Uncovering the cis-regulatory code that governs when and how much each gene is
transcribed in a given genome and cellular state remains a central goal of biology. Here, we …

Single-cell biology is facing a crisis of sorts. Vast numbers of single-cell molecular profiles
are being generated, clustered and annotated. However, this is overwhelmingly ad hoc, and …

Embryonic stem (ES) cells can undergo many aspects of mammalian embryogenesis in
vitro,,,–, but their developmental potential is substantially extended by interactions with …

Spatially resolved transcriptomic technologies are promising tools to study complex
biological processes such as mammalian embryogenesis. However, the imbalance between …

Metacells are cell groupings derived from single-cell sequencing data that represent highly
granular, distinct cell states. Here we present single-cell aggregation of cell states …

RNA velocity provides an approach for inferring cellular state transitions from single-cell
RNA sequencing (scRNA-seq) data. Conventional RNA velocity models infer universal …

Waddington's epigenetic landscape is a metaphor frequently used to illustrate cell
differentiation. Recent advances in single-cell genomics are altering our understanding of …

Single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for
recovering gene expression data from an exponentially scalable number of individual cells …

The development of the vertebrate eyes is a complex process starting from anterior-posterior
and dorso-ventral patterning of the anterior neural tube, resulting in the formation of the eye …

The four-dimensional nucleome (4DN) consortium studies the architecture of the genome
and the nucleus in space and time. We summarize progress by the consortium and highlight …