Artificial intelligence (AI) models based on deep learning now represent the state of the art
for making functional predictions in genomics research. However, the underlying basis on …

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 …

Gene regulation in the human genome is controlled by distal enhancers that activate specific
nearby promoters. A proposed model for this specificity is that promoters have sequence …

Enhancers play a central role in the spatiotemporal control of gene expression and tend to
work in a cell-type-specific manner. In addition, they are suggested to be major contributors …

Transcriptional enhancers act as docking stations for combinations of transcription factors
and thereby regulate spatiotemporal activation of their target genes. It has been a long …

Gene expression is in part controlled by cis-regulatory elements (CREs) such as enhancers
and repressive elements. Anecdotal evidence has indicated that a CRE and a promoter …

Gene expression is regulated by transcription factors that work together to read cis-
regulatory DNA sequences. The 'cis-regulatory code'—how cells interpret DNA sequences …

Recent advances in single-cell sequencing technologies have provided unprecedented
opportunities to measure the gene expression profile and RNA velocity of individual cells …

Genomes encode for genes and non-coding DNA, both capable of transcriptional activity.
However, unlike canonical genes, many transcripts from non-coding DNA have limited …

The inability to scalably and precisely measure the activity of developmental cis-regulatory
elements (CREs) in multicellular systems is a bottleneck in genomics. Here we develop a …