Most existing cell-cell communication methods use the product of ligand and receptor expression to indicate the strength of L-R interactions between two cell groups. But can we leverage the gene regulatory network-level information to infer significant L-R pairs? A thread 🧵

1/9 CPAis finally published. It can predict single-cell responses to combinatorial perturbation (drugs, CRISPR). This is a joint collab between @meta and Fabian Theis Helmholtz Munich | @HelmholtzMunich. Read the thread to understand the LEGO analogy! embopress.org/doi/full/10.15…

Videos from RECOMB-CCB 2023 are now available in our YouTube channel. We are waiting for permissions from a few more authors to release videos and we will update the list as we receive them. youtube.com/playlist?list=…

Prof. Gil Strang's last lecture is ... Monday! Watch it via live stream: grinfeld.org/strang/

Interpretable modeling of time-resolved single-cell gene-protein expression using CrossmodalNet biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

James Cai Xiaole Shirley Liu We have just uploaded a preprint on this topic where we predict surface protein profiles from scRNA-seq data with interpretability for temporal effects as well as gene-protein relationships. Xiaole Shirley Liu biorxiv.org/content/10.110…

CrossmodalNet: Interpretable modeling of time-resolved single-cell gene-protein expression biorxiv.org/content/10.110…

CodonBERT: Large Language Models for mRNA Design and Optimization biorxiv.org/content/10.110…

How to decipher subcellular gene patterns in spatial transcriptomics data? We're excited to share Bering, a graph neural network that harnesses subcellular gene colocalization graphs and transfer embeddings for joint cell segmentation and annotation (1/n) biorxiv.org/content/10.110….

These past few years have seen a rapid expansion of cell-cell communication research. Check out Erick Armingol's new Nature Reviews Genetics review of the diverse methods leveraging single-cell and spatial omics: rdcu.be/dwkND

vetmed.tamu.edu/news/press-rel… #GenKI #scTenifoldKnk #VituralKO Yoo

Controlled Noise: Evidence of Epigenetic Regulation of Single-Cell Expression Variability biorxiv.org/content/10.110…