Transcriptional enhancers act as docking stations for combinations of transcription factors
and thereby regulate spatiotemporal activation of their target genes. It has been a long …

Aspirations for high crop growth and yield, nutritional quality and bioproduction of materials
are challenged by climate change and limited adoption of new technologies. Here, we …

Measurements of gene expression or signal transduction activity are conventionally
performed using methods that require either the destruction or live imaging of a biological …

Massively parallel reporter assays (MPRAs) are powerful tools for quantifying the impacts of
sequence variation on gene expression. Reading out molecular phenotypes with …

The inability to scalably and precisely measure the activity of developmental cis-regulatory
elements (CREs) in multicellular systems is a bottleneck in genomics. Here we develop a …

Metabolic diseases are caused by a complex interplay between genetics and the
environment, yet many basic studies guiding our understanding of metabolism are confined …

Discrete diffusion or flow models could enable faster and more controllable sequence
generation than autoregressive models. We show that na\" ive linear flow matching on the …

Most mammalian genes have multiple polyA sites, representing a substantial source of
transcript diversity regulated by the cleavage and polyadenylation (CPA) machinery. To …

Regulatory DNA sequences within enhancers and promoters bind transcription factors to
encode cell type-specific patterns of gene expression. However, the regulatory effects and …

Motivation Promoters with desirable properties are crucial in biotechnological applications.
Generative AI (GenAI) has demonstrated potential in creating novel synthetic promoters with …