Statisticians in my field have been trying to improve statistical literacy in earnest since the early 20th century. The @royalstatsoc.bsky.social has an entire section on teaching statistics. We have the tools. The knowledge simply isn't valued enough. statsepi.substack.com/p/a-brief-hi...

Teaching scientists about statistics is not even that difficult. But it slows down how many papers get published, so we can't do it. I mean, why would we put any brakes on LLM produced papers by insisting scientists and reviewers understand the output!? Madness.

A new Nature Medicine study analyzing health records from >100 million people in the US offers compelling evidence that reactivation of varicella-zoster virus (VZV) ,the same virus that causes chickenpox and shingles may contribute to dementia risk. www.nature.com/articles/s41...

🦒Long read giraffe is out!🦒 Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2

Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe https://www.biorxiv.org/content/10.1101/2025.09.29.678807v1

Cowardice personified

One of my favorite anecdotes from THE PREHISTORY OF THE FAR SIDE: "That doesn't sound like the Jane Goodall we know."

There are millions of openly available microbial genomes, but searching them can be slow. Until now 🥁 Introducing LexicMap, a new alignment tool that lets scientists search these data in minutes, helping track antibiotic resistance, trace outbreaks, and more. www.ebi.ac.uk/about/news/r... 🦠

That's quite the chart annotation. www.nature.com/articles/d41...

When I was at NIH and shutdowns loomed, it was discovered that the administration was planning to shut down PubMed. The head of NCBI called the powers that be and pointed out that this would threaten patient safety Who knows what will happen now Just in case, remember Euruope-PMC (europepmc.org )

Just fuck off with this. How about start the conversation by highlighting how much immigrants contribute to the UK - not least by propping up the NHS and social care system! Also - forced volunteering is not volunteering, it's unpaid labour.

When you are able to publish bullshit in a #predatory journal: look at the title, author and affiliation, which the editor was unable (?) to identify.... The test was done by Thomas Schlacher #Research #Integrity

🚨 New Web Resource Alert! 🚨 We're delighted to share Viro3D a database of >85000 viral protein structure predictions from >4400 human & animal viruses. 🔗 viro3d.cvr.gla.ac.uk 📄 www.embopress.org/doi/full/10.... @molsystbiol.org @cvrinfo.bsky.social @uofgmvls.bsky.social #Virology #AlphaFold 🧪 🦠

Our former President Mary Robinson, told Channel 4 News that "the United States is complicit in this famine and unfolding genocide" of Palestinians in Gaza through its support of apartheid Israel. She's right, and shamefully the US uses Shannon Airport every day. #GazaGenocide Video Channel 4 News

🔍 The paper emphasizes that formal recognition of these competencies supports professional development, clearer career pathways, and effective leadership within bioinformatics core facilities, strengthening their long-term impact on research communities.

This work extends the ISCB competency framework to include six new competencies specific to bioinformatics core facilities: identifying and supporting user needs, managing projects, managing team members, engaging with collaborators, providing training, and leading the facility.

📘 Just out in Bioinformatics Advances: "Competencies for bioinformatics core facility scientists: Extension of the ISCB competency framework for bioinformatics" Explore the full study: https://doi.org/10.1093/bioadv/vbaf206 Authors include: @downingtim.bsky.social

I've written a short blog post introducing "The Art of Visualization with ggplot2"! This book is all about the end-to-end process of creating charts with #ggplot2 📊 including data wrangling, sketching, and styling your plots! nrennie.rbind.io/blog/art-of-... #RStats #DataViz #TidyTuesday

Sometimes you meet absolutely incredible bioinfo-magicians. It was a huge privilege when @shenwei356.bsky.social joined our group for a year on an @embl.org sabbatical. While here, he developed a new way of aligning to millions of bacteria, called LexicMap 1/n www.nature.com/articles/s41...

And here’s confirmation from @WHO: “Health authorities in the Democratic Republic of the Congo have declared an outbreak of Ebola virus disease in Kasai Province where 28 suspected cases and 15 deaths, including four health workers, have been reported as of 4 September 2025.” #IDsky 🧪

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io

New preprint from the group: @lucydillon.bsky.social analysis of 16,000+ genomes finds Bacteria cannot combine certain resistance genes as they are mutually exclusive, forcing them down incompatible evolutionary paths. biorxiv.org/content/10.1101/2025.08.20.671315v1 @jomcinerney.bsky.social

Is there only one "path" that evolution tends to take when a new trait arises? Or can the trait arise in more than one way? In other words, walking back from a particular evolutionary "destination", do we always take the same path? The answer might be "no", at least some of the time. In fact... 1/n

Very dissappointed the the #ISMB 2026 meeting will be in the USA next year. We all got an email about how moving it would be financially not possible, but in reality no one is going to go, hosting it in the USA is explicitly anti-inclusive ... iscb.bsky.social

Today, our article "The entities enabling scientific fraud at scale are large, resilient, and growing rapidly" is finally published in PNAS. I hope that it proves to be a wake-up-call for the whole scientific community. reeserichardson.blog/2025/08/04/a...

TIL the original paper describing CRISPR, by Francisco Mojica, was rejected by 4 journals and took 2 years to be published

📢 Calling all Postgrad Virologists! 🦠 Postgraduate Virologists Network are hosting their first conference for virology students, by virology students. 📍 @uofglasgow.bsky.social 📆 8-9 September Register and submit an abstract: www.postgradvirologistsnetwork.co.uk/2025-meeting

Just in case there was any doubt, ChatGPT 5.0 still makes up completely random citations that don't exist and should not be used for literature search.

We are also hiring a 4-year postdoc to study the dynamics and evolution of mobile genetic elements in the C-fixing Icelandic host-spring microbiomes Join our exciting multidisciplinary team funded by @ukri.org BBSRC sLoLa www.jobs.manchester.ac.uk/Job/JobDetai...

Scientists have found instances of sex reversal—where an individual has the physical features of one sex but the genetic makeup of the other—in five different Australian bird species. https://scim.ag/41Dvamo

1. "'Trusting the experts is not a feature of either a science or democracy," Kennedy said." It's literally a vital feature of both science and of representative democracy. I've written a fair bit about trust in expertise as a vital mechanism in the collective epistemology of science.

Data come in many different formats and are used in many different ways, but in many cases, a checklist like this (along with good data documentation) can help you verify if a dataset is in a usable format for most general purposes. osf.io/t8upr

music lessons don't make kids smarter, but many people have assumed that music lessons would have near-transfer effects, e.g. improving aspects of auditory perception big new study led by Andrew Oxenham says "nope". music lessons make kids better at music & that's good enough reason to do 'em !

Update on the Atlanta variant. It is unquestionably the same lineage we detected about at year ago. The lineage is a B.1.1-derivative. Probably B.1.1.29. That means it infected the person 4.5 years ago, and is currently the dominant signal in a sewershed with 190k people. More to come.

New blogpost. The shitshow that results when a publisher fails to check up on their peer reviewers, with authors caught up in a nightmare process. deevybee.blogspot.com/2025/07/trou...

Elon Musk casually, and illegally, dismantled USAID. According to a new study in the Lancet, that action will lead to *14 million* premature deaths between 2025 and 2030. Again: Elon Musk is directly responsible for 14 million coming deaths. 4.5 million will be children.

‘The nurse told me I couldn’t keep my baby’: how a controversial Danish ‘parenting test’ separated a Greenlandic woman from her children

A few months ago, Nature published how-to guide for using ChatGPT to write your peer reviews in 30 minutes. This is, of course, a horrible idea. Here’s my response with @jbakcoleman.bsky.social .

I’ve updated the iebabynames R package, which now contains baby name data (1964–2024) for Ireland, sourced from the Central Statistics Office. The data have proved valuable for teaching data wrangling and visualisation, and they reveal interesting patterns. ➡️ github.com/stefan-muell... #rstats

github.com/bede/deacon - by @bedec.bsky.social - nice to use a bioinformatics tool that attains the trifecta: (1) is easy to install, (2) actually works, & (3) does something useful. It can filter to keep or retain reads matching a FASTA query #filter #reads #genome

This sort of prejudice against Irish is exhausting from The Economist. It's not the first time. The Irish language is no more or less "unfathomable" than French, Spanish, Italian, Arabic, Portuguese etc. All languages are "fathomable" when you take the effort to learn them. Cc @shashj.bsky.social

Your genome is not a blueprint. A thread about misleading metaphors in science communication. 🧬🧪 1/n

New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search. github.com/bede/deacon

Hello everyone! I am pleased to share information on the first ever Computational Structural Virology Symposium, conducted August 4th on zoom and highlighting work in this emerging field. You can register for this event here: forms.gle/CNiqskMwQEuV.... Please re-post!

Here’s what I mean by being nicer while not changing meaning. Bloom’s Chinese colleagues “abused” his naively trusting American colleagues in his preprint. In the paper, all that changes is criticizing the American colleagues for allowing this abuse to occur.

Four years ago, Jesse Bloom announced the recovery of SARS-CoV-2 sequences and suggested they could come from very early COVID-19 patients. Zach Hensel and I found out that Bloom's claim relied on the deliberate omission of a January 30, 2020 collection date contradicting his narrative. 🧪 #PopGen

Jesse Bloom replied to our critique by painting Wang et al.'s data as unreliable. To do so, he once again omitted a critical piece of information that contradicted his narrative: five control samples had been mixed into a single one. This is part of a concerning pattern of misrepresentation: ▫️1/4

Yes, it was

Erm... This is data manipulation...

PhD opportunity: Understand how African swine fever virus (ASFV) interacts with the cellular immune response. This project is based at Pirbright and ‪@royalvetcollege.bsky.social‬ with an industry placement at ‪@boehringerglobal.bsky.social‬ Animal Health. 🔗 www.pirbright.ac.uk/careers-and-...