Networks—or graphs—are universal descriptors of systems of interacting elements. In
biomedicine and healthcare, they can represent, for example, molecular interactions …

In higher eukaryotic cells, chromosomes are folded inside the nucleus. Recent advances in
whole-genome map** technologies have revealed the multiscale features of 3D genome …

Long-range regulatory interactions among genomic regions are critical for controlling gene
expression, and their disruption has been associated with a host of diseases. However …

Background Alternative splicing is a widespread regulatory phenomenon that enables a
single gene to produce multiple transcripts. Among the different types of alternative splicing …

Despite accumulating evidence implicating noncoding variants in human diseases,
unraveling their functionality remains a significant challenge. Systematic annotations of the …

Motivation The technology of high-throughput chromatin conformation capture (Hi-C) allows
genome-wide measurement of chromatin interactions. Several studies have shown …

Chromatin features can reveal tissue-specific TF-DNA binding, which leads to a better
understanding of many critical physiological processes. Accurately identifying TF-DNA …

Epigenetics encompasses mechanisms that can alter the expression of genes without
changing the underlying genetic sequence. The epigenetic regulation of gene expression is …

Deep learning methods have been successfully applied to the tasks of predicting functional
genomic elements such as histone marks, transcriptions factor binding sites, non-B DNA …

Advances in high-throughput genome sequencing have enabled large-scale genome
sequencing in clinical practice and research studies. By analyzing genomic variants of …