AIMC Topic: Epigenome

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Graph embedding and unsupervised learning predict genomic sub-compartments from HiC chromatin interaction data.

Nature communications Mar 3, 2020
Chromatin interaction studies can reveal how the genome is organized into spatially confined sub-compartments in the nucleus. However, accurately identifying sub-compartments from chromatin interaction data remains a challenge in computational biolog...
Genomics Cluster Analysis Unsupervised Machine Learning Gene Expression Markov Chains Epigenome Data Analysis Algorithms Reproducibility of Results Humans Neural Networks, Computer K562 Cells Computer Graphics Chromatin
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scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles.

Genome biology Feb 3, 2020
Simultaneous measurements of transcriptomic and epigenomic profiles in the same individual cells provide an unprecedented opportunity to understand cell fates. However, effective approaches for the integrative analysis of such data are lacking. Here,...
Genetic Heterogeneity Humans Gene Expression Profiling Unsupervised Machine Learning Transcriptome A549 Cells Single-Cell Analysis Epigenome Genomics
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The predictive power of profiling the DNA methylome in human health and disease.

Epigenomics Jun 1, 2025
Early and accurate diagnosis significantly improves the chances of disease survival. DNA methylation (5mC), the major DNA modification in the human genome, is now recognized as a biomarker of immense clinical potential. This is due to its ability to ...
DNA Methylation Epigenome Genome-Wide Association Study Humans Epigenesis, Genetic Epigenomics Machine Learning Biomarkers
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Methylomes Reveal Recent Evolutionary Changes in Populations of Two Plant Species.

Genome biology and evolution May 30, 2025
Plant DNA methylation changes occur hundreds to thousands of times faster than DNA mutations and can be transmitted transgenerationally, making them useful for studying population-scale patterns in clonal or selfing species. However, a state-of-the-a...
Polymorphism, Single Nucleotide DNA Methylation Genome, Plant Linkage Disequilibrium Arabidopsis Brachypodium Evolution, Molecular Epigenome Gene Frequency
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A Guide to MethylationToActivity: A Deep Learning Framework That Reveals Promoter Activity Landscapes from DNA Methylomes in Individual Tumors.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2023
Genome-wide DNA methylomes have contributed greatly to tumor detection and subclassification. However, interpreting the biological impact of the DNA methylome at the individual gene level remains a challenge. MethylationToActivity (M2A) is a pipeline...
Epigenome Child DNA Methylation DNA Humans Adult Neoplasms Deep Learning
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Merged Affinity Network Association Clustering: Joint multi-omic/clinical clustering to identify disease endotypes.

Cell reports Apr 13, 2021
Although clinical and laboratory data have long been used to guide medical practice, this information is rarely integrated with multi-omic data to identify endotypes. We present Merged Affinity Network Association Clustering (MANAclust), a coding-fre...
Transcriptome Case-Control Studies Adolescent Male Middle Aged Gene Expression Profiling Proteomics Cluster Analysis Unsupervised Machine Learning Child, Preschool Child Feces Atlases as Topic Humans Nasal Cavity Precision Medicine Female Adult Epigenome Asthma Datasets as Topic Gene Expression Regulation Benchmarking Microbiota Allergens
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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 ...
Histone Code Linkage Disequilibrium Genetic Diseases, Inborn Chromatin Immunoprecipitation Organ Specificity Polymorphism, Single Nucleotide Epigenomics Humans Molecular Sequence Annotation Models, Genetic Deep Learning Binding Sites Transcription Factors Epigenome Genome-Wide Association Study Causality Datasets as Topic
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EWAS Atlas: a curated knowledgebase of epigenome-wide association studies.

Nucleic acids research Jan 8, 2019
Epigenome-Wide Association Study (EWAS) has become increasingly significant in identifying the associations between epigenetic variations and different biological traits. In this study, we develop EWAS Atlas (http://bigd.big.ac.cn/ewas), a curated kn...
Data Curation Genome-Wide Association Study DNA Methylation Genetic Association Studies Knowledge Bases Epigenesis, Genetic Epigenome Databases, Genetic
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