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Epigenesis, Genetic

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Deep learning approaches for non-coding genetic variant effect prediction: current progress and future prospects.

Briefings in bioinformatics
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...

m6ATM: a deep learning framework for demystifying the m6A epitranscriptome with Nanopore long-read RNA-seq data.

Briefings in bioinformatics
N6-methyladenosine (m6A) is one of the most abundant and well-known modifications in messenger RNAs since its discovery in the 1970s. Recent studies have demonstrated that m6A is involved in various biological processes, such as alternative splicing ...

A review of deep learning models for the prediction of chromatin interactions with DNA and epigenomic profiles.

Briefings in bioinformatics
Advances in three-dimensional (3D) genomics have revealed the spatial characteristics of chromatin interactions in gene expression regulation, which is crucial for understanding molecular mechanisms in biological processes. High-throughput technologi...

Insights to aging prediction with AI based epigenetic clocks.

Epigenomics
Over the past century, human lifespan has increased remarkably, yet the inevitability of aging persists. The disparity between biological age, which reflects pathological deterioration and disease, and chronological age, indicative of normal aging, h...

Predicting cell type-specific epigenomic profiles accounting for distal genetic effects.

Nature communications
Understanding how genetic variants affect the epigenome is key to interpreting GWAS, yet profiling these effects across the non-coding genome remains challenging due to experimental scalability. This necessitates accurate computational models. Existi...

Artificial intelligence and deep learning algorithms for epigenetic sequence analysis: A review for epigeneticists and AI experts.

Computers in biology and medicine
Epigenetics encompasses mechanisms that can alter the expression of genes without changing the underlying genetic sequence. The epigenetic regulation of gene expression is initiated and sustained by several mechanisms such as DNA methylation, histone...

AI-driven feature selection and epigenetic pattern analysis: A screening strategy of CpGs validated by pyrosequencing for body fluid identification.

Forensic science international
Identification of body fluid stain at crime scene is one of the important tasks of forensic evidence analysis. Currently, body fluid-specific CpGs detected by DNA methylation microarray screening, have been widely studied for forensic body fluid iden...

AI techniques have facilitated the understanding of epitranscriptome distribution.

Cell genomics
N-methyladenosine (m6A), the most prevalent internal mRNA modification in higher eukaryotes, plays diverse roles in cellular regulation. By incorporating both sequence- and genome-derived features, Fan et al. designed a novel Transformer-BiGRU framew...

Highlights of Precision Medicine, Genetics, Epigenetics and Artificial Intelligence in Pompe Disease.

International journal of molecular sciences
Pompe disease is a neuromuscular disorder caused by a deficiency of the enzyme acid alpha-glucosidase (), which leads to lysosomal glycogen accumulation and progressive development of muscle weakness. Two distinct isoforms have been identified. In th...