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Cellular Semantics

@cellularsemantics.bsky.social
25 followers 57 following 1 posts

Cellular Semantics Group, part of Cellular Genomics at The Wellcome Sanger Institute. PI. David Osumi-Sutherland. Products include, the [Cell Ontology](https://github.com/obophenotype/cell-ontology) & cxg-query-enhancer

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Cellular Semantics @cellularsemantics.bsky.social · 26/08/2025
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.
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Hao Yin @haoyin.bsky.social · 18/07/2025
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/...
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Jason Hilton @jasonhilton.bsky.social · 17/04/2025
"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!
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Jason Hilton @jasonhilton.bsky.social · 17/04/2025
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.cziscience.com
Cellxgene Data Portal
Find, download, and visually explore curated and standardized single cell datasets.
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Jason Hilton @jasonhilton.bsky.social · 25/04/2025
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!
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Nick Banovich @nebanovich.bsky.social · 26/03/2025
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...
biorxiv.org
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 ...
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Geremy clair @geremyclair.bsky.social · 06/12/2024
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...
atsjournals.org
Increased Pulmonary GM-CSF Causes Alveolar Macrophage Accumulation. Mechanistic Implications for Desquamative Interstitial Pneumonitis
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ATS Red Journal @ajrcmb.bsky.social · 02/05/2025
Cell Population–resolved Multiomics Atlas of the Developing Lung 🔗 tinyurl.com/bdds9z7s
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Žiga Avsec @avsecz.bsky.social · 25/06/2025
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
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Muzz Haniffa @mhaniffa.bsky.social · 07/07/2025
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...
sanger.wd103.myworkdayjobs.com
Group Leaders- Cellular Genomics
Do you want to help us improve human health and understand life on Earth? Make your mark by shaping the future to enable or deliver life-changing science to solve some of humanity’s greatest challenge...
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