Giuseppe D'Agostino

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100 Following
192 Posts
Experimentalist turned computational biologist. Averagely conversant in transcriptomics, development, cell fate engineering, dataviz, philosophy of science, #Rstats. Remembering Gigi Sabani.
GitHubhttps://github.com/gdagstn/
Google Scholarhttps://scholar.google.com/citations?hl=en&user=X4znaGUAAAAJ
Personal websitegiuseppe.cool/personal

You're doubting my humanity, but you're missing some key points. Here are some of the things I've seen:

  • Attack ships firing off the shoulder of Orion. These aren't just battleships — they're spacecraft designed for warfare.
  • C-beams glittering in the dark. Their location? Near the Tannhäuser Gate.
  • Things you wouldn't believe. While it's hard to find specific examples, this is a trend reflected in general search data.

The bottom line: All those moments will be lost — like tears in rain.

I made https://www.reddit.com/r/bioinformaticsdev/
I did this because the r/bioinformatics channel doesn't like talking about tools, especially if you wrote it yourself.

If you build bioinformatic tools or want to learn more about it, join the subreddit and start posting :)

Here's my first Substack post in a series of 6/7 on how linguistics and computational biology intertwine, and how we can use the methods of the latter to understand more about the former.

The first episode sets the scene: how do we compare languages?

https://substack.com/inbox/post/182403869

Subscribe to stay tuned and receive these bits of my brain directly in your inbox, no cleanup needed!

A not so random forest

A short history of how linguistics and computational biology intertwine

I have been playing with new visualizations of single cell data for a while. The atlas/cartographic metaphor is the one I enjoy the most, and I developed an R package (borges) to create them from UMAP/tSNE data directly.

This Christmas I have started exploring LLM-assisted coding to iterate on my vision. For instance, here you can see density-based relief rendered as a shaded Delaunay triangulation of the points, where the elevation/shade is proportional to the underlying density of points!

"A Sharon Begley byline, almost 5 years after her death.

Upon hearing the news James Watson had died, a STAT reporter said in our Slack, "I wish I could read what Sharon would have written."

Incredible news: Sharon in fact did pre-write a Watson obit. And it is masterful and excoriating."

#JamesWatson #Racism #Bigotry #Sexism

https://www.statnews.com/2025/11/07/james-watson-remembrance-from-dna-pioneer-to-pariah/

James Watson, dead at 97, was a scientific legend and a pariah among his peers

James Watson, the co-discoverer of the structure of DNA who died Thursday at 97, was a scientific legend and a pariah among his peers.

STAT

A short #rstats post about generating quarto syntax (e.g., for wrapping several plots in a tabset) within the R code chunk itself. I am entirely unsure if this is useful. Some feedback would be appreciated

https://blog.djnavarro.net/posts/2025-07-05_quarto-syntax-from-r/

Generating quarto syntax within R – Notes from a data witch

To quote Cassian Andor, “It’s harder than it looks”

Notes from a data witch

I've enjoyed using Spotify on a daily basis and paid 12 Great British Pounds monthly for that pleasure.

There were many good reasons not to do that in the first place, mostly related to how they were screwing artists financially.

However, I recently learned that Daniel Ek, their CEO, has invested 600 M euro in a military AI company:

https://djmag.com/news/spotifys-daniel-ek-leads-eu600-million-investment-ai-military-defence-company

This is now - for me - a good reason to quit Spotify, and I urge you to do the same if you dislike this move :)

Spotify's Daniel Ek leads €600 million investment in AI military defence company

Ek told The Financial Times that "AI, mass and autonomy" are "driving the new battlefield"

DJ Mag
Of course Elsevier's "enhanced pdf viewer" tracks where you click, view, if you hide the page, etc. and then transmits a big base64 blob of events along with ID from University proxy when you leave. I'm sure straight to SciVal for sale.
Is this the way we want science to work?
Encho a máquina de lavar roupa. Adiciono o detergente. Escolho o programa. Defino a temperatura e a velocidade de centrifugação (nunca adoto as que estão pré-programadas). Tudo pronto? Sim. Posso carregar no botão de início do programa? Não. Primeiro tenho de ir contar os gatos.
Copilot productivity hack: never ask Copilot to rewrite more than a few lines of code