Modelling multicellular coordination by bridging cell-cell communication and intracellular regulation through multilayer networks #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.01.20.700561v1

ReCoN: REconstruction of multicellular COrdination Network We are releasing a new tool to model multicellular coordination and cellular responses in tissu! 🫀🫁 The package is just out, and the preprint should follow within a few days😇 If you want to have a look already: github.com/cantinilab/R...

GitHub - cantinilab/ReCoN: Exploring multicellular coordination from single-cell gene expression / multi-omics using mutlilayer network representations

Exploring multicellular coordination from single-cell gene expression / multi-omics using mutlilayer network representations - cantinilab/ReCoN

github.com

I'm presenting #CIRCE, a Python package to infer co-accessible DNA region networks 🧬 Based on #Cicero 's algorithm (Pliner et al.), it runs ~150x faster, processing an atlas of 700k cells in less than 40 min! ⛷️ Short paper: doi.org/10.1101/2025... Code: github.com/cantinilab/CIRCE 1/5 ⬇️

I'm curious if other mid career PIs have considered completely abandoning the trad publication model. We've been making gradual moves towards that end goal. But it's been difficult to completely jump ship for one main reason for me at least. 1/

On Tuesday at 2025-02-04 18:00 CET, @jkobject will talk about scPrint, a transformer model that infers gene networks from scRNA-seq data, at our 2nd community meeting of 2025! For more information, check out the GitHub: https://buff.ly/40RJ3gT & pre-print https://buff.ly/4hwK4Av

GitHub - cantinilab/scPRINT: single cell foundation model for Gene network inference and more

single cell foundation model for Gene network inference and more - cantinilab/scPRINT

buff.ly

We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here 👇 Paper: doi.org/10.1101/2024.12.20.629764 Code: github.com/saezlab/greta

We present NetworkCommons, a unified platform 🪐 for network biology, providing access to omics data, knowledge, and contextualization methods, all with a consistent API 👇🧵 Paper: doi.org/10.1101/2024... Docs: networkcommons.readthedocs.io

Hey, this place is getting fun! Here is a new version of our latest preprint on oscillatory dynamics of mRNA metabolism and chromatin accessibility during the cell cycle: www.biorxiv.org/content/10.1...

Single-cell multiomics reveals the oscillatory dynamics of mRNA metabolism and chromatin accessibility during the cell cycle

The cell cycle is a tightly regulated process that requires precise temporal expression of hundreds of cell cycledependent genes. However, the genome-wide dynamics of mRNA metabolism throughout the ce...

biorxiv.org

What are the key disrupted multicellular processes in heart failure? In our new work we combine 23 years of molecular data with recent single-cell atlases to draw a cross-study patient map doi.org/10.1101/2024...