Recent progress in whole-genome mapping and imaging technologies has enabled the
characterization of the spatial organization and folding of the genome in the nucleus. In …

The present day's ongoing global warming and climate change adversely affect plants
through imposing environmental (abiotic) stresses and disease pressure. The major abiotic …

Background The largest sequence-based models of transcription control to date are
obtained by predicting genome-wide gene regulatory assays across the human genome …

Nuclear compartments are prominent features of 3D chromatin organization, but sequencing
depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally …

Genomic deep learning models can predict genome-wide epigenetic features and gene
expression levels directly from DNA sequence. While current models perform well at …

Higher-order chromatin structure is important for the regulation of genes by distal regulatory
sequences,. Structural variants (SVs) that alter three-dimensional (3D) genome organization …

Deep neural networks (DNNs) have greatly advanced the ability to predict genome function
from sequence. However, elucidating underlying biological mechanisms from genomic …

Investigating how chromatin organization determines cell-type-specific gene expression
remains challenging. Experimental methods for measuring three-dimensional chromatin …

Gene regulation is a central topic in cell biology. Advances in omics technologies and the
accumulation of omics data have provided better opportunities for gene regulation studies …

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 …