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 …

Assessment of single-cell gene expression (single-cell RNA sequencing) and adaptive
immune receptor (AIR) sequencing (scVDJ-seq) has been invaluable in studying …

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 …

Abstract Analysis across a growing number of single-cell perturbation datasets is hampered
by poor data interoperability. To facilitate development and benchmarking of computational …

Background Single-cell RNA-sequencing (scRNA-seq) measures gene expression in single
cells, while single-nucleus ATAC-sequencing (snATAC-seq) quantifies chromatin …

High-throughput single-cell profiling provides an unprecedented ability to uncover the
molecular states of millions of cells. These technologies are, however, destructive to cells …

Existing methods for gene regulatory network (GRN) inference rely on gene expression data
alone or on lower resolution bulk data. Despite the recent integration of chromatin …

Recently developed technologies to generate single-cell genomic data have made a
revolutionary impact in the field of biology. Multi-omics assays offer even greater …

Breast cancers are known to be driven by the transcription factor estrogen receptor and its
ligand estrogen. While the receptor's cis-binding elements are known to vary between …