Marco Grillo

We've just been awarded a grant to study the cellular basis of regeneration – to track the progenitors of sensory organs in the context of leg regeneration, in our favourite crustacean tinyurl.com/parhyale, based on live imaging and cell tracking. The project involves some cool collaborations... 1/3

Our latest work is now live on bioRxiv! We use copy number variation inference to uncover tumor clonality from imaging-based spatial transcriptomics data. Check it out: doi.org/10.1101/2025...

The cellular substrate of evolutionary novelty Joseph Parker and Matt Pennell propose gene expression programs — sets of co-expressed transcripts that collectively encode cellular subfunctions — as fundamental entities from which novel organismal ...

Useful perspective incorporating GRNs & gene modules into theory of evolutionary novelty

Parker & Pennell emphasise gene modules, not individual genes, as fundamental units of phenotypic evolution

Provides a needed evolutionary lens for analysing scRNAseq & cell types

www.cell.com/current-biol...

We're looking forward to another great day full of practicals and learning here at #EMBOSpatialOmics. We're having a great time so far, how about you? 😎

Let's see what you've been up to @maxjtelford.bsky.social ;)

Our colleague Prof. Benny (Ben Zion) Shilo passed away this morning @WeizmannScience . Benny worked at the forefront of world science in the study of molecular and developmental genetics. Among other things, he won the A.M.T. Prize in the field of genetics in 2013. He was also a great explainer of science, a kind teacher - and an artist photographer with a sharp eye and a sensitive soul. Benny, we will miss you very much. May his memory be blessed.

Our field has lost an amazing scientist, mentor, and old friend. Benny, along with Mike Hoffman, had a brilliant idea in the early 1980s. The first oncogenes were being cloned and they realized if we wanted to understand their roles in cancer, we needed to understand their normal function 1/n 🧪

Intelligence Evolved at Least Twice in Vertebrate Animals | Quanta Magazine Complex neural circuits likely arose independently in birds and mammals, suggesting that vertebrates evolved intelligence multiple times.

www.quantamagazine.org/intelligence...

Ok. This is the coolest i've read in a while

A study from @sergiomarcosalas.bsky.social @nilssonlab.org and colleagues presents a comprehensive evaluation of Xenium in situ datasets and provides recommendations on analysis workflows. @scilifelab.se

www.nature.com/articles/s41...

We offer three new positions to join BCA Phase 0:
1. A full-stack developer to work on the BCA database with @ebi.embl.org
2. A senior research technician to develop sc methods
3. A bioinformatician to analyze new atlases with @sangerinstitute.bsky.social

Details below.

Please, share and repost.

RNA xkcd.com/3056

Evolutionary convergence of sensory circuits in the pallium of amniotes The amniote pallium contains sensory circuits that are structurally and functionally equivalent, yet their evolutionary relationship remains unresolved. We used birthdating analysis, single-cell RNA a...

New paper alert! Led by the great Fernando Garcia Moreno, our lab's first venture into evolutionary developmental biology is out on @science.org
www.science.org/doi/10.1126/...

This paper here is the product of one of my funniest collaboration ever. Developmental biology, evolution, tech development, memes, gifs, improvised brainstorming sessions via WhatsApp, and so much more... Crazy things can happen when people with different skill sets have fun together!

Schematic overview on how MicroSpit operates. It can split superimposed structures in fluorescent image channels by using a suitably trained AI.

Concrete example for how MicroSplit unmixes four superimposed structures.

Immagine you could image two cellular structures in the same fluorescent channel and still reliably get them separated afterwards…
What would you do with this?

Now… what would you do if that also worked with 4 structures at once? 👇 #MicroSplit #preview🧵

Spatial omics meets theory.

cartoon of a fruit fly with a barcode overlaid on its abdomen

A genetic barcoding system lets scientists tag and track cells, making it easier than ever to map gene expression (#transcriptomics) and decode behaviour.
https://elifesciences.org/reviewed-preprints/88334?utm_source=bluesky&utm_medium=social&utm_campaign=organic

scRNA-seq data sets exploding in number and size - check out scanpy & anndata for >1b cells: new experimental update includes APIs for scaling with dask from anndata, integrated with lots of scanpy and rapids-singlecell functions.
gist.github.com/ilan-gold/98...

I made a #BioImageAnalysis #GPT 🎉

Compared to #chatGPT it provides more concise hints for processing fluorescence microscopy images using Python libraries my collaborators and yours truly maintain. Thanks to all contributors and as usual: Feedback is 💚ly welcome! 🤗

chat.openai.com/g/g-psAohb1O...