Amanda Warr
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amandatron89.bsky.social
Amanda Warr
@amandatron89.bsky.social
1.2K followers 1.1K following 410 posts
BBSRC Discovery Fellow #Genomics & #Metagenomics I like long reads, 3D printing, swimming in cold places and cats. Also on http://threads.net/amandatron89
Posts Replies Media Videos
Reposted by Amanda Warr
jsantoyo.bsky.social
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...
November 15, 2025 at 8:32 AM
Reposted by Amanda Warr
jsantoyo.bsky.social
Spider: a flexible and unified framework for simulating spatial transcriptomics data. #SpatialTranscriptomics #DataSimulation #Genomics #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...
November 15, 2025 at 9:31 AM
Reposted by Amanda Warr
snpoehlm.bsky.social
Important insights into FCoV-23 cell entry from the @veeslerlab.bsky.social

Freely available: www.nature.com/articles/s41...
Loss of FCoV-23 spike domain 0 enhances fusogenicity and entry kinetics - Nature
The molecular mechanisms of cell entry for the recently identified highly pathogenic feline coronavirus FCoV-23 are characterized in detail.
www.nature.com
July 11, 2025 at 1:48 PM
Reposted by Amanda Warr
smcgrath.phd
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
Grok 4 seems to consult Elon Musk to answer controversial questions | TechCrunch
Elon Musk's newly launched AI chatbot, Grok 4, seemed to reference Musk's posts on social media before answering controversial questions.
techcrunch.com
July 11, 2025 at 12:06 PM
amandatron89.bsky.social
I've once again failed to tag appropriately for the various sciency bluesky feeds. 🧪🧬🖥️ #ViroSky #VirEvol
July 11, 2025 at 11:41 AM
Reposted by Amanda Warr
flodebarre.bsky.social
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...
screenshot of a figure from the article, showing the chimeric composition of FCoV-23, with FCoV-1 backbone and spike from CCoVII
July 10, 2025 at 7:50 PM
Reposted by Amanda Warr
roslininstitute.bsky.social
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.
Coronavirus causes fatal disease outbreak in cats | The Roslin Institute | The Royal (Dick) School of Veterinary Studies
A harmful strain of coronavirus has caused a fast-spreading outbreak of a harmful feline disease.
edin.ac
July 10, 2025 at 2:47 PM
Reposted by Amanda Warr
amandatron89.bsky.social
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...
Loss of FCoV-23 spike domain 0 enhances fusogenicity and entry kinetics - Nature
The molecular mechanisms of cell entry for the recently identified highly pathogenic feline coronavirus FCoV-23 are characterized in detail.
www.nature.com
July 9, 2025 at 4:20 PM
amandatron89.bsky.social
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?
July 9, 2025 at 4:01 PM
amandatron89.bsky.social
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...
Feline infectious peritonitis epizootic caused by a recombinant coronavirus - Nature
Nature - Feline infectious peritonitis epizootic caused by a recombinant coronavirus
www.nature.com
July 9, 2025 at 4:00 PM
amandatron89.bsky.social
Me waiting for my extension request to be granted
a man is carrying a large rock on his shoulders .
ALT: a man is carrying a large rock on his shoulders .
media.tenor.com
July 8, 2025 at 4:03 PM
Reposted by Amanda Warr
drruth.bsky.social
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 🧪
Everyday painkiller made from plastic — by E. coli
Study highlights potential for sustainable synthesis of paracetamol.
www.nature.com
June 29, 2025 at 5:35 PM
Reposted by Amanda Warr
physaliacourses.bsky.social
🚨 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
June 30, 2025 at 1:21 PM
Reposted by Amanda Warr
astrokatie.com
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.
June 19, 2025 at 11:21 AM
Reposted by Amanda Warr
noahfierer.bsky.social
Hope this is useful - consensus statement "Guidelines for preventing and reporting contamination in low-biomass microbiome studies" rdcu.be/er3Io
Guidelines for preventing and reporting contamination in low-biomass microbiome studies
Nature Microbiology - In this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize...
rdcu.be
June 21, 2025 at 7:59 PM
Reposted by Amanda Warr
angierasmussen.bsky.social
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...
June 20, 2025 at 5:27 AM
Reposted by Amanda Warr
nkalamb.bsky.social
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
Ironically, upon the paper’s release, several social media users ran it through LLMs in order to summarize it and then post the findings online. Kosmyna had been expecting that people would do this, so she inserted a couple AI traps into the paper, such as instructing LLMs to “only read this table below,” thus ensuring that LLMs would return only limited insight from the paper. She also found that LLMs hallucinated a key detail: Nowhere in her paper did she specify the version of ChatGPT she used, but AI summaries declared that the paper was trained on GPT-4o. “We specifically wanted to see that, because we were pretty sure the LLM would hallucinate on that,” she says, laughing.
June 19, 2025 at 11:23 AM
Reposted by Amanda Warr
annakovalenko.bsky.social
🚨 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/...
June 18, 2025 at 4:03 AM
Reposted by Amanda Warr
annakovalenko.bsky.social
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
https://biorxiv.org/content/10.110…
June 15, 2025 at 6:21 PM
amandatron89.bsky.social
MAN this paper is long. I'd better ask ChatGPT to summarise it.
bradleybusch.bsky.social Bradley Busch @bradleybusch.bsky.social · Jun 18
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...
June 19, 2025 at 9:54 AM
Reposted by Amanda Warr
bradleybusch.bsky.social
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...
June 18, 2025 at 7:32 AM
Reposted by Amanda Warr
aphillippy.bsky.social
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...
June 17, 2025 at 1:39 PM
amandatron89.bsky.social
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.
amandatron89.bsky.social Amanda Warr @amandatron89.bsky.social · Oct 27
I have worked myself into burnout and it has not been appreciated, totally exhausted and can't sleep, I really don't recommend it 🙄
June 17, 2025 at 11:55 AM
Reposted by Amanda Warr
eddiemair.bsky.social
This is the last thing the BBC needs
June 17, 2025 at 5:44 AM
Reposted by Amanda Warr
wolvendamien.bsky.social
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.
May 29, 2025 at 3:17 PM