Is the purpose of science and 🧪 training to churn out papers or to create a healthy knowledge community? In a @nature.com comment, @mjcrockett.bsky.social and I check in on how AI helps with the former while jeopardizing the latter 1/

A gentle reminder that if your customers are scientists, your products and claims will be extensively (and rightfully) scrutinized.

of many projects Craig Venter led, of personal significance was the fly genome, a unique and i think unexpected collaboration of his company Celera Genomics and the BDGP, led by my pd advisor Gerry Rubin. the power of a shotgun sequenced metazoan, benchmarked to a physical map, transformed genomics.

Using light-activated CRISPR in zebrafish, we triggered synchronized DNA breaks and track the repair process. ⚡🐟⚡ 

 Well ... DNA repair is very different in embryos compared to tissue culture cells. Embryos repair DNA breaks incredibly fast - within minutes! www.biorxiv.org/content/10.6...

At @szndohrn.bsky.social, the floor tiles have stitching and segmentation artifacts :) Just finished teaching the marvels of spatial omics to the great group of PhD students of @zoocell.biologists.social.ap.brid.gy, together with @alvarocrevenna.bsky.social. What a week! 🔬🍕🍝🍷🧪

New Pre-Print Alert! Evolving initial conditions: an alternative developmental route to morphological diversity with Shannon Taylor and @jamesehammond.bsky.social www.biorxiv.org/content/10.6...

As mentioned elsewhere, I've been dreaming of solving this problem for a looooooooong time. Nice to see that my dreams were also the dreams of a very talented team! Slightly different approach, same problem, similar logic. Loving this!

Capturing somatic mutations in single-cell probe-based assays (ie. 10X Flex) is a hard task, especially if you don't know *exactly* the mutations you want to capture, or if your target sequence is a mutational hotspot with many possible alternative alleles. Here's the way we pulled this off. Enjoy!

Why so serious? 🃏 Marco Grillo, Anna Nam and yours truly 𝗚𝗼𝗧 𝗮 𝗙𝗶𝗹𝗹𝗶𝗻𝗴 that will make you happy 😃 No more limitations. Maximum flexibility. Something is coming. Stay tuned. #singlecellwithaplus

Let me introduce you to KaroSpace, which is a rapid-access framework for interactive exploration of multi-sample spatial omics data. The preprint can be accessed here: www.biorxiv.org/content/10.6...

Do you work with a strange model species and are frustrated by the lack of antibodies for immunos? Here's a web app that does some computational pre-screening for you. sixpack-abscan.serve.scilifelab.se

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

#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

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...

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...

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

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...

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 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 🧪

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

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!

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.

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...