Cellular Semantics
@cellularsemantics.bsky.social
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
PI. David Osumi-Sutherland.
Products include, the [Cell Ontology](https://github.com/obophenotype/cell-ontology) & cxg-query-enhancer
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.
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...
rBio: Reasoning Model Trained on Virtual Cell Simulations
Scientists can ask complex biological questions in plain language and get predictions about gene interactions.
chanzuckerberg.com
August 26, 2025 at 9:59 AM
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.
Reposted by Cellular Semantics
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/...
#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/...
July 18, 2025 at 12:23 PM
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/...
#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/...
Reposted by Cellular Semantics
"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!
Very cool to see how they leveraged the ontological relationships to refine many labels!
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...
www.nature.com/artic...
scPRINT: pre-training on 50 million cells allows robust gene network predictions
Nature Communications - Authors present a state-of-the-art cell foundation model trained on 50 million cells. They show that the model generates a meaningful gene network and has zero-shot...
www.nature.com
April 17, 2025 at 3:55 PM
"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!
Very cool to see how they leveraged the ontological relationships to refine many labels!
Reposted by Cellular Semantics
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...
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
April 17, 2025 at 7:58 PM
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...
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...
Reposted by Cellular Semantics
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!
April 25, 2025 at 10:58 PM
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!
Reposted by Cellular Semantics
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...
@davisjmcc.bsky.social
www.biorxiv.org/content/10.1...
March 26, 2025 at 6:04 PM
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...
@davisjmcc.bsky.social
www.biorxiv.org/content/10.1...
Reposted by Cellular Semantics
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...
Increased Pulmonary GM-CSF Causes Alveolar Macrophage Accumulation. Mechanistic Implications for Desquamative Interstitial Pneumonitis
www.atsjournals.org
December 6, 2024 at 6:08 PM
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...
Reposted by Cellular Semantics
May 2, 2025 at 8:09 PM
Reposted by Cellular Semantics
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
June 25, 2025 at 2:29 PM
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
Reposted by Cellular Semantics
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...
Please share with your networks and do contact me if you would like to find out more
sanger.wd103.myworkdayjobs.com/en-US/Wellco...
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...
sanger.wd103.myworkdayjobs.com
July 7, 2025 at 9:14 AM
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...
Please share with your networks and do contact me if you would like to find out more
sanger.wd103.myworkdayjobs.com/en-US/Wellco...