Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples: Cell Reports Methods
cell.com/cell-reports-m…

Delighted to receive the Levy-Plumb Fund for the Humanities grant from Christ's College to travel to China to explore rich traditions of porcelain

En route to Shanghai 🇨🇳

Local heterogeneity of tissues can define their function and predict clinical outcomes. We introduce Kasumi 💻biorxiv.org/content/10.110… to identify spatially localized neighborhoods of intra and intercellular relationships from spatial omics persistent across samples & conditions

What would happen if you got vaccinated against the same antigen over and over again? In The Lancet Infectious Diseases, we now report on a hypervaccinated individual from Magdeburg (HIM) who received 217 vaccinations within 29 months against SARS-CoV-2. 👇 1/19 thelancet.com/journals/lanin…

Pre-trained using over 33 million single cell RNA-seq profiles, scGPT is a foundation model facilitating a broad spectrum of downstream single-cell analysis tasks by transfer learning. Bo Wang Haotian Cui ChloeXWang University of Toronto Vector Institute University Health Network

nature.com/articles/s4159…

Next Tuesday at 2024-03-05 18:00 CET will be another community meeting!

Robert Petryszak will talk about about CellPhoneDB, and how to infer cell-cell communication from single-cell multiomics data. For more information, check the GitHub repository: github.com/ventolab/Cellp…

Excited to share our experience and perspectives on spatial transcriptomics and omics data deconvolution in Nature Methods. Delighted to collaborate with leaders in the field, especially Sarah Teichman's and Lana Garmire's labs. nature.com/articles/s4159…

We’re excited to share a directory of models & embeddings in CZ #CellxGene Census!

It’s a centralized hub for exploration, collaboration & improvement of models integrating up to 36M cells, giving a more comprehensive picture of cell states bit.ly/475Qi4A

The diversification of methods for studying cell–cell interactions and communication go.nature.com/491i6Zi #Review by Erick Armingol, Hratch M Baghdassarian & Nathan Lewis LewisLabUCSD UC San Diego Continuing Professional Development

Our latest review is now on Nature Reviews Genetics, focusing on the evolution of methods in cell-cell interaction research. It updates and complements our previous review on the foundations of inferring cell-cell interactions from transcriptomics.
nature.com/articles/s4157…

1) 📚 Looking for flexible and user-friendly resources on metabolite-mediated interactions in cell-cell communication? Check our new database, MetalinksDB, described in our recent preprint: tinyurl.com/mldbpprnt

Thrilled to share our manuscript on single-cell whole-embryo phenotyping of mouse mutants in its final form out in nature: nature.com/articles/s4158…
Here is a brief summary of some results:

Thanks for a great week !

Moon jar 🌙

Small bud vase, given as gift

A few from ceramics summer workshop Bedford this week with Mandy

I had a fantastic week with Anne at Kaolin Studio, Utrecht working with porcelain and stoneware 🇳🇱

📢Our preprint ‘RNA allelic frequencies of somatic mutations encode substantial functional information in cancers’ is out today. Excited to tell you all about it, and our new tool, RVdriver: biorxiv.org/content/10.110… (1/8)

Experimenting with new glazes, quick espresso cups, buff clay stoneware #ceramics

I am very grateful to UMR-INSERM 1064 CHU de Nantes and Nantes Université Nantes Université for hosting me for a visiting fellowship in translational immunology, had a fantastic time and learnt a lot. Thank you Christophe Masset !