Davide CIttaro
@daweonline.bsky.social
Coordinator of λ-lab @ Center for Omics Sciences, Milan | Assistant professor of bioinformatics @unisr.bsky.social
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]
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]
January 30, 2026 at 4:58 PM
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]
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]
“You’d be the smallest fucking province in the Russian Empire”
Trump in Davos, Switzerland:
"Without us, right now you'd all be speaking German".
German is the main language of Switzerland.
"Without us, right now you'd all be speaking German".
German is the main language of Switzerland.
January 24, 2026 at 3:53 AM
“You’d be the smallest fucking province in the Russian Empire”
I see so many physicists approaching biology, and then there’s the absolute genius of @zachweinersmith.bsky.social
10 points to anyone who tries this argument in real life.
COMIC ◆ www.smbc-comics.com/comic/unifie...
PATREON ◆ www.patreon.com/ZachWeinersm...
STORE ◆ smbc-store.myshopify.com
COMIC ◆ www.smbc-comics.com/comic/unifie...
PATREON ◆ www.patreon.com/ZachWeinersm...
STORE ◆ smbc-store.myshopify.com
January 23, 2026 at 5:03 PM
I see so many physicists approaching biology, and then there’s the absolute genius of @zachweinersmith.bsky.social
How long would you survive with no DNA?
YouTube video by xkcd's What If?
youtu.be
January 20, 2026 at 6:21 PM
Reposted by Davide CIttaro
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...
Client Challenge
www.nature.com
January 14, 2026 at 5:01 PM
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...
Reposted by Davide CIttaro
A transposase-derived gene required for human brain development | Science Advances www.science.org/doi/10.1126/...
A transposase-derived gene required for human brain development
PGBD5 is required for brain development in humans and mice through genetic and nongenetic mechanisms.
www.science.org
January 15, 2026 at 3:00 AM
A transposase-derived gene required for human brain development | Science Advances www.science.org/doi/10.1126/...
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...
www.bio-itworld.com/news/2026/01...
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!
www.bio-itworld.com
January 14, 2026 at 10:48 AM
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...
www.bio-itworld.com/news/2026/01...
Reposted by Davide CIttaro
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/abs/2601.05065
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...
arxiv.org
January 10, 2026 at 11:52 PM
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/abs/2601.05065
Reposted by Davide CIttaro
Rare microbial relict sheds light on an ancient eukaryotic supergroup www.nature.com/articles/s41... - so cool!
January 9, 2026 at 8:28 AM
Rare microbial relict sheds light on an ancient eukaryotic supergroup www.nature.com/articles/s41... - so cool!
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! 🤞
December 22, 2025 at 4:57 PM
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! 🤞
Reposted by Davide CIttaro
CUT&ID for simultaneous profiling of protein-DNA and protein-protein interactions https://www.biorxiv.org/content/10.64898/2025.12.11.693662v1
December 12, 2025 at 11:16 PM
CUT&ID for simultaneous profiling of protein-DNA and protein-protein interactions https://www.biorxiv.org/content/10.64898/2025.12.11.693662v1
Third failed attempt of getting funds from Italian Association for Cancer Research.
December 1, 2025 at 1:19 PM
Third failed attempt of getting funds from Italian Association for Cancer Research.
Is this marble a fossil trace of some sea urchin or something?
November 26, 2025 at 7:39 AM
Is this marble a fossil trace of some sea urchin or something?
Somehow I feel biology went from the age of research to the age of scaling
So, the ”age” of scaling was about 3 years or so?
Ilya!!!!
www.dwarkesh.com/p/ilya-sutsk...
www.dwarkesh.com/p/ilya-sutsk...
November 26, 2025 at 6:49 AM
Somehow I feel biology went from the age of research to the age of scaling
I feel like I’m on sabbatical without being on sabbatical
November 20, 2025 at 7:21 AM
I feel like I’m on sabbatical without being on sabbatical
Can you believe I haven’t read this in 6 years? I made amends, one less on the (still long) reading list
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Gene expression across mammalian organ development - Nature
The transcriptomes of seven major organs across developmental stages from several mammalian species are used for comparative analyses of gene expression and evolution across organ development.
www.nature.com
November 13, 2025 at 6:19 AM
Can you believe I haven’t read this in 6 years? I made amends, one less on the (still long) reading list
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Great job. The most interesting part? The initial design that leverages good quality data (L1000), not single cell data. Also an apparently simpler AI architecture.
🚀 Our new Science paper is out (w/ B DeMeo, D Burkhardt, A Shalek, M Cortes): www.science.org/doi/10.1126/...
We show that active learning + transcriptomic perturbations can guide which exps to run next, boosting phenotypic hit rates >13x. AI not just predicting bio, but designing it. 🔁
We show that active learning + transcriptomic perturbations can guide which exps to run next, boosting phenotypic hit rates >13x. AI not just predicting bio, but designing it. 🔁
October 27, 2025 at 1:41 PM
Great job. The most interesting part? The initial design that leverages good quality data (L1000), not single cell data. Also an apparently simpler AI architecture.
Any sufficiently advanced technology is indistinguishable from magic.
[PHLOWER] leverages the harmonic component of the Hodge decomposition on simplicial complexes to infer trajectory embeddings from single-cell multimodal data.
www.nature.com/articles/s41...
[PHLOWER] leverages the harmonic component of the Hodge decomposition on simplicial complexes to infer trajectory embeddings from single-cell multimodal data.
www.nature.com/articles/s41...
PHLOWER leverages single-cell multimodal data to infer complex, multi-branching cell differentiation trajectories - Nature Methods
PHLOWER leverages single-cell multimodal data to infer complex, multi-branching cell differentiation trajectories.
www.nature.com
October 24, 2025 at 9:39 AM
Any sufficiently advanced technology is indistinguishable from magic.
[PHLOWER] leverages the harmonic component of the Hodge decomposition on simplicial complexes to infer trajectory embeddings from single-cell multimodal data.
www.nature.com/articles/s41...
[PHLOWER] leverages the harmonic component of the Hodge decomposition on simplicial complexes to infer trajectory embeddings from single-cell multimodal data.
www.nature.com/articles/s41...
the three mice di 鼠鼠鼠 su Apple Music
Album · 2024 · 7 brani
music.apple.com
October 21, 2025 at 6:48 AM
How much current foundation models for scRNA are bound to the technology used to produce data (10x or Parse)? How much to the processing pipeline?
October 17, 2025 at 6:44 AM
How much current foundation models for scRNA are bound to the technology used to produce data (10x or Parse)? How much to the processing pipeline?
Dear reviewer 2, could you please try to be more specific on your points? Saying “something is not enough” isn’t actually enough.
Sincerely,
Reviewer 1
Sincerely,
Reviewer 1
October 16, 2025 at 4:22 PM
Dear reviewer 2, could you please try to be more specific on your points? Saying “something is not enough” isn’t actually enough.
Sincerely,
Reviewer 1
Sincerely,
Reviewer 1