The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …

The rapid development of precision medicine in recent years has started to challenge
diagnostic pathology with respect to its ability to analyze histological images and …

Generative pretrained models have achieved remarkable success in various domains such
as language and computer vision. Specifically, the combination of large-scale diverse …

Joint profiling of chromatin accessibility and gene expression in individual cells provides an
opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present …

Understanding cellular responses to genetic perturbation is central to numerous biomedical
applications, from identifying genetic interactions involved in cancer to developing methods …

This protocol explains how to perform a fast SCENIC analysis alongside standard best
practices steps on single-cell RNA-sequencing data using software containers and Nextflow …

RNA velocity has enabled the recovery of directed dynamic information from single‐cell
transcriptomics by connecting measurements to the underlying kinetics of gene expression …

Cell–cell communication is a fundamental process that shapes biological tissue. Historically,
studies of cell–cell communication have been feasible for one or two cell types and a few …

Deciphering the functional interactions of cells in tissues remains a major challenge. Here
we describe DIALOGUE, a method to systematically uncover multicellular programs (MCPs) …

Abstract The Gene Expression Omnibus (GEO) is an international public repository that
archives gene expression and epigenomics data sets generated by next-generation …