Background: Drug discovery, which is the process of discovering new candidate
medications, is very important for pharmaceutical industries. At its current stage, discovering …

The forthcoming massive genome data generated by the Earth BioGenome Project will open
up a new era of comparative genomics, for which genome synteny analysis provides an …

Determining the effect of DNA methylation on chromatin structure and function in higher
organisms is challenging due to the extreme complexity of epigenetic regulation. We studied …

Proximity-ligation methods such as Hi-C allow us to map physical DNA–DNA interactions
along the genome, and reveal its organization into topologically associating domains …

Over the past decade, methods for predicting three-dimensional (3-D) chromosome and
genome structures have proliferated. This has been primarily due to the development of high …

ABSTRACT Three-dimensional (3D) organization of the human genome plays an essential
role in all DNA-templated processes, including gene transcription, gene regulation, and …

Motivation Recent experiments have provided Hi-C data at resolution as high as 1 kbp.
However, 3D structural inference from high-resolution Hi-C datasets is often computationally …

High-resolution reconstruction of spatial chromosome organizations from chromatin contact
maps is highly demanded, but is hindered by extensive pairwise constraints, substantial …

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

The new advances in various experimental techniques that provide complementary
information about the spatial conformations of chromosomes have inspired researchers to …