Eukaryotic transcription factors (TFs) from the same structural family tend to bind similar DNA
sequences, despite the ability of these TFs to execute distinct functions in vivo. The cell …

Enhancers are genomic DNA elements controlling spatiotemporal gene expression. Their
flexible organization and functional redundancies make deciphering their sequence-function …

Short tandem repeats (STRs) are enriched in eukaryotic cis-regulatory elements and alter
gene expression, yet how they regulate transcription remains unknown. We found that STRs …

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

INTRODUCTION Enzymes possess extraordinary catalytic proficiency and specificity. These
properties ultimately derive from interactions not just between the active-site residues and …

Over the last decade, a rich variety of massively parallel assays have revolutionized our
understanding of how biological sequences encode quantitative molecular phenotypes …

Deep learning has been successful at predicting epigenomic profiles from DNA sequences.
Most approaches frame this task as a binary classification relying on peak callers to define …

Promoters serve a critical role in establishing baseline transcriptional capacity through the
recruitment of proteins, including transcription factors. Previously, a paucity of data for cis …

Genome-wide association studies (GWAS) have mapped over 90% of disease-and
quantitative-trait-associated variants within the non-coding genome. Non-coding regulatory …

Deep neural networks have demonstrated improved performance at predicting the
sequence specificities of DNA-and RNA-binding proteins compared to previous methods …