iiinova — where your digital self keeps evolving

Amanda Warr @amandatron89.bsky.social · 28/09/2026

Just thinking about how totally normal my office is.

Shelf with minion sequencers, nanopore stickers, wooden dinosaur models, a model of a pig riding a Champaign bottle, and a guitar from the Philippines.

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Rob Noble @robjohnnoble.bsky.social · 02/09/2026

Figure 3 makes it plain

Respondents were asked to indicate the degree and direction of the impact of federal and state policies since January 20, 2025 on the categories of "Impact on my field of science", "Impact on my Department and Institution", "Impact on my research", "Impact on my career prospects", and "Impact on my personal life". A percentage of respondents reported positive impacts in each category (~1-2%). 79.7% of respondents said that federal policies since January 20, 2025 had "extremely negative impact" or "irreparable harm" on their field of science (Figure 3, top row), with a total of 96.8% of respondents saying the impacts have been negative. Over half of respondents said the effects on their department/institution were "extremely negative" or "irreparable harm" (54.8%), with a total of 91.9% responding that the impacts have been negative (Figure 3, second row). Most respondents reported "slightly negative" to "extremely negative" effects on their research (78.4%) and career prospects (70.9%), with about 15-22% reporting no impact and 5-6% reporting irreparable harm in both categories (Figure 3, third and forth rows). A majority of respondents reported slightly negative to extremely negative effects on their personal life (82.3%), with 5.3% reporting irreparable harm and 11.1% reporting no impact (Figure 3, fifth row).

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Flo Débarre @flodebarre.eurosky.social · 29/07/2026

New set of documents released by Rand Paul's staff before Fauci's hearing today. They found nothing. Paul and other conspiracy theorists keep talking about a lab leak cover-up, but to have one, you need something to coverup. They have not found any evidence, in spite of all their subpoenas.

paul.senate.gov

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Amanda Warr @amandatron89.bsky.social · 22/07/2026

I love the game of "where did the notification ding come from?" while working with multiple windows and a remote desktop that also has multiple windows.

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Amanda Warr @amandatron89.bsky.social · 20/07/2026

School is bringing in a literal hostage negotiator to teach conflict resolution to the staff and students. Sounds about right.

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David Eccles 🌻🇵🇸7x🩹🛡️ @gringene.org · 14/07/2026

If only Flongle were still a viable option: * Run reagent consumable cost of $78.50 (Flongle flow cell + Rapid Barcoding kit); that's quite a cheap sequencing run. That gives barcodes for up to 24 samples; less than $5 per bacteriophage.

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Albert Vilella, PhD. @albertvilella.bsky.social · 13/07/2026

I am doing more investigating on the uptake of @bsky.app by the #Bioinformatics and #ComputationalBiology community. I found 2114 accounts where the Bio contains the words "Bioinformatics" or "Computational Biology", out of which the large majority are personal but there are some institutional ones.

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 01/07/2026

We’re happy to introduce phageFACTor (Functional Annotation and Curation Tool) 👩‍💻Developed by Tanaïs Moreau, our most recent PhD candidate, and building on Phold, we were able to improve annotation of prophage genes by as much as 50% 🧬 You should check it out github.com/TMs-code/pha...

In this example, we're showing the improvement in the percentage of annotated genes from prophage "Maintenon" from Clostridium innocuum (doi: 10.1186/s40168-023-01541-x) using the phageFACTor pipeline

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 08/06/2026

Is @nanoporetech.com hac v6 better than 5.2.0 sup? The short answer is no. But are a few errors in a genome worth 5 times more basecalling compute? github.com/Kirk3gaard/M...

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Ryan Wick @rrwick.bsky.social · 11/06/2026

New blog post! I analyse the new hac@v6.0.0 basecalling model from @nanoporetech.com and discuss the conspicuous lack of a new sup model: rrwick.github.io/2026/06/11/d...

rrwick.github.io

Dorado v2.0.0: no more sup?

a blog for miscellaneous bioinformatics stuff

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Amanda Warr @amandatron89.bsky.social · 24/06/2026

Anyone have a favourite tool for simulating nanopore reads at current error profile? Still badread?

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David Eccles 🌻🇵🇸7x🩹🛡️ @gringene.org · 15/06/2026

From the presentations I watched, RNA barcoding does seem to be working fine. Yes, ONT's claim is that the new HAC is better than the old SUP, so there's no need to improve further. I don't agree. There is substantial marketing benefit from catering to the people who want higher accuracy.

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Amanda Warr @amandatron89.bsky.social · 15/06/2026

Also keen to hear about any new(ish) host depletion kit options. I have a lot of (unfortunately very frozen) intestinal samples (fortunately with glycerol) that are (unfortunately) bonkers littered with host cells.

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Amanda Warr @amandatron89.bsky.social · 15/06/2026

I'm just back at work after an 11 month absence. What did I miss? Nanopore stuff? Virus stuff? Microbiome stuff? Important new tools? Fill me in.

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Amanda Warr @amandatron89.bsky.social · 08/04/2026

Has anyone ever been awarded the Nobel Peace Prize after threatening genocide? Asking for a not friend.

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Amanda Warr @amandatron89.bsky.social · 18/03/2026

Just over 8 months ago I was on here announcing the publication of my first Nature paper, exactly a week later I found a lump. A lump that alarmingly doubled in 24h. A very stressful few weeks later I was diagnosed with an aggressive lymphoma.

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Dr Emma Hodcroft @firefoxx66.bsky.social · 10/03/2026

1/5 Introducing SimPlot-CL! 🧬 Recombination plays an important role in viral evolution. Similarity plots are a great way to visualize recombination patterns, but generating them across many genomes can be cumbersome (Work with my student, Keno Strotjohann!) 📂 github.com/hodcroftlab/simplot-cl

A figure showing a 'Simplot' which plots the similarity of a genome to other genomes across a graph, with similarity on the Y-axis and the genome position on the x-axis. Many coloured lines show the sequences being compared - those closest to the top (similarity of 1) are the closest matches in different parts of the genome.

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NY Times Pitchbot @nytpitchbot.bsky.social · 14/02/2026

Doctors say that vaccines protect children from dangerous diseases. A nepo baby who barbecues dogs and snorts cocaine off toilet seats says that vaccines make children vulnerable to 5G radiation. For busy parents, it can be hard to know who to trust.

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Julie K. Brown @jkbjournalist.bsky.social · 01/02/2026

Troublemaker is my middle name.

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BK. Titanji @boghuma.bsky.social · 27/01/2026

There is a cost to science denial.

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Adam Kucharski @adamjkucharski.bsky.social · 25/01/2026

Quickly telling someone you’ve liked something they’ve done (e.g. telling a writer you like their writing, or a researcher you like their research, or a teacher you like their teaching) has a phenomenally high effort-to-impact ratio.

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Dimitri Drekonja, MD, MS @dimitridrekonja.bsky.social · 24/01/2026

Alex Pretti was a colleague at the VA. We hired him to recruit for our trial. He became an ICU nurse- I lover working with him. He was a good kind person who lived to help and these fuckers executed him. White. Hot. Rage.

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Amanda Warr @amandatron89.bsky.social · 20/01/2026

"I know we'll come to (Nato's) rescue, but I just really do question whether or not they'll come to ours"- Trump Mate, article 5 has been invoked exactly once and guess who it was in aide of...

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Javier Santoyo @jsantoyo.bsky.social · 15/11/2025

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...

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Javier Santoyo @jsantoyo.bsky.social · 15/11/2025

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

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Scott McGrath @smcgrath.phd · 11/07/2025

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

techcrunch.com

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.

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Amanda Warr @amandatron89.bsky.social · 11/07/2025

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

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Flo Débarre @flodebarre.eurosky.social · 10/07/2025

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

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The Roslin Institute @roslininstitute.bsky.social · 10/07/2025

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.

edin.ac

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.

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Amanda Warr @amandatron89.bsky.social · 09/07/2025

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...

nature.com

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.

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Amanda Warr @amandatron89.bsky.social · 09/07/2025

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?

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Ruth Ann Crystal @drruth.bsky.social · 29/06/2025

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 🧪

nature.com

Everyday painkiller made from plastic — by E. coli

Study highlights potential for sustainable synthesis of paracetamol.

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Physalia-courses@ONLINE @physaliacourses.bsky.social · 30/06/2025

🚨 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

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Katie Mack @astrokatie.com · 19/06/2025

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.

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Angie Rasmussen @angierasmussen.bsky.social · 20/06/2025

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...

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Nathan Kalman-Lamb @nkalamb.bsky.social · 19/06/2025

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.

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Anna (Ganna) Kovalenko @annakovalenko.bsky.social · 18/06/2025

🚨 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/...

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Anna (Ganna) Kovalenko @annakovalenko.bsky.social · 15/06/2025

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

biorxiv.org

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Amanda Warr @amandatron89.bsky.social · 19/06/2025

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

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Bradley Busch @handle.invalid · 18/06/2025

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...

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Adam Phillippy @aphillippy.bsky.social · 17/06/2025

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...

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