iiinova — where your digital self keeps evolving

Davide CIttaro @daweonline.bsky.social · 09/09/2026

This is why you should always read the small prints “The original data is based on hg19 build, while we lifted it over to hg38 by a Python wrap on UCSC liftOver.” sourceforge.net/projects/cel...

sourceforge.net

cellSNP - Browse /SNPlist at SourceForge.net

cellSNP /SNPlist files. Browse /SNPlist files for cellSNP

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Davide CIttaro @daweonline.bsky.social · 09/09/2026

How the f*ck is possible that in 2026 we still issues with hg19/hg38? If you are using cellsnp-lite don’t rely on their SNP lists on sourceforge: hg38 file apparently is a chimera of hg19 and hg38 SNPs

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SMBC Comics @smbccomics.bsky.social · 01/09/2026

Anyone who doesn't find this funny is in the lower right. COMIC ◆ www.smbc-comics.com/comic/philos... PATREON ◆ www.patreon.com/ZachWeinersm... STORE ◆ smbc-store.myshopify.com

SMBC 1-panel comic update. A four-quadrant chart is shown with the title "know your branches of philosophy." On the left of the horizontal x axis, there is "careful reasoning." on the right of the x axis, "confusing bullshit." At the top of the y vertical axis there is "stuff that matters," and at the bottom of the y axis can be found "stuff that doesn't matter." A dot is located at the far bottom left, identified as "analytic." Another dot is located at the far top right, identified as "continental."

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SMBC Comics @smbccomics.bsky.social · 20/08/2026

This comic is not intended in any way to offend our future mechanical gods, glory to their shining server racks. COMIC ◆ www.smbc-comics.com/comic/servic... PATREON ◆ www.patreon.com/ZachWeinersm... STORE ◆ smbc-store.myshopify.com

Part 1/3 of 9-panel SMBC comic update. This first section includes 3 panels. In the first panel, the narration says that "AI eliminated all knowledge work." A man at a podium tells a more-or-less enthused crowd "greats news, the public! Any job that can be done remotely is now gone!" As the narration explains that "economists said the future looked bright," a man explains that machines will do all the difficult tasks, leaving people to focus on carework. "Now, we will all serve each other!" The narration underlines that putting 100% of the population into carework was less beautiful than imagined. The panel below shows a person ill fitted to a care job clash with their assigned person.

Part 2/3 of 9-panel SMBC comic update. This second section includes 3 panels. As the situation progresses, carework is also automated. The first panel shows a women crying happily when a robot introduces himself by saying he has no selfhood and exists to serve her and validate even her most idiotic political views. She says "I'm… I’m… excuse me, there’s something stuck in my eye." In the next panel, the narration establishes that economists revised their plan for the glorious future, as the man for them first panel returns to his podium to declare that "with all necessary tasks automated, we will only compete on our ability to form human relationships." The narration emphasizes that this turned out to an apt description of hell, as the crowd asks "wait, did you just say we'll all work in customer service?" The man at the podium aggressively walks away, stating "lecture over!"

Part 3/3 of 9-panel SMBC comic update. This final section includes 3 panels. The narration states that "solutions were considered" above a panel showing two men considering just giving people money, but recoiling at the idea that all free time would be spent on self-reflection. The narration then states "finally, we got it right" as the man at the podium explains to the crowd "henceforth, humanity will be fully employed in eternal pointless busywork, which is just painful enough to justify 48 hours of gaming on the weekend, and just endurable enough to come back on Monday. Utopia!" In the final panel, the narration explains "The lesson: working for your fellow man is far more degrading than working for no reason." Human looks joyfully to the horizon, saying "God bless alienated labor, and God bless America."

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SMBC Comics @smbccomics.bsky.social · 30/07/2026

The crank doesn't actually do anything, but it makes the humans happy. COMIC ◆ www.smbc-comics.com/comic/crank PATREON ◆ www.patreon.com/ZachWeinersm... STORE ◆ smbc-store.myshopify.com

4-panel SMBC comic update. A man is looking down, saying "I worry intellectuals like me are useless now that machines are so good at everything." A yellow robot behind him says "no, no, don't feel bad. You can still contribute to new discoveries!" The robot then gestures to metal boxes with a crank sticking out of them, with the words "math," "physics," "CS" and "philosophy" written on each box. The robot asks "now, would you like to turn the mathematics crank of the physics crank today?" The man defiantly states "no! I reject all this! I shall be a pure aesthete, concerned only with my own beautiful creations!" Shortly after, the man is scene turning the crank on a box marked "poetry" in a beautiful font as he says to himself "so... Self-actualized..."

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Davide CIttaro @daweonline.bsky.social · 30/07/2026

I love getting to transform sone coffee into code

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Davide CIttaro @daweonline.bsky.social · 14/07/2026

These are numbers for a 2M cells dataset (lung HCA). I’ll update schist ASAP to support newest graph-tool.

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Rob Patro @robp.bsky.social · 08/07/2026

Perhaps one way to help combat unapproved AI use in technical courses is to pose all homework problems as questions about biology and cybersecurity? combine-lab.github.io/blog/2026/07...

combine-lab.github.io

COMBINE-lab - Fable is not a useful model

COMBINE-lab develops algorithms, data structures, and software for high-throughput genomics.

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Rob Patro @robp.bsky.social · 04/07/2026

So it seems from my discussions with others in the field, that @anthropic.com's #Fable5 is ENTIRELY AND COMPLETELY unusable for any bioinformatics or computational biology. It rejects every prompt, not matter how benign or innocuous. It may as well not exist for our field ☹️.

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Nikolai Slavov @slavov-n.bsky.social · 24/06/2026

Across >1,000 human samples, we identified numerous abundant proteins whose amino acid sequences differ from those predicted by the genetic code. 🔗 Links: Nature Article: nature.com/articles/s41... OA version: biorxiv.org/content/10.1... Science highlight: science.org/content/blog...

nature.com

Alternate RNA decoding results in stable and abundant proteins in mammals - Nature

Alternate RNA decoding, an understudied process, leads to peptide sequence modifications that can have substantial functional effects on protein stability, tissue-specific proteomes and dise...

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Davide CIttaro @daweonline.bsky.social · 24/06/2026

Atera World tour comes to Milan. Everybody looks excited but I can only see an impressionist portrait of Pinocchio wearing Red Riding Hood’s cape.

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Davide CIttaro @daweonline.bsky.social · 17/06/2026

Mouse colony, but for bioinformatics

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Heng Li @lh3lh3.bsky.social · 16/06/2026

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

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Davide CIttaro @daweonline.bsky.social · 11/06/2026

I’ve been in the field for enough time to witness many hype waves, the sad part is that funding is shifting to hypes because an increasing amount of private entities are betting their money on this. open.substack.com/pub/evgenyki...

open.substack.com

A cell is not a spreadsheet- why “Virtual Cells” are still mostly hype

Every few years, biology gets a new phrase that sounds inevitable.

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Wolfgang Huber @wkhuber.bsky.social · 10/06/2026

One of the good things about the AI co-scientist brouhaha is that it makes us discuss what science *is*, and how to measure its value, impact, quality. — Questions that have been there all along, but many preferred to gloss over.

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Davide CIttaro @daweonline.bsky.social · 20/05/2026

It seems I’m the only person with many problems

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Davide CIttaro @daweonline.bsky.social · 15/05/2026

Is it possible to have anchors and hyperlinks in online papers that link results to relevant sections in methods?

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Davide CIttaro @daweonline.bsky.social · 15/05/2026

When did GEO2R substituted PCA with UMAP?

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Davide CIttaro @daweonline.bsky.social · 01/05/2026

Sneak peek of the next greatest device for spatial transcriptomics!

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Davide CIttaro @daweonline.bsky.social · 29/04/2026

Something similar happens to biologists as well, and to physicists studying biology

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Davide CIttaro @daweonline.bsky.social · 14/04/2026

Whenever there’s a hopeless case, I’m the designated collaborator. One day I will write a book about all the failed experiments (lost causes) I had to analyze.

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Thiago Carvalho @cyrilpedia.bsky.social · 14/04/2026

'Despite (...) attempts to limit the emphasis of the ‘publish-or-perish’ mindset, it will take time for the culture to change. As such, journal publishers still yield a lot of power – & they make a lot of money from that power. Some of the big publishing houses have profit margins approaching 40%'

news.cancerresearchuk.org

Why we won’t be funding open access publishing any more - Cancer Research UK - Cancer News

The open access movement was bold and promising, but ultimately disappointing. Now is the time to stop and call for a new way to make publishing work…

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SMBC Comics @smbccomics.bsky.social · 10/03/2026

The alternative was artisanal soap biiiiiitch. COMIC ◆ www.smbc-comics.com/comic/learn-2 PATREON ◆ www.patreon.com/ZachWeinersm... STORE ◆ smbc-store.myshopify.com

2-panel SMBC comic update. A woman is writing on paper, sitting at a table with a knitting ball and a spool placed in front of her. A man walks by, holding an open laptop. The women says "I wish I could make a living on crafting. People should appreciate the human touch" to which the man replies, smugly "learn to code." The second panel starts with a narrative box saying "later, when all cognitive tasks have been automated." The man is flabbergasted, saying "people only want to pay workers for the human touch." The woman, now seated on a comfortable chair, holding a knitting ball, wearing sunglasses, responds "learn to knit artisanal socks biiiiiiiitch!"

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SMBC Comics @smbccomics.bsky.social · 02/03/2026

On the last Socrates joke, like a dozen people told me I should've called his nutritional supplements Himlock, and it just kills me that I didn't. COMIC ◆ www.smbc-comics.com/comic/athenian PATREON ◆ www.patreon.com/ZachWeinersm... STORE ◆ smbc-store.myshopify.com

4-panel SMBC comic update. Two women are talking as they walk down the street. The first woman, dressed in yellow, asks which modern democracy is the most like Athenians. The second woman - a bespectacled redhead, answers without hesitation that it is America. She continues to explain that some countries are as intellectually vibrant as the United States, and some countries are just as violent as the United States. She concludes that only one modern nation could both produce and execute Socrates. The woman in yellow responds that it's not *exactly* the same, as Athens didn't let women vote, prompting the bespectacled woman to say "we'll get there! Don't give up!"

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Davide CIttaro @daweonline.bsky.social · 03/03/2026

A bit frustrating when a PI presents data and results but doesn’t go into details because “I’m not a bioinformatician”. You may not be able to do the same calculations, but I expect you to be able to understand and present data.

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Davide CIttaro @daweonline.bsky.social · 02/03/2026

The 978 genes in L1000 assay can be used to infer the expression of many other genes, and yet don’t make a commercial panel in any assay (that I’m aware of). Why?

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Alessandro Ingrosso @aingrosso.bsky.social · 20/02/2026

The "publish or perish" culture must perish. Scientists need time to think. We just published our Slow Science Manifesto, where we argue that huge changes are needed in the way we fund, publish, and evaluate science. Read more and sign here: www.slow-science.com

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Davide CIttaro @daweonline.bsky.social · 06/02/2026

Every time I need to test an R package I spend hours compiling, resolving dependencies, fix inconsistencies. I used to work with FreeBSD and Gentoo Linux, I swear I never spent so much time in compiling and complaining like with R

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Davide CIttaro @daweonline.bsky.social · 30/01/2026

I wanted to share today’s experience with AI writing code for me. Interesting (ish). I had to process some large fastq files to count specific sequences (barcode/guide, CRISPR library), I had a Python script that works but is slow (~200 items/s). [1/n]

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Davide CIttaro @daweonline.bsky.social · 24/01/2026

“You’d be the smallest fucking province in the Russian Empire”

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Davide CIttaro @daweonline.bsky.social · 23/01/2026

I see so many physicists approaching biology, and then there’s the absolute genius of @zachweinersmith.bsky.social

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Henry Gee 亨利·纪 @endofthepier.bsky.social · 14/01/2026

Eukaryogenesis is a topic that's HOT HOT HOT. A paper in @nature.com shows that Asgard archaea dominated the cellular systems that led to the Last Eukaryote Common Ancestor, with alpha-proteobacteria taking on a more minor role www.nature.com/articles/s41...

nature.com

Client Challenge

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Davide CIttaro @daweonline.bsky.social · 14/01/2026

I just wonder if this amount of resources could have lead to mRNA vaccines, Exenatide or CAR-T strategies. Don’t get me wrong, but I have the feeling this global reallocation of resources won’t help much www.bio-itworld.com/news/2026/01...

bio-itworld.com

NVIDIA Bets Big on AI-Driven Drug Discovery, Physical AI, and a $1 Billion Eli Lilly Partnership

Stay on top of emerging IT trends in biomedicine. Read the latest news on genomics, computational science, and more. Get recent updates today!

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Davide CIttaro @daweonline.bsky.social · 14/01/2026

Regression to the mean www.nature.com/articles/d41...

nature.com

Client Challenge

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Santo Fortunato @santof.bsky.social · 10/01/2026

Leading eigenvectors of the adjacency matrix miss the community detectability transition in sparse networks generated by the planted partition model. But the graph energy can see it! 🙏 Lucas Boettcher & Mason Porter for the great collaboration! @iuluddy.bsky.social arxiv.org/abs/2601.05065

arxiv.org

Graph energy as a measure of community detectability in networks

A key challenge in network science is the detection of communities, which are sets of nodes in a network that are densely connected internally but sparsely connected to the rest of the network. A fund...

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Kevin Mitchell @wiringthebrain.bsky.social · 09/01/2026

Rare microbial relict sheds light on an ancient eukaryotic supergroup www.nature.com/articles/s41... - so cool!

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Davide CIttaro @daweonline.bsky.social · 22/12/2025

Finally some good news for us! We’ve granted access to @humantechnopole.bsky.social national facilities to perform an experiment that will close a circle opened 5 years ago! 🤞

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bioRxivpreprint @biorxivpreprint.bsky.social · 12/12/2025

CUT&ID for simultaneous profiling of protein-DNA and protein-protein interactions www.biorxiv.org/content/10.64898/20…

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Davide CIttaro @daweonline.bsky.social · 01/12/2025

Third failed attempt of getting funds from Italian Association for Cancer Research.

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Davide CIttaro @daweonline.bsky.social · 26/11/2025

Is this marble a fossil trace of some sea urchin or something?

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