Regulation of genome organization and gene expression by nuclear mechanotransduction
It is well established that cells sense chemical signals from their local microenvironment and
transduce them to the nucleus to regulate gene expression programmes. Although a number …
transduce them to the nucleus to regulate gene expression programmes. Although a number …
Machine learning meets omics: applications and perspectives
The innovation of biotechnologies has allowed the accumulation of omics data at an
alarming rate, thus introducing the era of 'big data'. Extracting inherent valuable knowledge …
alarming rate, thus introducing the era of 'big data'. Extracting inherent valuable knowledge …
Enter the matrix: factorization uncovers knowledge from omics
Omics data contain signals from the molecular, physical, and kinetic inter-and intracellular
interactions that control biological systems. Matrix factorization (MF) techniques can reveal …
interactions that control biological systems. Matrix factorization (MF) techniques can reveal …
Dissecting super-enhancer hierarchy based on chromatin interactions
Recent studies have highlighted super-enhancers (SEs) as important regulatory elements
for gene expression, but their intrinsic properties remain incompletely characterized …
for gene expression, but their intrinsic properties remain incompletely characterized …
Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation
Dynamic changes in the expression of transcription factors (TFs) can influence the
specification of distinct CD8+ T cell fates, but the observation of equivalent expression of TFs …
specification of distinct CD8+ T cell fates, but the observation of equivalent expression of TFs …
DeepYY1: a deep learning approach to identify YY1-mediated chromatin loops
Abstract The protein Yin Yang 1 (YY1) could form dimers that facilitate the interaction
between active enhancers and promoter-proximal elements. YY1-mediated enhancer …
between active enhancers and promoter-proximal elements. YY1-mediated enhancer …
Epigenetics analysis and integrated analysis of multiomics data, including epigenetic data, using artificial intelligence in the era of precision medicine
To clarify the mechanisms of diseases, such as cancer, studies analyzing genetic mutations
have been actively conducted for a long time, and a large number of achievements have …
have been actively conducted for a long time, and a large number of achievements have …
DeepTACT: predicting 3D chromatin contacts via bootstrap** deep learning
Interactions between regulatory elements are of crucial importance for the understanding of
transcriptional regulation and the interpretation of disease mechanisms. Hi-C technique has …
transcriptional regulation and the interpretation of disease mechanisms. Hi-C technique has …
A supervised learning framework for chromatin loop detection in genome-wide contact maps
Accurately predicting chromatin loops from genome-wide interaction matrices such as Hi-C
data is critical to deepening our understanding of proper gene regulation. Current …
data is critical to deepening our understanding of proper gene regulation. Current …
Predicting enhancer‐promoter interaction from genomic sequence with deep neural networks
Background In the human genome, distal enhancers are involved in regulating target genes
through proximal promoters by forming enhancer‐promoter interactions. Although recently …
through proximal promoters by forming enhancer‐promoter interactions. Although recently …