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 …

CD8+ T cells specific for cancer cells are detected within tumours. However, despite their
presence, tumours progress. The clinical success of immune checkpoint blockade and …

Emerging spatial technologies, including spatial transcriptomics and spatial epigenomics,
are becoming powerful tools for profiling of cellular states in the tissue context,,,–. However …

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 …

Cellular function in tissue is dependent on the local environment, requiring new methods for
spatial mapping of biomolecules and cells in the tissue context. The emergence of spatial …

Spatially resolved genomic technologies have allowed us to study the physical organization
of cells and tissues, and promise an understanding of local interactions between cells …

Charting an organs' biological atlas requires us to spatially resolve the entire single-cell
transcriptome, and to relate such cellular features to the anatomical scale. Single-cell and …

Single-cell transcriptomic approaches have revolutionised the study of complex biological
systems, with the routine measurement of gene expression in thousands of cells enabling …

Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied
characteristic of the eukaryotic genome. As active regulatory DNA elements are generally …

Recent advances in single-cell technologies have led to the discovery of thousands of brain
cell types; however, our understanding of the gene regulatory programs in these cell types is …