It's out! The LIN code approach for genomic taxonomy of microbial strains and its applications in genomic epidemiology journals.plos.org/plosbiology/...

Life Identification Numbers: A strain nomenclature approach to aid epidemiological surveillance of bacterial pathogens

Unified bacterial strain taxonomies are needed for coherent communication of findings in microbiological research. This Essay provides an overview of a novel bacterial strain taxonomy and describes ho...

journals.plos.org

They stole the internet’s knowledge and all the work that went into it and they want to sell it back to us for a fee. What a business model.

Thrilled to announce that the Department of Microbiology at the University of Washington, School of Medicine is hiring at the Assistant Professor level (tenure-track)! The Pacific Northwest is an awesome place to live and do science 🧪🦠. Join us! apply.interfolio.com/185622 Applications due 8/1.

Just a shout-out to the folks over at @pathoplexus.org and, importantly, all the scientists sharing genomic data with such amazing speed. It's great to see the field having moved to a new platform, with non-transparent platforms being a thing of the past. Fantastic.

🚨New preprint from the lab!🚨 Check @gazollavolpiano.bsky.social 's thread on our latest study looking at bacterial diversity and strain dynamics in the early-life respiratory microbiome 🫁🧫🧬👶 🔗 www.biorxiv.org/content/10.6... cc @bakerresearchau.bsky.social @uniofbath.bsky.social @lshtm.bsky.social

Camila Gazolla Volpiano, PhD@gazollavolpiano.bsky.social · 3mo ago

New preprint! The first first-author work of my postdoc at the Baker! So, babies' airways are colonised from birth, and our group has shown that early colonisers shape respiratory health. 1/7 www.biorxiv.org/content/10.6...

⏰ Registration closing soon! Join us in Manchester for a 1-day meeting on Therapeutics & Antimicrobial Resistance (AMR). Talks, panels, ECR sessions, speed networking & a WAAW sandpit. Don’t miss out 👉 https://microb.io/TherAMR26

New preprint! The first first-author work of my postdoc at the Baker! So, babies' airways are colonised from birth, and our group has shown that early colonisers shape respiratory health. 1/7 www.biorxiv.org/content/10.6...

A new study led by Harry Veillard, MSc student @lshtm.bsky.social, found that nurse and pharmacist prescribing could improve access to care, reduce treatment delays, and ease pressure on primary care. The study also highlights the need for training and support. Read more 👉 bit.ly/4tERrvi

Having just finished my MCSA Fellowship with him, I would really encourage those looking to do a postdoc in microbial adaptation to check out Alex Couces lab in Madrid. Alex is a gifted researcher, and Madrid is a wonderful city to live in :) Details in link below: evoldir.net/brian/evoldi...

Being a PI is an intricate juggling act that requires tough decisions – intellectual, financial, strategic. Yet we are expected to navigate these dangerous waters with very little support. The solo PI model is deeply problematic. My latest blog post #AcademicSky occamstypewriter.org/mindthegap/2...

Rapid release of multiplex PCR amplicon scheme for Andes hantavirus whole genome sequencing validated on control material: www.biorxiv.org/content/10.6... @scalene.bsky.social @stevepullan.bsky.social @ukhsa.bsky.social output from HPRU in Public Health Genomics

🚨🧪 Our UK Public Health Rapid Support Team has deployed a fully functioning mobile laboratory to one of the world’s most remote locations to support the hantavirus outbreak response. Read our blog post for the full story 🔗 https://bit.ly/4wxnlwo

Yes! Now do it for other pre-print servers, grant applications, social media posts and wedding speeches.

Mel Andrews@bayesianboy.bsky.social · 3mo ago

Finally, some good news for once. ArXiV will no longer tolerate hallucinated content in submitted works, with real, enforceable consequences.

Finally, some good news for once. ArXiV will no longer tolerate hallucinated content in submitted works, with real, enforceable consequences.

Mark Riedl@markriedl.bsky.social · 3mo ago

ArXiV has a new LLM policy (Screenshots with alt text so you don’t have to click through to the other place and see all the stupid responses)

@katholt.bsky.social gives the keynote @target-amr.bsky.social speech on interpretive standards for AMR genotypes #TARGetAMR26

To anyone who works in the biomedical research space, and knows the ethical & regulatory hoops that REAL healthcare guidance & decision-support tools have to (rightly!) go through before being unleashed, this is just so bizarre. It can NOT be a fix-by-lawsuit situation, it MUST be regulated.

Maggie Harrison Dupré@mharrisondupre.bsky.social · 3mo ago

OpenAI is being sued by the family of a 19-yo student who overdosed after ChatGPT wrongly advised him to consume a deadly mix of substances. The lawsuit seeks to halt access to "ChatGPT Health," a health "support" product that outside experts have found grave flaws in: futurism.com/artificial-i...

Wake up! The House of Commons Education Committee says fifty - yes fifty - Higher Education Institutions are at risk of insolvency within the next three years. Wake up! committees.parliament.uk/work/9012/hi...

“A very serious problem”: No clear government plan for universities risking insolvency, MPs find in new report - Committees - UK Parliament

Today MPs on the Education Committee warn that the government has no clear plan for universities facing insolvency and that protections for students are inadequate, as the Committee publishes a new re...

committees.parliament.uk

Since launching support for the Andes virus species of hantavirus two days ago, we have already received submissions from four countries' sequencing teams. This is a testament to the rapid response of researchers, sharing real-time data. Read more in our news post: pathoplexus.org/news/2026-05...

Pathoplexus | Andes virus: supporting response to the current hantavirus outbreak

Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

pathoplexus.org

How much do you want to bet that the second Meta agrees to pay Elsevier, all the complaints about integrity and intellectual property will vanish? Bet number 2: of all the money Meta will pay Elsevier, exactly 0% will go to the authors of the papers.

the severe misread of youth by ai prophets is that at 22 you’re starving for agency. all your life you’ve waited to call your own shots. the idea that what you get instead is “tell the machine to draw a horse” is inherently offensive

Prof Gavin Yamey MD MPH@gavinyamey.bsky.social · 3mo ago

Yup. It's so tiring hearing that we (as teachers) MUST "prepare our students for an AI future" & "get on the AI train or else be left behind," & I'm aware that some professors are using AI for grading or creating AI lectures using avatars of themselves, but I think if "AI is the future" we're fucked

1/ 🚀 Pathoplexus now supports the Andes variant of Hantavirus (ANDV). ANDV is the variant identified in the recent MV Hondius cases, & the Hantavirus variant previously identified as having occasional human-to-human transmission. pathoplexus.org/andv #hantavirus #hondius

If your brain is struggling due to anxiety,sadness,the way others have behaved,ADHD, autism,burnout,chronic illness &/or because the world’s too full of grimness then hi,me too. Research shows my photo’ll provide relief for your thoughts-pause & zoom into the details-& keep going, you’re not alone 🌿

This is such a stupidly good experiment. I've generally seen analysis of a limited dataset to be one of the strongest non-coding use cases for LLMs — and I think that is probably still true — but this makes it clear that how much you can expect from that analysis is potentially very limited.

Adam Kucharski@adamjkucharski.bsky.social · 3mo ago

"Based on the dataset you shared, US and UK responses differ mainly in tone, intensity, and wording style, even though they express similar emotional states" New post on what happened when I got Copilot to do some data analysis: kucharski.substack.com/p/real-signa...

If you can’t write a grant proposal without AI, why should you be awarded a grant? Why should anyone believe you are capable to execute the work, if you can’t even write the proposal yourself? Should funders just skip a step and run their own AI research agents? (you know it’s coming)

I've spent yesterday and today talking to researchers across the globe trying to understand the hantavirus outbreak aboard the cruise ship MV Hondius. My story in @science.org is here (and some threaded thoughts coming): www.science.org/content/arti... 🧪 #IDsky

Cruise ship’s hantavirus outbreak puts researchers in uncharted territory

Questions about the culprit virus and its route of spread remain as health officials make plans for stranded passengers

science.org

You can make a long, LONG list of technologies that were supposed to make stupid brick and mortar institutions of higher education obsolete. Printed books. Radio. Television. Personal computers. CD-ROMs. The Internet. MOOCs. Write the story once, and you can re-use it every five years!

😱 Take-home message: hospital sinks are perfectly safe if you don’t run the taps! #IDSky

Alan McNally@alanmcn1.bsky.social · 3mo ago

Latest paper out today with the IPC team in Birmingham. Where we show the 2m splash zone of a hospital sink is awash with Gram negs, including a Citrobacter containing our Birmingham KPC-2 plasmid pQEB1 www.sciencedirect.com/science/arti...

An interesting essay by educationalist Will Ellis - raising serious concerns about AI, with studies showing that cognitive engagement shrinks in direct proportion to the degree of AI assistance - with adolescent brains particularly vulnerable: reclaimchildhoodmedia.substack.com/p/the-cost-o...

The Cost of No Friction

Adolescence happens once.

reclaimchildhoodmedia.substack.com

For no particular reason this week… If you want to know how close we came to having the human genome sequence behind a paywall, & the very concept of using gene sequences to benefit health (e.g. as diagnostic or drug targets) locked up behind patents, read this: www.worldofbooks.com/en-gb/produc...

The Common Thread

John Sulston was director of the Sanger Centre in Cambridge from 1993 to 2000. There he led the British arm of the international team selected to map the entire human DNA sequence, a feat that was pul...

worldofbooks.com

Nice summary of MTB surveillance in the United States and detection/response to large outbreaks. The US sees almost 10k domestic cases each year, and a number of large outbreaks or clusters. AMD Platform is the bioinformatic engine that drives this genomic surveillance. www.cdc.gov/mmwr/volumes...

Large Tuberculosis Outbreaks — United States, 2017–2023

This report describes 50 large tuberculosis outbreaks in 23 states during 2017–2023.

cdc.gov