ArticleNature genetics2019
An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences.
Article in Nature genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 24 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
24 citing papers in PubMed, 1 synthesis or guideline pooled it.
- GhostKnockoff inference empowers identification of putative causal variants in genome-wide association studies.Nature communications · 2022Pooled it
- Integrative multi-cohort analysis of DNA methylation profiles for pancreatic ductal adenocarcinoma biomarker discovery and prognosis.Frontiers in bioinformatics · 2026Article
- Endogenous fine-mapping and prioritization of functional regulatory elements in complex genetic loci.Cell genomics · 2025Article
- Stratifying variant deleteriousness and trait-modulating effect under human recent adaptation using the FIND model.Genome biology · 2025Article
- Disease-specific prioritization of non-coding GWAS variants based on chromatin accessibility.HGG advances · 2024Article
- In silico generation and augmentation of regulatory variants from massively parallel reporter assay using conditional variational autoencoder.bioRxiv : the preprint server for biology · 2024Article
- Nitrogen sensing and regulatory networks: it's about time and space.The Plant cell · 2024Review
- VarCards2: an integrated genetic and clinical database for ACMG-AMP variant-interpretation guidelines in the human whole genome.Nucleic acids research · 2024Article
- Multiomics-integrated deep language model enables in silico genome-wide detection of transcription factor binding site in unexplored biosamples.Bioinformatics (Oxford, England) · 2024Article
- Performance Comparison of Computational Methods for the Prediction of the Function and Pathogenicity of Non-coding Variants.Genomics, proteomics & bioinformatics · 2023Article
- Transcription factor binding sites are frequently under accelerated evolution in primates.Nature communications · 2023Article
- TVAR: assessing tissue-specific functional effects of non-coding variants with deep learning.Bioinformatics (Oxford, England) · 2022Article
- Extreme purifying selection against point mutations in the human genome.Nature communications · 2022Article
- Exploiting deep transfer learning for the prediction of functional non-coding variants using genomic sequence.Bioinformatics (Oxford, England) · 2022Article
- VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases.Nucleic acids research · 2022Article
- Impact of Genetic Variation in Gene Regulatory Sequences: A Population Genomics Perspective.Frontiers in genetics · 2021Review
- Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations.Nature communications · 2020Article
- Ultrafast and scalable variant annotation and prioritization with big functional genomics data.Genome research · 2020Article
- Unified inference of missense variant effects and gene constraints in the human genome.PLoS genetics · 2020Article
- Annotations capturing cell type-specific TF binding explain a large fraction of disease heritability.Human molecular genetics · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
2 authors.
Funding
Abstract
Here we ask the question "How much information do epigenomic datasets provide about human genomic function?" We consider nine epigenomic features across 115 cell types and measure information about function as a reduction in entropy under a probabilistic evolutionary model fitted to human and nonhuman primate genomes. Several epigenomic features yield more information in combination than they do individually. We find that the entropy in human genetic variation predominantly reflects a balance between mutation and neutral drift. Our cell-type-specific FitCons scores reveal relationships among cell types and suggest that around 8% of nucleotide sites are constrained by natural selection.
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.