Rémi Trimbour

CIRCE predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data, improving speed and memory use compared to Cicero.

ReCoN models multicellular coordination by integrating cell-cell communication and intracellular regulation to predict cellular responses to perturbations.

The paper benchmarks methods for inferring gene regulatory networks from multimodal single-cell data and introduces a framework called GRETA to evaluate their performance and limitations.

HuMMuS infers regulatory mechanisms from single-cell multi-omics data, improving predictions of TF targets, binding motifs, and regulatory regions.