Recent advancements in high-throughput sequencing technologies have significantly enhanced our ability to unravel the intricacies of gene regulatory processes. A critical challenge in this endeavor is the identification of variant effects, a key fact...
Epigenetic changes serve as a cellular memory for cumulative cold recognition in both herbaceous and tree species, including bud dormancy. However, most studies have discussed predicted chromatin structure with respect to histone marks. In the presen...
DNA methylation is a fundamental epigenetic modification involved in various biological processes and diseases. Analysis of DNA methylation data at a genome-wide and high-throughput level can provide insights into diseases influenced by epigenetics, ...
Silencers are noncoding DNA sequence fragments located on the genome that suppress gene expression. The variation of silencers in specific cells is closely related to gene expression and cancer development. Computational approaches that exclusively r...
Enhancers are crucial cis-regulatory elements that control gene expression in a cell-type-specific manner. Despite extensive genetic and computational studies, accurately predicting enhancer activity in different cell types remains a challenge, and t...
Accurate prediction of deoxyribonucleic acid (DNA) modifications is essential to explore and discern the process of cell differentiation, gene expression and epigenetic regulation. Several computational approaches have been proposed for particular ty...
Nihon yakurigaku zasshi. Folia pharmacologica Japonica
Jan 1, 2022
We are constructing the "Percellome Database" containing many transcriptomes of mice exposed to a series of chemicals to elucidate the molecular mechanism of toxicity and to develop toxicity prediction technology. Acute toxicity of a chemical can be ...
MOTIVATION: DNA methylation plays an important role in epigenetic modification, the occurrence, and the development of diseases. Therefore, identification of DNA methylation sites is critical for better understanding and revealing their functional me...
The accumulation of large epigenomics data consortiums provides us with the opportunity to extrapolate existing knowledge to new cell types and conditions. We propose Epitome, a deep neural network that learns similarities of chromatin accessibility ...
The exploration of three-dimensional chromatin interaction and organization provides insight into mechanisms underlying gene regulation, cell differentiation and disease development. Advances in chromosome conformation capture technologies, such as h...