AIMC Topic: Epigenesis, Genetic
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Inference of Developmental Hierarchy and Functional States of Exhausted T Cells from Epigenetic Profiles with Deep Learning.
Journal of chemical information and modeling
Mar 28, 2024
Exhausted T cells are a key component of immune cells that play a crucial role in the immune response against cancer and influence the efficacy of immunotherapy. Accurate assessment and measurement of T-cell exhaustion (TEX) are critical for understa...
Deciphering the fibrotic process: mechanism of chronic radiation skin injury fibrosis.
Frontiers in immunology
Feb 15, 2024
This review explores the mechanisms of chronic radiation-induced skin injury fibrosis, focusing on the transition from acute radiation damage to a chronic fibrotic state. It reviewed the cellular and molecular responses of the skin to radiation, high...
Biologically informed deep learning for explainable epigenetic clocks.
Scientific reports
Jan 15, 2024
Ageing is often characterised by progressive accumulation of damage, and it is one of the most important risk factors for chronic disease development. Epigenetic mechanisms including DNA methylation could functionally contribute to organismal aging, ...
Epigenetic target identification strategy based on multi-feature learning.
Journal of biomolecular structure & dynamics
Oct 12, 2023
The identification of potential epigenetic targets for a known bioactive compound is essential and promising as more and more epigenetic drugs are used in cancer clinical treatment and the availability of chemogenomic data related to epigenetics incr...
Precision epigenetics provides a scalable pathway for improving coronary heart disease care globally.
Epigenomics
Sep 13, 2023
Coronary heart disease (CHD) is the world's leading cause of death. Up to 90% of all CHD deaths are preventable, but effective prevention of this mortality requires more scalable, precise methods for assessing CHD status and monitoring treatment resp...
EpiTEAmDNA: Sequence feature representation via transfer learning and ensemble learning for identifying multiple DNA epigenetic modification types across species.
Computers in biology and medicine
May 11, 2023
Methylation is a major DNA epigenetic modification for regulating the biological processes without altering the DNA sequence, and multiple types of DNA methylations have been discovered, including 6mA, 5hmC, and 4mC. Multiple computational approaches...
A Grid Search-Based Multilayer Dynamic Ensemble System to Identify DNA N4-Methylcytosine Using Deep Learning Approach.
Genes
Feb 25, 2023
DNA (Deoxyribonucleic Acid) N4-methylcytosine (4mC), a kind of epigenetic modification of DNA, is important for modifying gene functions, such as protein interactions, conformation, and stability in DNA, as well as for the control of gene expression ...
Laplacian Regularized Sparse Representation Based Classifier for Identifying DNA N4-Methylcytosine Sites via L-Matrix Norm.
IEEE/ACM transactions on computational biology and bioinformatics
Feb 3, 2023
N4-methylcytosine (4mC) is one of important epigenetic modifications in DNA sequences. Detecting 4mC sites is time-consuming. The computational method based on machine learning has provided effective help for identifying 4mC. To further improve the p...
MultiScale-CNN-4mCPred: a multi-scale CNN and adaptive embedding-based method for mouse genome DNA N4-methylcytosine prediction.
BMC bioinformatics
Jan 18, 2023
N4-methylcytosine (4mC) is an important epigenetic mechanism, which regulates many cellular processes such as cell differentiation and gene expression. The knowledge about the 4mC sites is a key foundation to exploring its roles. Due to the limitatio...
CFA: An explainable deep learning model for annotating the transcriptional roles of cis-regulatory modules based on epigenetic codes.
Computers in biology and medicine
Nov 29, 2022
Metazoa gene expression is controlled by modular DNA segments called cis-regulatory modules (CRMs). CRMs can convey promoter/enhancer/insulator roles, generating additional regulation layers in transcription. Experiments for understanding CRM roles a...
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