PROMINENT: AN INTERPRETABLE DEEP LEARNING METHOD TO PREDICT PHENOTYPES USING DNA METHYLATION

L Zhang - 2024 - d-scholarship.pitt.edu
DNA methylation (DNAm) is an epigenetic mark that regulates genome function and is
important for normal development in mammals. To understand the complex interplay …

MLACNN: an attention mechanism-based CNN architecture for predicting genome-wide DNA methylation

JG Bai, H Yang, CD Wu - Theory in Biosciences, 2023 - Springer
Methylation is an important epigenetic regulation of methylation genes that plays a crucial
role in regulating biological processes. While traditional methods for detecting methylation in …

DeepMethyGene: a deep-learning model to predict gene expression using DNA methylations

W Li, S Wang, T Huang - 2024 - researchsquare.com
Gene expression influences various physiological functions and plays a critical role in
disease progression. One of the key mechanisms governing gene expression is DNA …

Predicting locus-specific DNA methylation based on deep neural network

B Ma, J Dong, S Zhang, H Yan, J Pan, C Li… - Bio-Inspired Computing …, 2021 - Springer
The next generation sequencing technologies have enabled DNA methylation levels to be
assayed at single-base resolution in the whole genome, but this method is relatively …

MethylNet: an automated and modular deep learning approach for DNA methylation analysis

JJ Levy, AJ Titus, CL Petersen, Y Chen, LA Salas… - BMC …, 2020 - Springer
Background DNA methylation (DNAm) is an epigenetic regulator of gene expression
programs that can be altered by environmental exposures, aging, and in pathogenesis …

iDNA-OpenPrompt: OpenPrompt learning model for identifying DNA methylation

X Yu, J Ren, H Long, R Zeng, G Zhang, A Bilal… - Frontiers in …, 2024 - frontiersin.org
Introduction: DNA methylation is a critical epigenetic modification involving the addition of a
methyl group to the DNA molecule, playing a key role in regulating gene expression without …

iDNA-ABT: advanced deep learning model for detecting DNA methylation with adaptive features and transductive information maximization

Y Yu, W He, J Jin, G Xiao, L Cui, R Zeng, L Wei - Bioinformatics, 2021 - academic.oup.com
Motivation DNA methylation plays an important role in epigenetic modification, the
occurrence, and the development of diseases. Therefore, identification of DNA methylation …

NCAE: data-driven representations using a deep network-coherent DNA methylation autoencoder identify robust disease and risk factor signatures

D Martínez-Enguita, SK Dwivedi… - Briefings in …, 2023 - academic.oup.com
Precision medicine relies on the identification of robust disease and risk factor signatures
from omics data. However, current knowledge-driven approaches may overlook novel or …

Predicting the impact of non-coding variants on DNA methylation

H Zeng, DK Gifford - Nucleic acids research, 2017 - academic.oup.com
DNA methylation plays a crucial role in the establishment of tissue-specific gene expression
and the regulation of key biological processes. However, our present inability to predict the …

[PDF][PDF] Discovering DNA motifs and genomic variants associated with DNA methylation

H Zeng, DK Gifford - bioRxiv, 2016 - pdfs.semanticscholar.org
DNA methylation plays a crucial role in establishing tissue-specific gene expression.
However, our incomplete understanding of the cis elements that regulate DNA methylation …