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Reposted by Rémi Trimbour - MD-PhD student

#SingleCell preprints @prepub-singlecell.bsky.social · 23/01/2026

Modelling multicellular coordination by bridging cell-cell communication and intracellular regulation through multilayer networks #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.64898/20…

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Rémi Trimbour - MD-PhD student @remitrimbour.bsky.social · 20/01/2026

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.com

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

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Rémi Trimbour - MD-PhD student @remitrimbour.bsky.social · 30/09/2025

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 ⬇️

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Reposted by Rémi Trimbour - MD-PhD student

Anshul Kundaje @anshulkundaje.bsky.social · 16/09/2025

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/

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Reposted by Rémi Trimbour - MD-PhD student

scverse @scverse.bsky.social · 31/01/2025

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: buff.ly/40RJ3gT & pre-print buff.ly/4hwK4Av

buff.ly

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

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Reposted by Rémi Trimbour - MD-PhD student

Saez-Rodriguez Group @saezlab.bsky.social · 23/12/2024

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

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Reposted by Rémi Trimbour - MD-PhD student

Saez-Rodriguez Group @saezlab.bsky.social · 26/11/2024

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

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Reposted by Rémi Trimbour - MD-PhD student

Saez-Rodriguez Group @saezlab.bsky.social · 11/11/2024

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...

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