ArticleGenome biology2022
Universal annotation of the human genome through integration of over a thousand epigenomic datasets.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
90 citing papers in PubMed, 1 synthesis or guideline pooled it.
- DNA methylation aging and transcriptomic studies in horses.Nature communications · 2022Pooled it
- Interactions of LINE-1 ORF1p with proteins and chromatin suggest a role in neuronal physiology.Life science alliance · 2026Article
- Whole-genome 5-hydroxymethylation profiling of human neurons for regulatory and biological insight.Epigenetics & chromatin · 2026Article
- Clonal hematopoiesis-associated DNMT3A mutations derepress bivalent Polycomb target genes and enhance macrophage migration.bioRxiv : the preprint server for biology · 2026Article
- Enhancing the performance and interpretability of epigenetic clocks.Nucleic acids research · 2026Article
- EpiATLAS - a reference for human epigenomic research.bioRxiv : the preprint server for biology · 2026Article
- Article
- Circulating DNA reveals nucleosome occupancy patterns that are associated with nucleosome-DNA affinity and are affected in cancer.Genome medicine · 2026Article
- Pervasive cryptic selection in the human noncoding genome.bioRxiv : the preprint server for biology · 2026Article
- Pan-cell type continuous chromatin state annotation of 1,698 epigenomes from the International Human Epigenome Consortium.Genome biology · 2026Article
- Causal inference clarifies the roles of background selection and mutation rate variation in shaping human genetic diversity.bioRxiv : the preprint server for biology · 2026Article
- A scalable Tn5-based method for genome-wide DNA methylation profiling in development and disease.Nature communications · 2026Article
- ChromBERT: A foundation model for learning interpretable representations for context-specific transcriptional regulatory networks.Cell genomics · 2026Article
- Article
- AP-1 promotes oncogenic transcription in lung cancer cells by bridging promoter-enhancer interactions.Cancer gene therapy · 2026Article
- chromIDEAS reveals epigenetic dynamics via multi-dimensional clustering of chromatin states.Nucleic acids research · 2026Article
- MissenseHMM: state-based annotations for missense variants through joint modeling of pathogenicity scores.bioRxiv : the preprint server for biology · 2026Article
- Learning a pairwise epigenomic and transcription factor binding association score across the human genome.Bioinformatics (Oxford, England) · 2026Article
- A Single-Cell and Spatial 3D Multi-omic Atlas of Developing Human Basal Ganglia and Inhibitory Neurons.bioRxiv : the preprint server for biology · 2026Article
- Chromatin state dynamics during the Plasmodium falciparum intraerythrocytic development cycle.BMC genomics · 2026Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
backgroundGenome-wide maps of chromatin marks such as histone modifications and open chromatin sites provide valuable information for annotating the non-coding genome, including identifying regulatory elements. Computational approaches such as ChromHMM have been applied to discover and annotate chromatin states defined by combinatorial and spatial patterns of chromatin marks within the same cell type. An alternative "stacked modeling" approach was previously suggested, where chromatin states are defined jointly from datasets of multiple cell types to produce a single universal genome annotation based on all datasets. Despite its potential benefits for applications that are not specific to one cell type, such an approach was previously applied only for small-scale specialized purposes. Large-scale applications of stacked modeling have previously posed scalability challenges.
resultsUsing a version of ChromHMM enhanced for large-scale applications, we apply the stacked modeling approach to produce a universal chromatin state annotation of the human genome using over 1000 datasets from more than 100 cell types, with the learned model denoted as the full-stack model. The full-stack model states show distinct enrichments for external genomic annotations, which we use in characterizing each state. Compared to per-cell-type annotations, the full-stack annotations directly differentiate constitutive from cell type-specific activity and is more predictive of locations of external genomic annotations.
conclusionsThe full-stack ChromHMM model provides a universal chromatin state annotation of the genome and a unified global view of over 1000 datasets. We expect this to be a useful resource that complements existing per-cell-type annotations for studying the non-coding human genome.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.