AIMC Topic: Epigenomics

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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...
Epigenomics DNA Methylation Models, Statistical Neural Networks, Computer Machine Learning Sequence Analysis, RNA Humans Histone Code CCCTC-Binding Factor Transcription Elongation, Genetic Histones Binding Sites RNA Splice Sites
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Integrating single-cell multimodal epigenomic data using 1D convolutional neural networks.

Bioinformatics (Oxford, England) Dec 26, 2024
MOTIVATION: Recent experimental developments enable single-cell multimodal epigenomic profiling, which measures multiple histone modifications and chromatin accessibility within the same cell. Such parallel measurements provide exciting new opportuni...
Animals Mice Humans Convolutional Neural Networks Epigenomics Neural Networks, Computer Single-Cell Analysis
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LOGOWheat: deep learning-based prediction of regulatory effects for noncoding variants in wheats.

Briefings in bioinformatics Nov 22, 2024
Identifying the regulatory effects of noncoding variants presents a significant challenge. Recently, the accumulation of epigenomic profiling data in wheat has provided an opportunity to model the functional impacts of these variants. In this study, ...
Computational Biology Epigenomics Triticum Software Deep Learning Genetic Variation Genome, Plant
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A review of deep learning models for the prediction of chromatin interactions with DNA and epigenomic profiles.

Briefings in bioinformatics Nov 22, 2024
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...
Deep Learning Genomics Computational Biology Humans Chromatin Epigenesis, Genetic Epigenomics DNA
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Biomarkers of aging - current state of knowledge.

Casopis lekaru ceskych Jan 1, 2023
Aging is a process of gradual decline in the functional capacity of the human body that leads to a significant increase in the risk of death over time. Although it is a process universal to all animals, its rate is not the same. Biomarkers of aging a...
Epigenomics Humans Artificial Intelligence Biomarkers Animals Aging
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Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches.

Briefings in bioinformatics May 20, 2021
The multi-omics molecular characterization of cancer opened a new horizon for our understanding of cancer biology and therapeutic strategies. However, a tumor biopsy comprises diverse types of cells limited not only to cancerous cells but also to tum...
Genetic Heterogeneity Genomics Humans Computational Biology Epigenomics Machine Learning Algorithms Neoplasms Prognosis Gene Expression Profiling
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Predicting regulatory variants using a dense epigenomic mapped CNN model elucidated the molecular basis of trait-tissue associations.

Nucleic acids research Jan 11, 2021
Assessing the causal tissues of human complex diseases is important for the prioritization of trait-associated genetic variants. Yet, the biological underpinnings of trait-associated variants are extremely difficult to infer due to statistical noise ...
Datasets as Topic Organ Specificity Molecular Sequence Annotation Deep Learning Binding Sites Genome-Wide Association Study Linkage Disequilibrium Chromatin Immunoprecipitation Polymorphism, Single Nucleotide Genetic Diseases, Inborn Histone Code Humans Transcription Factors Epigenomics Causality Models, Genetic Epigenome
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Artificial Intelligence for Epigenetics: Towards Personalized Medicine.

Current medicinal chemistry Jan 1, 2021
Epigenetics is a field of biological sciences focused on the study of reversible, heritable changes in gene function, not due to modifications of the genomic sequence. These changes are the result of a complex cross-talk between several molecular mec...
Epigenomics Artificial Intelligence Humans Precision Medicine Genome Epigenesis, Genetic
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Graph convolutional networks for epigenetic state prediction using both sequence and 3D genome data.

Bioinformatics (Oxford, England) Dec 30, 2020
MOTIVATION: Predictive models of DNA chromatin profile (i.e. epigenetic state), such as transcription factor binding, are essential for understanding regulatory processes and developing gene therapies. It is known that the 3D genome, or spatial struc...
Neural Networks, Computer Epigenesis, Genetic Epigenomics Genome Chromatin
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Imputing missing RNA-sequencing data from DNA methylation by using a transfer learning-based neural network.

GigaScience Jul 1, 2020
BACKGROUND: Gene expression plays a key intermediate role in linking molecular features at the DNA level and phenotype. However, owing to various limitations in experiments, the RNA-seq data are missing in many samples while there exist high-quality ...
High-Throughput Nucleotide Sequencing Reproducibility of Results CpG Islands Machine Learning Epigenesis, Genetic Neoplasms Gene Expression Regulation Computational Biology Epigenomics Humans Algorithms DNA Methylation Neural Networks, Computer Prognosis
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