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...
Haploinsufficiency, wherein a single allele is not enough to maintain normal functions, can lead to many diseases including cancers and neurodevelopmental disorders. Recently, computational methods for identifying haploinsufficiency have been develop...
MOTIVATION: N7-methylguanosine (m7G) is an important epigenetic modification, playing an essential role in gene expression regulation. Therefore, accurate identification of m7G modifications will facilitate revealing and in-depth understanding their ...
Machine learning methods have been widely applied to big data analysis in genomics and epigenomics research. Although accuracy and efficiency are common goals in many modeling tasks, model interpretability is especially important to these studies tow...
DNA N6-methyladenine (6mA) represents important epigenetic modifications, which are responsible for various cellular processes. The accurate identification of 6mA sites is one of the challenging tasks in genome analysis, which leads to an understandi...
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