Many enhancers play a crucial role in regulating gene expression by assembling regulatory
factor (RF) clusters, also referred to as condensates. This process is essential for facilitating …

The advent of single-cell sequencing techniques has not only revolutionized the
investigation of biological processes but also significantly contributed to unraveling cellular …

Here we frame the cis-regulatory code (that connects the regulatory functions of non-coding
regions, such as promoters and UTRs, to their DNA sequences) as a representation building …

Single nucleus ATAC-seq (snATAC-seq) experimental designs have become increasingly
complex with multiple factors that might affect chromatin accessibility, including genotype …

Summary Transcription factor (TF)-cofactor (COF) interactions define dynamic, cell-specific
networks that govern gene expression; however, these networks are understudied due to a …

The Myb proto-oncogene encodes the transcription factor c-MYB, which is critical for
hematopoiesis. Distant enhancers of Myb form a hub of interactions with the Myb promoter …

Machine learning methods that fully exploit the dual modality of single-cell RNA+ ATAC-seq
techniques are still lacking. Here, we developed ChromatinHD, a pair of models that uses …

An important and largely unsolved problem in synthetic biology is how to target gene
expression to specific cell types. Here, we apply iterative deep learning to design synthetic …

Regulatory elements are important constituents of plant genomes that have shaped ancient
and modern crops. Their identification, function, and diversity in crop genomes however are …

Enhancers, through the combinatorial action of transcription factors (TFs), dictate both the
spatial specificity and the levels of gene expression, and their aberrations can result in …