Sequence-specific transcription factors (TFs) regulate gene expression by binding to cis-
regulatory elements in promoter and enhancer DNA. While studies of TF–DNA binding have …

Most complex trait-associated variants are located in non-coding regulatory regions of the
genome, where they have been shown to disrupt transcription factor (TF)-DNA binding …

Abstract Design of de novo synthetic regulatory DNA is a promising avenue to control gene
expression in biotechnology and medicine. Using mutagenesis typically requires screening …

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 …

The cistrome is the complete set of transcription factor (TF) binding sites (cis-elements) in an
organism, while an epicistrome incorporates tissue-specific DNA chemical modifications and …

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 …

Kernel-based support vector machines (SVMs) are supervised machine learning algorithms
for classification and regression problems. We introduce a method to train SVMs on a D …

Transcription factors regulate gene expression, but how these proteins recognize and
specifically bind to their DNA targets is still debated. Machine learning models are effective …

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

Understanding the mechanisms of protein-DNA binding is critical in comprehending gene
regulation. Three-dimensional DNA structure, also described as DNA shape, plays a key …