ArticleGenome biology2019
A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 61 citations in OpenAlex.
- Pan-cell type continuous chromatin state annotation of 1,698 epigenomes from the International Human Epigenome Consortium.Genome biology · 2026Article
- Endogenous fine-mapping and prioritization of functional regulatory elements in complex genetic loci.Cell genomics · 2025Article
- Epilogos: information-theoretic navigation of multi-tissue functional genomic annotations.bioRxiv : the preprint server for biology · 2025Article
- Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation.PLoS computational biology · 2024Article
- Genome wide clustering on integrated chromatin states and Micro-C contacts reveals chromatin interaction signatures.NAR genomics and bioinformatics · 2024Article
- Robust chromatin state annotation.Genome research · 2024Article
- Epigenomic insights into common human disease pathology.Cellular and molecular life sciences : CMLS · 2024Review
- A High-Throughput PIXUL-Matrix-Based Toolbox to Profile Frozen and Formalin-Fixed Paraffin-Embedded Tissues Multiomes.Laboratory investigation; a journal of technical methods and pathology · 2024Article
- SilenceREIN: seeking silencers on anchors of chromatin loops by deep graph neural networks.Briefings in bioinformatics · 2023Article
- Toward a comprehensive catalog of regulatory elements.Human genetics · 2023Review
- Evolution of Resistance to Irinotecan in Cancer Cells Involves Generation of Topoisomerase-Guided Mutations in Non-Coding Genome That Reduce the Chances of DNA Breaks.International journal of molecular sciences · 2023Article
- Managing the Steady State Chromatin Landscape by Nucleosome Dynamics.Annual review of biochemistry · 2022Review
- Continuous chromatin state feature annotation of the human epigenome.Bioinformatics (Oxford, England) · 2022Article
- GREEN-DB: a framework for the annotation and prioritization of non-coding regulatory variants from whole-genome sequencing data.Nucleic acids research · 2022Article
- Mouse genomic and cellular annotations.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Review
- Aristotle: stratified causal discovery for omics data.BMC bioinformatics · 2022Article
- Coupling high-throughput mapping with proteomics analysis delineates cis-regulatory elements at high resolution.Nucleic acids research · 2022Article
- Universal annotation of the human genome through integration of over a thousand epigenomic datasets.Genome biology · 2022Article
- Analysis of the landscape of human enhancer sequences in biological databases.Computational and structural biotechnology journal · 2022Article
- Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns.PLoS computational biology · 2021Review
Corrections and comments
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Authors and funding
6 authors at 5 institutions in 2 countries.
Funding
Abstract
Semi-automated genome annotation methods such as Segway take as input a set of genome-wide measurements such as of histone modification or DNA accessibility and output an annotation of genomic activity in the target cell type. Here we present annotations of 164 human cell types using 1615 data sets. To produce these annotations, we automated the label interpretation step to produce a fully automated annotation strategy. Using these annotations, we developed a measure of the importance of each genomic position called the "conservation-associated activity score." We further combined all annotations into a single, cell type-agnostic encyclopedia that catalogs all human regulatory elements.
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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.