Very cool work. I curious about how a model like this might leverage knowledge of what processes and components are known to be active/present in specific cell types.

Chris Mungall@cmungall.bsky.social · last yr.

Very exciting to see the research from @cziscience.bsky.social on the rBio distilling a black box foundation model (in this case a "virtual cell" perturbation model) into a smaller reasoner LLM. And it uses ontologies as part of RL! chanzuckerberg.com/blog/rbio-re...

STOmicsDB #SpatialTranscriptomics repository Coding-free visualization & re-analysis of published ST datasets (if you have a specific question) 361 datasets 128 tissues 17 species db.cngb.org/stomics/ @narjournal.bsky.social 2023 academic.oup.com/nar/article/...

"Fortunately, cellxgene classes follow an ontology, a robust structure that defines relationships among the labels." 😍 Very cool to see how they leveraged the ontological relationships to refine many labels!

Jeremie Kalfon 👨‍💻🧬🤖🚀@jkobject.com · last yr.

I am super happy to annonce that after 9 months under review the first paper of my PhD: scPRINT is finally available on Nature Comms! 🎉🧬 www.nature.com/artic...

Big CELLxGENE news! No longer just human & mouse data. Now supported: #celegans #zebrafish #drosophila #rat #pig #rabbit and several non-human primates Please see info on how to contribute data: cellxgene.cziscience.com/docs/032__Co...

Cellxgene Data Portal

Find, download, and visually explore curated and standardized single cell datasets.

cellxgene.cziscience.com

Another fun CELLxGENE update from this week: We now support ATAC-seq fragments files. You can download the fragments file for all unpaired scATAC-seq datasets and many multiome datasets. More ATAC-seq features (and data) are coming. Happy #DNADay!

Excited to share Ruqian has developed a package for this transcript based niche analysis. Check out the preprint and the package! This is a flexible approach and we're working on extending this for other spatial analyses! @davisjmcc.bsky.social www.biorxiv.org/content/10.1...

SpatialRNA: a python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomics dataset

Image-based spatial transcriptomics deliver gene expression measurements of RNA transcripts in tissue slices with single-molecule resolution and spatial context preserved. Modern Graph Neural Network ...

biorxiv.org

Nick Banovich@nebanovich.bsky.social · 2y ago

To go beyond manual annotations, we computationally identified multicellular spatial “niches” both using Seurat v5 and with a custom, transcript-based approach developed by co-first author @Ruqian_lyu using the GraphSAGE framework.

New publication 🫁 📊 🔬 ! We performed proteomics and transcriptomics of lung sorted cells from human (0 to 8 years). We discovered new cell markers and pathway modulated during development. A must-read for #teamMassSpec enthusiasts focused on development www.atsjournals.org/doi/abs/10.1...

Cell Population–resolved Multiomics Atlas of the Developing Lung 🔗 tinyurl.com/bdds9z7s

Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind

Great faculty opportunities within the Cellular Genomics Programme @sangerinstitute.bsky.social Please share with your networks and do contact me if you would like to find out more sanger.wd103.myworkdayjobs.com/en-US/Wellco...