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

Mapping single-cell sequencing profiles to comprehensive reference datasets provides a
powerful alternative to unsupervised analysis. However, most reference datasets are …

Biological systems are immensely complex, organized into a multi-scale hierarchy of
functional units based on tightly regulated interactions between distinct molecules, cells …

Harmonizing cell types across the single-cell community and assembling them into a
common framework is central to building a standardized Human Cell Atlas. Here, we present …

Although multiple pancreatic islet single-cell RNA-sequencing (scRNA-seq) datasets have
been generated, a consensus on pancreatic cell states in development, homeostasis and …

The advent of high-throughput single-cell genomics technologies has fundamentally
transformed biological sciences. Currently, millions of cells from complex biological tissues …

Factor analysis decomposes single-cell gene expression data into a minimal set of gene
programs that correspond to processes executed by cells in a sample. However, matrix …

Advancements in cytometry technologies have enabled quantification of up to 50 proteins
across millions of cells at single cell resolution. Analysis of cytometry data routinely involves …

Early organogenesis represents a key step in animal development, during which pluripotent
cells diversify to initiate organ formation. Here, we sampled 300,000 single-cell …

Cell signaling plays a critical role in regulating cellular behavior and fate. While multimodal
single-cell sequencing technologies are rapidly advancing, scalable and flexible profiling of …