iiinova — where your digital self keeps evolving

Davide CIttaro @daweonline.bsky.social · 09/10/2026

Again, if you want to have fun ask a chatbot to solve a rebus

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Davide CIttaro @daweonline.bsky.social · 02/10/2026

Ross could also be glutamate as well, because of unagi

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Davide CIttaro @daweonline.bsky.social · 02/10/2026

I thought proline was Janice, proline is the most annoying aa. Monica and Chandler are both cysteine, bonding

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

IDK if there’s data in other examples (not really my field), but I guess you can have U, C and D states anyway (I mean, you can see them also in very stupid cases, like when you drive with clutch after years of automatic transmission and the gears ground…)

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

Very interesting reading. Are there (or have been in history) examples of similar behavior applied to adoption of other technologies? I’m thinking, for example, to adoption of smartphones and the ability to memorize stuff

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

WTF?!? You shall not liftover SNPs! It’s in genomics 101!

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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

The VCF released with the tool is “well formed” (ish), I simply suspect a weird liftover from hg19 plus some integration with the dbSNP table from UCSC genome browser.

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

Note that the VCF is referenced by other tools for single cell CNV profiling, such as numbat

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

We’ve just made the horrible discovery and still evaluating the impact on our single cell data, hopefully not a big issue as many SNPs seem to be hg38 ones

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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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Reposted by Davide CIttaro

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 · 27/07/2026

See here bsky.app/profile/dawe...

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Davide CIttaro @daweonline.bsky.social · 27/07/2026

Precisely! I’m sure I have to modify schist to fully support gt-3, once back from holidays…

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

It’s 2282447 nodes and 51427121 edges. Took 7082.49s with simple init and 29069.77s with default init

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Davide CIttaro @daweonline.bsky.social · 13/07/2026

Nested SBM (simple_init) took only 2 hours (32 cores) 😱😱😱😱

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Davide CIttaro @daweonline.bsky.social · 13/07/2026

I’ve managed to run a simple test on a 2M nodes network, PPBlockState for a quick evaluation: 13 h => 15 minutes (16 cores). I’m speechless, congratulations for this milestone! I’m leaving for holidays with other models running, I’ll come back with lots of things to do! 🙏🙏🙏

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Reposted by Davide CIttaro

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

Yep. I see why many are moving to Rust

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

Will you post alerts for each and any manuscript under review/preparation mentioned in this one?

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Reposted by Davide CIttaro

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 · 25/06/2026

Are there people who design their talks to be understood by a minority of the audience on purpose?

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

I didn’t take other pictures but I saw the map of coastal Croatia and a baby dragon sleeping under sheets

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

And it has been falling since 2020 academic-freedom-index.net

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

I understand it is also based on BWT indexing. Is minibwa retrocompatible with genomes indexed for bwa?

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Reposted by Davide CIttaro

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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Reposted by Davide CIttaro

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 · 07/06/2026

Ahahaha! Also any Bioconductor package

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Davide CIttaro @daweonline.bsky.social · 04/06/2026

I love the fact that when everyone moves to virtual cells, there’s still somebody working on better algorithms and tools for sequence analysis

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

I see, so the throughput increases bc of greater area/number of slides, time for imaging hasn’t been improved. Good to know, thank you

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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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