CellPhoneDB v5: inferring cell–cell communication from single-cell multiomics data www.nature.com/articles/s4...

CellPhoneDB v5 is officially published!
nature.com/articles/s41...

Very happy to have played a small role in it by developing some tools to help visualise the complex cell-cell interaction data!

#SingleCell

🔥 18-19/9/25 🔥 Computational Biology Symposium in Lausanne! Meet the speakers: Roser Vento-Tormo @sangerinstitute.bsky.social has pioneered computational approaches to study cell-cell interactions with the now legendary CellPhoneDB www.cellphonedb.org #bioinformatics #SingleCell #compbio

News & Views discussing the latest implementation of the computational tool #CellPhoneDB for inferring #cellcellcommunication from #singlecelldata bit.ly/42gSmXi

A major overinterpretation is that CellPhoneDB predicts ligand-receptor interactions. It does not demonstrate actual signalling or activation. "EBV+ B cells activate T cells" is a stronger conclusion than the data support.
The autoimmune parallels are real, but not specific.
8/10

#NewNProt: Protocol Update of #CellPhoneDB, describing an expanded database of molecular interactors and new approaches to infer, prioritise and visualise the results bit.ly/4lbG2Af and see associated News & Views article

CellPhoneDB v5 expands the database to nonpeptide ligands and includes several strategies to prioritize and visualize interactions, incorporating information from epigenomics and spatial transcriptomics modalities.

Benchmarking sequencing-based #SpatialTranscriptomic methods

#10xVisium
#HDST
#BMKMANUS1000
#SlideseqV2
#Stereoseq
#PIXELseq
#DBiTseq

Different ST methods yield inconsistent cell-cell communication results by #CellChat #CellPhoneDB

bioRxiv 2023
www.biorxiv.org/content/10.1...

Advancing cell–cell communication analysis from single-cell genomics data

www.nature.com/articles/s41...

ktplotspy (Python)
github.com/zktuong/ktpl...