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 …

Cis-regulatory elements (CREs) control gene expression, orchestrating tissue identity,
developmental timing, and stimulus responses, which collectively define the thousands of …

The epigenome—the chemical modifications and chromatin-related packaging of the
genome—enables the same genetic template to be activated or repressed in different …

Cooperative DNA-binding by transcription factor (TF) proteins is critical for eukaryotic gene
regulation. In the human genome, many regulatory regions contain TF-binding sites in close …

Motivation Supervised deep learning is used to model the complex relationship between
genomic sequence and regulatory function. Understanding how these models make …

This article examines the structure and functions of the plant synthetic promoters frequently
used to precisely regulate complex regulatory routes. It details the composition of native …

Cis-regulatory elements (CREs) direct gene expression in health and disease, and models
that can accurately predict their activities from DNA sequences are crucial for biomedicine …

Neural networks have emerged as immensely powerful tools in predicting functional
genomic regions, notably evidenced by recent successes in deciphering gene regulatory …

We present regLM, a framework to design synthetic CREs with desired properties, such as
high, low or cell type-specific activity, using autoregressive language models in conjunction …

Genomic sequence-to-activity models are increasingly utilized to understand gene
regulatory syntax and probe the functional consequences of regulatory variation. Current …