The proper activities of enhancers and gene promoters are essential for coordinated
transcription within a cell. Although diverse methodologies have been developed to identify …

Cell type-specific gene expression relies on transcription factors (TFs) binding DNA
sequence motifs embedded in chromatin. Understanding how motifs are accessed in …

Transcription factors (TFs) are key regulators of intrinsic cellular processes, such as
differentiation and development, and of the cellular response to external perturbation …

The human gene catalogue is essentially complete, but we lack an equivalently vetted
inventory of bona fide human enhancers. Hundreds of thousands of candidate enhancers …

Access to DNA is a prerequisite to the execution of essential cellular processes that include
transcription, replication, chromosomal segregation, and DNA repair. How the proteins that …

DNA can determine where and when genes are expressed, but the full set of sequence
determinants that control gene expression is unknown. Here, we measured the …

The gene regulatory code and grammar remain largely unknown, precluding our ability to
link phenotype to genotype in regulatory sequences. Here, using a massively parallel …

Designing promoters with desirable properties is essential in synthetic biology. Human
experts are skilled at identifying strong explicit patterns in small samples, while deep …

Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively
parallel reporter assays, test thousands of sequence variants in a single experiment. Despite …

Each language has standard books describing that language's grammatical rules. Biologists
have searched for similar, albeit more complex, principles relating enhancer sequence to …