Hox genes play key roles in axial patterning and regulating the regional identity of cells and
tissues in a wide variety of animals from invertebrates to vertebrates. Nested domains of Hox …

Eukaryotic genomes are organized into chromatin domains. The molecular mechanisms
driving the formation of these domains are difficult to dissect in vivo and remain poorly …

Eukaryotic genomes are organized into 3D structures, which range from small-scale
nucleosome arrays to large-scale chromatin domains. These structures have an important …

The linear sequence of DNA provides invaluable information about genes and their
regulatory elements along chromosomes. However, to fully understand gene function and …

Abstract The three-dimensional (3D) genome structure plays a fundamental role in gene
regulation and cellular functions. Recent studies in 3D genomics inferred the very basic …

Motivation: We present a user-friendly 3D chromatin simulation model for the human
genome based on OpenMM, addressing the challenges posed by existing models with use …

The spatial organization of the genome modulates nuclear processes, including
transcription, replication, and DNA repair,. Eukaryotic genomes are organized into distinct …

Chromatin architecture is orchestrated, and plays crucial roles during the developmental
process by regulating gene expression. In embryonic stem cells (ESCs), three types of …

The three-dimensional structure of chromatin has emerged as an important feature of
eukaryotic gene regulation. Recent technological advances in DNA sequencing-based …

Gene expression and cell fate determination require precise and coordinated epigenetic
regulation. The complex three-dimensional (3D) genome organization plays a critical role in …