With hundreds of epigenomic maps, the opportunity arises to exploit the correlated nature of epigenetic signals, across both marks and samples, for large-scale prediction of additional datasets. Here, we undertake epigenome imputation by leveraging such correlations through an ensemble of regression trees. We impute 4,315 high-resolution signal maps, of which 26% are also experimentally observed. Imputed signal tracks show overall similarity to observed signals and surpass experimental datasets in consistency, recovery of gene annotations and enrichment for disease-associated variants. We use the imputed data to detect low-quality experimental datasets, to find genomic sites with unexpected epigenomic signals, to define high-priority marks for new experiments and to delineate chromatin states in 127 reference epigenomes spanning diverse tissues and cell types. Our imputed datasets provide the most comprehensive human regulatory region annotation to date, and our approach and the ChromImpute software constitute a useful complement to large-scale experimental mapping of epigenomic information.
Mutation of the PAX2 gene in a family with optic nerve colobomas, renal anomalies and vesicoureteral reflux
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology
Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods
Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser
HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease
A donor-specific epigenetic classifier for acute graft-versus-host disease severity in hematopoietic stem cell transplantation
Reprint of "Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction"
Epigenomic mapping and effect sizes of noncoding variants associated with psychotropic drug response
A glutamatergic network mediates lithium response in bipolar disorder as defined by epigenome pathway analysis
Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction
De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles
Across-Platform Imputation of DNA Methylation Levels Incorporating Nonlocal Information Using Penalized Functional Regression
GenomeRunner web server: regulatory similarity and differences define the functional impact of SNP sets
PINCAGE: probabilistic integration of cancer genomics data for perturbed gene identification and sample classification
Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN
Aberrant DNA Methylation in Human iPSCs Associates with MYC-Binding Motifs in a Clone-Specific Manner Independent of Genetics
DIRECTION: a machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes
Large-scale determination and characterization of cell type-specific regulatory elements in the human genome
Deep learning of the splicing (epi)genetic code reveals a novel candidate mechanism linking histone modifications to ESC fate decision
Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant
Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas.
Noncoding Genome-Wide Association Studies Variant for Obesity: Inroads Into Mechanism: An Overview From the AHA's Council on Functional Genomics and Translational Biology
Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks
A massively parallel reporter assay dissects the influence of chromatin structure on cis-regulatory activity
Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines
Integrative Genomics Analysis Identifies ACVR1B as a Candidate Causal Gene of Emphysema Distribution
Identification of an emphysema-associated genetic variant near TGFB2 with regulatory effects in lung fibroblasts
A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types
Disrupting MLV integrase:BET protein interaction biases integration into quiescent chromatin and delays but does not eliminate tumor activation in a MYC/Runx2 mouse model
GWAS for systemic sclerosis identifies multiple risk loci and highlights fibrotic and vasculopathy pathways.
Interactions between core histone marks and DNA methyltransferases predict DNA methylation patterns observed in human cells and tissues.
Annotations capturing cell type-specific TF binding explain a large fraction of disease heritability.
Leveraging mouse chromatin data for heritability enrichment informs common disease architecture and reveals cortical layer contributions to schizophrenia
Prediction and identification of transcriptional regulatory elements at the lung cancer-specific DKK1 locus
Identification of key genes by integrating DNA methylation and next-generation transcriptome sequencing for esophageal squamous cell carcinoma
Genome-wide association analysis of pain severity in dysmenorrhea identifies association at chromosome 1p13.2, near the nerve growth factor locus
An efficient method to transcription factor binding sites imputation via simultaneous completion of multiple matrices with positional consistency
A global transcriptional network connecting noncoding mutations to changes in tumor gene expression.
Maternal 5m CpG Imprints at thePARD6G-AS1 andGCSAML Differentially Methylated Regions Are Decoupled From Parent-of-Origin Expression Effects in Multiple Human Tissues
BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues
Discovery of the first genome-wide significant risk loci for attention deficit/hyperactivity disorder.
Early-Life Exposure to the Chinese Famine Is Associated with Higher Methylation Level in the INSR Gene in Later Adulthood.
DNA methylation analysis of multiple imprinted DMRs in Sotos syndrome reveals IGF2-DMR0 as a DNA methylation-dependent, P0 promoter-specific enhancer
Identification of recurrent combinatorial patterns of chromatin modifications at promoters across various tissue types
Incorporating Functional Annotations for Fine-Mapping Causal Variants in a Bayesian Framework Using Summary Statistics
A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies
Single-cell and single-molecule epigenomics to uncover genome regulation at unprecedented resolution
Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts
Reverse gene-environment interaction approach to identify variants influencing body-mass index in humans
Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples.
EPIGENE: genome-wide transcription unit annotation using a multivariate probabilistic model of histone modifications.
A computational tool (H-MAGMA) for improved prediction of brain-disorder risk genes by incorporating brain chromatin interaction profiles
Epigenomic annotation-based interpretation of genomic data: from enrichment analysis to machine learning
Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer's disease
AIControl: replacing matched control experiments with machine learning improves ChIP-seq peak identification
Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D
eRFSVM: a hybrid classifier to predict enhancers-integrating random forests with support vector machines
Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome.
Genome-Wide Association Study: Functional Variant rs2076295 Regulates Desmoplakin Expression in Airway Epithelial Cells.
Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations.
Prioritizing transcriptomic and epigenomic experiments using an optimization strategy that leverages imputed data.
3D promoter architecture re-organization during iPSC-derived neuronal cell differentiation implicates target genes for neurodevelopmental disorders.
Common schizophrenia risk variants are enriched in open chromatin regions of human glutamatergic neurons.
Identification of epigenetic memory candidates associated with gestational age at birth through analysis of methylome and transcriptional data.
Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities
Converging genetic and epigenetic drivers of paediatric acute lymphoblastic leukaemia identified by an information-theoretic analysis.
Sarcomere function activates a p53-dependent DNA damage response that promotes polyploidization and limits in vivo cell engraftment.
Advances in Genomic Discovery and Implications for Personalized Prevention and Medicine: Estonia as Example.
Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes.
Cell-type-specific effects of genetic variation on chromatin accessibility during human neuronal differentiation.
Zero-shot imputations across species are enabled through joint modeling of human and mouse epigenomics
Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.
STING Receptor Agonists
Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.
Chronic Fatigue Syndrome
Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.
Hereditary Sensory Autonomic Neuropathy
Hereditary Sensory Autonomic Neuropathies are a group of inherited neurodegenerative disorders characterized clinically by loss of sensation and autonomic dysfunction. Here is the latest research on these neuropathies.
Spatio-Temporal Regulation of DNA Repair
DNA repair is a complex process regulated by several different classes of enzymes, including ligases, endonucleases, and polymerases. This feed focuses on the spatial and temporal regulation that accompanies DNA damage signaling and repair enzymes and processes.
Glut1 deficiency, an autosomal dominant, genetic metabolic disorder associated with a deficiency of GLUT1, the protein that transports glucose across the blood brain barrier, is characterized by mental and motor developmental delays and infantile seizures. Follow the latest research on Glut1 deficiency with this feed.
Separation anxiety is a type of anxiety disorder that involves excessive distress and anxiety with separation. This may include separation from places or people to which they have a strong emotional connection with. It often affects children more than adults. Here is the latest research on separation anxiety.
KIF1A Associated Neurological Disorder
KIF1A associated neurological disorder (KAND) is a rare neurodegenerative condition caused by mutations in the KIF1A gene. KAND may present with a wide range and severity of symptoms including stiff or weak leg muscles, low muscle tone, a lack of muscle coordination and balance, and intellectual disability. Find the latest research on KAND here.
Regulation of Vocal-Motor Plasticity
Dopaminergic projections to the basal ganglia and nucleus accumbens shape the learning and plasticity of motivated behaviors across species including the regulation of vocal-motor plasticity and performance in songbirds. Discover the latest research on the regulation of vocal-motor plasticity here.