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 …

Large serine recombinases (LSRs) are DNA integrases that facilitate the site-specific
integration of mobile genetic elements into bacterial genomes. Only a few LSRs, such as …

The arrangement (syntax) of transcription factor (TF) binding motifs is an important part of the
cis-regulatory code, yet remains elusive. We introduce a deep learning model, BPNet, that …

Heritable variation in gene expression is common within and between species. This
variation arises from mutations that alter the form or function of molecular gene regulatory …

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 …

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 …

Background The largest sequence-based models of transcription control to date are
obtained by predicting genome-wide gene regulatory assays across the human genome …

To elucidate principles operating in native biological systems and to develop novel
biotechnologies, synthetic biology aims to build and integrate synthetic gene circuits within …

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 …