AIMC Topic: DNA Methylation

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Deep6mA: A deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species.

PLoS computational biology
N6-methyladenine (6mA) is an important DNA modification form associated with a wide range of biological processes. Identifying accurately 6mA sites on a genomic scale is crucial for under-standing of 6mA's biological functions. However, the existing ...

Sarcoma classification by DNA methylation profiling.

Nature communications
Sarcomas are malignant soft tissue and bone tumours affecting adults, adolescents and children. They represent a morphologically heterogeneous class of tumours and some entities lack defining histopathological features. Therefore, the diagnosis of sa...

MethylationToActivity: a deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors.

Genome biology
Although genome-wide DNA methylomes have demonstrated their clinical value as reliable biomarkers for tumor detection, subtyping, and classification, their direct biological impacts at the individual gene level remain elusive. Here we present Methyla...

The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome.

Nature cancer
We report a systematic analysis of the DNA methylation variability in 1,595 samples of normal cell subpopulations and 14 tumor subtypes spanning the entire human B-cell lineage. Differential methylation among tumor entities relates to differences in ...

Machine learning analysis of DNA methylation in a hypoxia-immune model of oral squamous cell carcinoma.

International immunopharmacology
BACKGROUND: Hypoxia status and immunity are related with the development and prognosis of oral squamous cell carcinoma (OSCC). Here, we constructed a hypoxia-immune model to explore its upstream mechanism and identify potential CpG sites.

Predicting Deep Learning Based Multi-Omics Parallel Integration Survival Subtypes in Lung Cancer Using Reverse Phase Protein Array Data.

Biomolecules
Mortality attributed to lung cancer accounts for a large fraction of cancer deaths worldwide. With increasing mortality figures, the accurate prediction of prognosis has become essential. In recent years, multi-omics analysis has emerged as a useful ...

Identification of an epigenetic signature in human induced pluripotent stem cells using a linear machine learning model.

Human cell
The use of human induced pluripotent stem cells (iPSCs), used as an alternative to human embryonic stem cells (ESCs), is a potential solution to challenges, such as immune rejection, and does not involve the ethical issues concerning the use of ESCs ...

Automatic Prediction of MGMT Status in Glioblastoma via Deep Learning-Based MR Image Analysis.

BioMed research international
Methylation of the O-methylguanine methyltransferase (MGMT) gene promoter is correlated with the effectiveness of the current standard of care in glioblastoma patients. In this study, a deep learning pipeline is designed for automatic prediction of M...

Machine Learning-Based DNA Methylation Score for Fetal Exposure to Maternal Smoking: Development and Validation in Samples Collected from Adolescents and Adults.

Environmental health perspectives
BACKGROUND: Fetal exposure to maternal smoking during pregnancy is associated with the development of noncommunicable diseases in the offspring. Maternal smoking may induce such long-term effects through persistent changes in the DNA methylome, which...