018 1. Introduction 2. Be Consistent 3. Choose Good Names for Things 4. Write Dates as YYYY-MM-DD 5. No Empty Cells 6. Put Just One Thing in a Cell 7. Make it a Rectangle 8. Create a Data Dictionary 9. No Calculations in the Raw Data Files 10. Do Not Use Font Color or Highlighting as Data 11. Make Backups 12. Use Data Validation to Avoid Errors 13. Save the Data in Plain Text Files ABSTRACT Spreadsheets are widely used software tools for data entry, storage, analysis, and visualization. Focusing on the data entry and storage aspects, this article offers practical recommendations for organizing spreadsheet data to reduce errors and ease later analyses. The basic principles are: be consistent, write dates like YYYY-MM-DD, do not leave any cells empty, put just one thing in a cell, organize the data as a single rectangle (with subjects as rows and variables as columns, and with a single header row), create a data dictionary, do not include calculations in the raw data files, do not use font color or highlighting as data, choose good names for things, make backups, use data validation to avoid data entry errors, and save the data in plain text files.

Every day is a good day for sharing one of the most useful papers about research data ever written. PLEASE get your people to understand and follow this advice.

www.tandfonline.com/doi/full/10....

GitHub - downingtim/Panalyze Contribute to downingtim/Panalyze development by creating an account on GitHub.

💻 Panalyze is available at

Panalyze is a workflow for constructing & analyzing viral pangenome variation graphs to better capture genomic diversity w/o reference bias. The tool automates graph construction, exploration, & annotation to support scalable analysis of viral genome variation in lightweight computing environments.

🧬 New in Bioinformatics Advances: "Panalyze: Automated virus pangenome variation graph construction, analysis and annotation" 

Read the paper:  https://doi.org/10.1093/bioadv/vbag071

Authors include: @downingtim.bsky.social

Germany does not lack talent, and it does not lack funding. But we are trapping 21st-century minds inside 19th-century academic hierarchies. We are asking brilliant young scientists to build the future of the German economy, but refusing to give them the lab space, the job security, or the scientific independence to actually do it. If we want to reclaim our place as an industrial superpower, we have to stop the rat race of trying to keep every technology and structure alive that made us successful in the 20th century. Instead, we must fix our system that pushes our most ambitious scientists away. The money is there. The talent can be there. Now, we also need the courage to fix what’s broken.

“we are trapping 21st-century minds inside 19th-century academic hierarchies.” This essay gets a lot right about problems with German science. I would add that the hierarchies and precarious contracts lead also to systemic abuse and scientific misconduct. open.substack.com/pub/realimag...

Our paper "Panalyze: automated virus pangenome variation graph construction, analysis and annotation" is out in Bioinformatics Advances, link below

#pangenome #virus #pathogen #genomics

academic.oup.com/bioinformati...

Imprinting by influenza virus infection in children can cause a deleterious shift of nearly the entire memory recall response against key, conserved epitopes @nature.com @weillcornell.bsky.social
www.nature.com/articles/s41...

Dynamics of natural selection preceding human viral epidemics and pandemics Using a phylogenetic framework to characterize natural selection, we investigate the hypothesis that zoonotic viruses require adaptation prior to zoon…

There's a common misconception that zoonotic viruses require significant adaptation to jump from animals to cause human epidemics.

Not so 👇.

Further, we see clear signs of 1977 flu experiencing cell passage, prior to epidemic.

SARS-CoV-2? Business as usual.

www.sciencedirect.com/science/arti...