Marco Grillo

In animals with large genomes, finding cis-regulatory elements can be very challenging. Enhancers can be located tens/hundreds of kb away from their target promoters. We face this challenge in Parhyale, with >3 Gbp genome.
We just published a preprint describing how we are tackling this problem. /1

I am very happy (and a bit scared) to present to you what we have been working on over the last 4 years. This manuscript is exactly what I dreamt of when I started the lab and I could not be happier and prouder of the outcome!

Mastodon: the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets https://www.biorxiv.org/content/10.64898/2025.12.10.693416v1

A cloning strategy as depicted in the OpenCloning website

#OpenCloning is a an Open Source alternative to SnapGene/Benchling that supports automation and integration with other software

✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨‍🔬 Built by a researcher — for researchers!

👉 Check it out at opencloning.org

Hierarchical lineage architecture of human and avian spinal cord revealed by single-cell genomic barcoding The formation of neural circuits depends on the precise spatial and temporal organisation of neuronal populations during development. In the vertebrate spinal cord, progenitors are patterned into mole...

Thrilled to share my main postdoc work with @jamesbriscoe.bsky.social

We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇

www.biorxiv.org/content/10.1...

FlyBase secures funding for year, but future still uncertain The FlyBase team’s fundraising efforts have proven successful in the short term, but restoration of its federal grant remains uncertain.

There is still “an urgent need for donations from the community,” says Eric Lai, president of the Fly Board.

By @callimcflurry.bsky.social

#neuroskyence

www.thetransmitter.org/community/fl...

Reaffirming the value of model organisms in training scientific minds - Nature Cell Biology As biomedical research prioritizes human models and translational promise, classic model organisms are increasingly dismissed. Here we argue that they have a lasting value, both in enabling discovery and in cultivating scientific thinking, by training researchers in systems reasoning, integrative thinking and independent inquiry.

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

Here it is! Postdoctoral position to identify the progenitors sensory organs in the regenerating legs of Parhyale

apply here: www.averof-lab.org/pages/tracman

1/3

🔬🧬🔍 If you're interested in spatial omics and miRNAs, don’t miss our latest review!

We explore where the early field of spatial miRNomics stands, what’s missing, and why incorporating miRNAs matters for building richer spatial transcriptomic maps.

#SpatialOmics #miRNA #GeneRegulation

Doktorand i biokemi Institutionen för biokemi och biofysik. SciLifeLab ( SciLifeLab ) är ett nationellt center för molekylära biovetenskaper med fokus på forskning inom hälsa och miljö. Centret kombinerar ledande

We're looking for a PhD student!
Join the team to develop new technologies for targeted spatial omics.
More info and instruction on how to apply at the following link:
su.varbi.com/what:job/job...

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...