OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis. #StructuralVariants #SVs #SVcomparison #SVidentification #Bioinformatics 🧪🧬 🖥️ academic.oup.com/bioinformati...

Spider: a flexible and unified framework for simulating spatial transcriptomics data. #SpatialTranscriptomics #DataSimulation #Genomics #Bioinformatics 🧬 🖥️ academic.oup.com/bioinformati...

Important insights into FCoV-23 cell entry from the @veeslerlab.bsky.social Freely available: www.nature.com/articles/s41...

Grok 4 appears to consult Elon Musk's X posts and news about him when addressing controversial subjects like immigration or the Israel-Palestine conflict. This design choice, aiming to align with Musk's views, raises questions about Grok's stated goal of being a "maximally truth-seeking AI." #MLSky

I've once again failed to tag appropriately for the various sciency bluesky feeds. 🧪🧬🖥️ #ViroSky #VirEvol

A lab is not required to generate chimeric coronaviruses, with a spike of a different virus: they can emerge naturally ▫️1/2 (from newly published paper by Attipa & @amandatron89.bsky.social et al.; preprinted in 2023) www.nature.com/articles/s41...

A hybrid coronavirus, formed of cat and dog coronaviruses, caused a severe outbreak of disease among cats in Cyprus, researchers found. Their work, in Nature, showed how this new virus was able to cause widespread cases of Feline Infectious Peritonitis (FIP) among the island’s cats.

For more on the domain 0 deletion in the spike gene, see another paper, also out today in Nature, looking at how the deletion enhances fusogenicity and entry kinetics. www.nature.com/articles/s41...

As a side note, Nature including "Thank you for choosing to publish your work with us." In an acceptance email is wild. I'm not convinced we were the ones doing the choosing, but you're welcome?

I am paw-sitively thrilled to say that out latest work is out in Nature today! #Virology #Genomics #Coronavirus #AnimalHealth #InfectiousDisease #Sequencing #FIP #FCoV23 www.nature.com/articles/s41...

Me waiting for my extension request to be granted

Wow! Scientists engineered E. coli to convert plastic waste (PET) into pain medicine paracetamol (acetaminophen or Tylenol) in under 24 hours with up to 92% yield. www.nature.com/articles/d41... #medsky #pharmsky 🧪

🚨 Join us for the Environmental Metagenomics course (Oct 13–17, online) with @oskolkov.bsky.social & @aroneys.bsky.social ! 🔬 Hands-on training on read-based & assembly-based methods, MAGs, and integrating short & long-read @nanoporetech.com data. shorturl.at/HOm6X

Chatbots — LLMs — do not know facts and are not designed to be able to accurately answer factual questions. They are designed to find and mimic patterns of words, probabilistically. When they’re “right” it’s because correct things are often written down, so those patterns are frequent. That’s all.

Hope this is useful - consensus statement "Guidelines for preventing and reporting contamination in low-biomass microbiome studies" rdcu.be/er3Io

Do you like sex? How about viral pathogenesis? If you’re like me & the answer is both, we have got the preprint for you! Led by Marin Habbick in collaboration with our brilliant colleagues at RML, we showed that when it comes to MERS-CoV, it sucks to be male! www.biorxiv.org/content/10.1...

Amazing: MIT researchers revealed how ChatGPT etc are destroying our brains and booby-trapped the report to expose those who want to use AI to ostensibly summarize the results. t.co/JXeTALBPds

🚨 Tularemia mystery solved in stranded belugas in Alaska! thanks to smart-9N metagenomics & nanopore sequencing 🔬🐋 #wildhealth #onehealth Well done @bortz-virology.bsky.social and Team!! wwwnc.cdc.gov/eid/article/...

Ever had to pause genomic surveillance due to enzyme shortages?🫣 Happy to share our new preprint with the solution inside 🦹‍♀️💪 biorxiv.org/content/10.110… @scalene.bsky.social @chris.primalscheme.com @pathogenomenick.bsky.social @articnetwork.bsky.social @nanoporetech.com

MAN this paper is long. I'd better ask ChatGPT to summarise it.

New research from MIT found that those who used ChatGPT can’t remember any of the content of their essays. Key takeaway: the product doesn’t suffer, but the process does. And when it comes to essays, the process *is* how they learn. arxiv.org/pdf/2506.088...

Congrats to @dantipov.bsky.social et al. on the publication of Verkko2! The team put a ton of work into this making it the first assembler that deals with the complexity of human acrocentric chromosomes. Lots of interesting discoveries to come! genome.cshlp.org/content/earl...

Fun story: This wasn't really burnout. It was a several year long B12 deficiency. To anyone who spoke to me over the last couple of years, I might have seemed unusually tired and unenthusiastic. A lot of injections later, I'm more fun to be around now (I think...). I don't recommend this either.

This is the last thing the BBC needs

This regime is using "generative AI" to write its policy papers, and they are are not checking the outputs, and the results are literally exactly what we warned you they would be. I mean we literally warned you about exactly this. JFC.

RFK Jr's "MAHA" report is filled with references to studies that literally do not exist, or that completely misinterpret the studies' findings. “We did not publish a paper.. on this topic with that co-author group, or with that title,” says one cited researcher. www.notus.org/health-scien...

One problem with the speed of Nanopore improvement is that we have to do significant, time consuming updates to this course every year. Sitting here watching London Calling updates, I'm resigning myself to the idea that this year we might have to just write the whole thing from scratch...

And now #ColossalBioSci admit they did not deëxtinct dire wolves, the whole thing was PR #DisInformation campaign. Extinction is (mostly) forever… www.newscientist.com/article/2481...

I did not have Harvard suing Trump on my bingo card

Absolutely thrilled to announce the launch of ARTIC2 - a £5.5M 5 year project funded by @wellcometrust.bsky.social to build on the ARTIC approach of low-cost, globally accessible genome sequencing for surveillance of outbreaks, epidemics and endemic diseases: www.birmingham.ac.uk/news/2025/am...

Ok Microsoft

Sad to be missing #nanoporeconf this year, but I'll catch up online! Have fun everyone!

Live from London Calling 2025! Speakers, attendees and the Oxford Nanopore crew are starting to fill into Old Billingsgate! Ready for Gordon to kick things off for the 11th time! Make sure you keep your posts coming using: #nanoporeconf

Really pleased that this paper is out - academic.oup.com/neuro-oncolo... thanks to all our collaborators far and wide who have helped and of course @nanoporetech.com

Assembling Genomes with Oxford Nanopore: A Hands-On Guide to Long-Read Sequencing with @amandatron89.bsky.social & Nat Ring Learn to go from raw @nanoporetech.com data to polished, high-quality genome assemblies—no matter your experience level. www.physalia-courses.org/courses-work...

If both of the Microsoft office programs I am using freeze for no reason at 4:30 pm, I can just give up and go home, right?

An astronomy professor colleague of mine once relayed trying to explain to his students why it was important that they actually write their class reports themselves. “The point is not to teach ME about neutron stars,” he said.

Even accepting the premise that AI produces useful writing (which no one should), using AI in education is like using a forklift at the gym. The weights do not actually need to be moved from place to place. That is not the work. The work is what happens within you.

Our new preprint characterizing the red grouse microbiota for the first time using metagenomics: doi.org/10.1101/2025.... The red grouse microbiota is really interesting, as these birds rely on a very high fibre plant species (heather) for the majority of their diet. #microbiota

This banner is showing up on NIH data repositories. If you use data from these archives you may want to consider what you need access to in the near and far term for your research

Our comms team was the best to ever do it! They are also the kind of people who, even while saying goodbyes, kept making me smile. I'm going to miss them terribly. If you're in need of some stellar folks, get in touch

james surowiecki has discovered where the completely fabricated trump tariff rate has come from for each country "...for every country, they just took our trade deficit with that country and divided it by the country's exports to us."

Trump is imposing a 10% tariff on the Heard and McDonald Islands. The Heard and McDonald Islands are uninhabited.

I just said "Thanks" to Gemini and it said "I'm not able to help with that, as I'm only a language model." Yes you are, Gemini, yes you are...

Good morning! You're at risk of redundancy again, btw. Good morning to you too, academia...

Do you (like me) create a bunch of conda environments, then later forget what they're for, when they were last updated, or which tools are in them? If so, you might this little project: github.com/rrwick/conda...

Let's do an exercise to show how this error can cause spurious associations Here is plot of live births and cell phone usage in Sri Lanka from 2001-2009 We will ask, "Is cell phone use associated with live birth percentage in Sri Lanka?" and make the same case/control design mistake made by Geier

David Geier has apparently been commissioned by HHS secretary RFK, Jr. to study potential links between vaccination and autism. He and his father have 2 papers in 2017/2016 claiming to show Hep-B vaccination greatly increases risk of autism/obesity. However, their studies have FATAL FLAW...

I have confirmation from several sources now that all T32s, many F30s and F31s, and most or all Center awards (P30, P50) have been terminated at Columbia. This is quite damaging to research and to individuals. This is pure terrorism and cannot be legal. But litigation will take time...