AIMC Topic: DNA Methylation

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[Construction and preliminary validation of machine learning predictive models for cervical cancer screening based on human DNA methylation].

Zhonghua zhong liu za zhi [Chinese journal of oncology] Feb 23, 2025
Using methylation characteristics of human genes to construct machine learning predictive models for screening cervical cancer and precancerous lesions. Human DNA methylation detection was performed on 224 cervical exfoliated cell specimens from th...
Papillomavirus Infections Support Vector Machine DNA Methylation Uterine Cervical Dysplasia Early Detection of Cancer Bayes Theorem Adult Uterine Cervical Neoplasms Middle Aged Machine Learning Algorithms Female Humans
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Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data.

Nucleic acids research Feb 8, 2025
Rates of transcription elongation vary within and across eukaryotic gene bodies. Here, we introduce new methods for predicting elongation rates from nascent RNA sequencing data. First, we devise a probabilistic model that predicts nucleotide-specific...
Histones Binding Sites RNA Splice Sites Transcription Elongation, Genetic Histone Code Humans Sequence Analysis, RNA DNA Methylation CCCTC-Binding Factor Neural Networks, Computer Epigenomics Models, Statistical Machine Learning
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Deep learning-based classifier for carcinoma of unknown primary using methylation quantitative trait loci.

Journal of neuropathology and experimental neurology Feb 1, 2025
Cancer of unknown primary (CUP) constitutes between 2% and 5% of human malignancies and is among the most common causes of cancer death in the United States. Brain metastases are often the first clinical presentation of CUP; despite extensive patholo...
Male Middle Aged Deep Learning DNA Methylation Retrospective Studies Female Aged Quantitative Trait Loci Neoplasms, Unknown Primary Humans
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Leveraging molecular-QTL co-association to predict novel disease-associated genetic loci using a graph convolutional neural network.

PloS one Jan 1, 2025
Genome-wide association studies (GWAS) have successfully uncovered numerous associations between genetic variants and disease traits to date. Yet, identifying significantly associated loci remains a considerable challenge due to the concomitant multi...
Humans Neural Networks, Computer Polymorphism, Single Nucleotide DNA Methylation CpG Islands Quantitative Trait Loci Convolutional Neural Networks Genome-Wide Association Study Genetic Predisposition to Disease
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Integrative analysis of epigenetic subtypes in acute myeloid Leukemia: A multi-center study combining machine learning for prognostic and therapeutic insights.

PloS one Jan 1, 2025
BACKGROUND: Acute Myeloid Leukemia (AML) exhibits significant heterogeneity in clinical outcomes, yet current prognostic stratification systems based on genetic alterations alone cannot fully capture this complexity. This study aimed to develop an in...
Machine Learning Prognosis Female Aged Humans Transcriptome Male Epigenesis, Genetic Middle Aged DNA Methylation Gene Expression Profiling Mutation Adult Tumor Microenvironment Leukemia, Myeloid, Acute
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HD-6mAPred: a hybrid deep learning approach for accurate prediction of N6-methyladenine sites in plant species.

PeerJ Jan 1, 2025
BACKGROUND: N6-methyladenine (6mA) is an important DNA methylation modification that serves a crucial function in various biological activities. Accurate prediction of 6mA sites is essential for elucidating its biological function and underlying mech...
Deep Learning DNA Methylation DNA, Plant Arabidopsis Neural Networks, Computer Oryza Adenine Adenosine
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GD-Net: An Integrated Multimodal Information Model Based on Deep Learning for Cancer Outcome Prediction and Informative Feature Selection.

Journal of cellular and molecular medicine Dec 1, 2024
Multimodal information provides valuable resources for cancer prognosis and survival prediction. However, the computational integration of this heterogeneous data information poses significant challenges due to the complex interactions between molecu...
Neoplasms Deep Learning Liver Neoplasms DNA Methylation MicroRNAs Computational Biology Gene Expression Regulation, Neoplastic Algorithms Prognosis Biomarkers, Tumor Humans
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Inferring tumor purity using multi-omics data based on a uniform machine learning framework MoTP.

Briefings in bioinformatics Nov 22, 2024
Existing algorithms for assessing tumor purity are limited to a single omics data, such as gene expression, somatic copy number variations, somatic mutations, and DNA methylation. Here we proposed the machine learning Multi-omics Tumor Purity predict...
Humans DNA Methylation DNA Copy Number Variations Algorithms Bayes Theorem Neoplasms Genomics Neural Networks, Computer Computational Biology Machine Learning Multiomics
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Raman-based machine-learning platform reveals unique metabolic differences between IDHmut and IDHwt glioma.

Neuro-oncology Nov 4, 2024
BACKGROUND: Formalin-fixed, paraffin-embedded (FFPE) tissue slides are routinely used in cancer diagnosis, clinical decision-making, and stored in biobanks, but their utilization in Raman spectroscopy-based studies has been limited due to the backgro...
Mutation Isocitrate Dehydrogenase Brain Neoplasms Spectrum Analysis, Raman Humans Machine Learning Glioma Biomarkers, Tumor DNA Methylation
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Precision DNA methylation typing via hierarchical clustering of Nanopore current signals and attention-based neural network.

Briefings in bioinformatics Sep 23, 2024
Decoding DNA methylation sites through nanopore sequencing has emerged as a cutting-edge technology in the field of DNA methylation research, as it enables direct sequencing of native DNA molecules without the need for prior enzymatic or chemical tre...
Nanopores Nanopore Sequencing Humans DNA Methylation Neural Networks, Computer Cluster Analysis Sequence Analysis, DNA DNA
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