Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …

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

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 …

The relationship between the human placenta—the extraembryonic organ made by the
fetus, and the decidua—the mucosal layer of the uterus, is essential to nurture and protect …

The recent development of experimental methods for measuring chromatin state at single-
cell resolution has created a need for computational tools capable of analyzing these …

Single-cell omics technologies have revolutionized the study of gene regulation in complex
tissues. A major computational challenge in analyzing these datasets is to project the large …

Cell type-specific gene expression patterns and dynamics during development or in disease
are controlled by cis-regulatory elements (CREs), such as promoters and enhancers …

Understanding kidney disease relies on defining the complexity of cell types and states, their
associated molecular profiles and interactions within tissue neighbourhoods. Here we …

To the Editor—Methods for analyzing single-cell data 1–4 perform a core set of
computational tasks. These tasks include dimensionality reduction, cell clustering, cell-state …

Realizing the full utility of brain organoids to study human development requires
understanding whether organoids precisely replicate endogenous cellular and molecular …