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Index and biological spectrum of accessible DNA elements in the human genome

https://doi.org/10.1101/822510
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/s00467-010-1749-xopenalex-snapshot
Patterning and early cell lineage decisions in the developing kidney: the role of Pax genes
inferredcites →https://doi.org/10.1016/0092-8674(80)90631-5openalex-snapshot
Tissue-specific DNA cleavages in the globin chromatin domain introduced by DNAase I
inferredcites →https://doi.org/10.1016/0092-8674(81)90359-7openalex-snapshot
A 200 base pair region at the 5$prime; end of the chicken adult $beta;-globin gene is accessible to nuclease digestion
inferredcites →https://doi.org/10.1016/0092-8674(93)80052-gopenalex-snapshot
A 5′ element of the chicken β-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila
inferredcites →https://doi.org/10.1016/j.ajhg.2014.10.004openalex-snapshot
Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases
inferredcites →https://doi.org/10.1016/j.cell.2006.12.048openalex-snapshot
Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome
inferredcites →https://doi.org/10.1016/j.cell.2007.12.014openalex-snapshot
High-Resolution Mapping and Characterization of Open Chromatin across the Genome
inferredcites →https://doi.org/10.1016/j.cell.2013.07.020openalex-snapshot
Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes
inferredcites →https://doi.org/10.1016/j.cell.2018.01.029openalex-snapshot
The Human Transcription Factors
inferredcites →https://doi.org/10.1016/j.placenta.2003.10.014openalex-snapshot
Decreased Placental GCM1 (Glial Cells Missing) Gene Expression in Pre-eclampsia
inferredcites →https://doi.org/10.1016/j.tig.2018.07.003openalex-snapshot
Enter the Matrix: Factorization Uncovers Knowledge from Omics
inferredcites →https://doi.org/10.1016/s0168-9525(01)02366-6openalex-snapshot
CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease
inferredcites →https://doi.org/10.1038/286854a0openalex-snapshot
The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I
inferredcites →https://doi.org/10.1038/306809a0openalex-snapshot
DNase I hypersensitive sites in the chromatin of human μ immunoglobulin heavy-chain genes
inferredcites →https://doi.org/10.1038/44565openalex-snapshot
Learning the parts of objects by non-negative matrix factorization
inferredcites →https://doi.org/10.1038/nature07829openalex-snapshot
Histone modifications at human enhancers reflect global cell-type-specific gene expression
inferredcites →https://doi.org/10.1038/nature09906openalex-snapshot
Mapping and analysis of chromatin state dynamics in nine human cell types
inferredcites →https://doi.org/10.1038/nature11232openalex-snapshot
The accessible chromatin landscape of the human genome
inferredcites →https://doi.org/10.1038/nature13972openalex-snapshot
Conservation of trans-acting circuitry during mammalian regulatory evolution
inferredcites →https://doi.org/10.1038/nature14248openalex-snapshot
Integrative analysis of 111 reference human epigenomes
inferredcites →https://doi.org/10.1038/nature21683openalex-snapshot
KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks
inferredcites →https://doi.org/10.1038/nbt.2024openalex-snapshot
Targeted RNA sequencing reveals the deep complexity of the human transcriptome
inferredcites →https://doi.org/10.1038/nbt.3853openalex-snapshot
CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome
inferredcites →https://doi.org/10.1038/ng.759openalex-snapshot
Chromatin accessibility pre-determines glucocorticoid receptor binding patterns
inferredcites →https://doi.org/10.1038/nmeth.1937openalex-snapshot
Unsupervised pattern discovery in human chromatin structure through genomic segmentation
inferredcites →https://doi.org/10.1038/nmeth.3768openalex-snapshot
Genomic footprinting
inferredcites →https://doi.org/10.1038/nmeth890openalex-snapshot
Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays
inferredcites →https://doi.org/10.1038/nrg3017openalex-snapshot
Determinants and dynamics of genome accessibility
inferredcites →https://doi.org/10.1038/s41467-018-03751-6openalex-snapshot
Massive mining of publicly available RNA-seq data from human and mouse
inferredcites →https://doi.org/10.1038/s41586-018-0579-zopenalex-snapshot
The UK Biobank resource with deep phenotyping and genomic data
inferredcites →https://doi.org/10.1038/s41588-018-0081-4openalex-snapshot
Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types
inferredcites →https://doi.org/10.1038/s41588-018-0196-7openalex-snapshot
Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk
inferredcites →https://doi.org/10.1038/s41588-018-0316-4openalex-snapshot
Fast and accurate genomic analyses using genome graphs
inferredcites →https://doi.org/10.1073/pnas.0307540100openalex-snapshot
Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites
inferredcites →https://doi.org/10.1073/pnas.0407387101openalex-snapshot
Discovery of functional noncoding elements by digital analysis of chromatin structure
inferredcites →https://doi.org/10.1073/pnas.1016071107openalex-snapshot
Histone H3K27ac separates active from poised enhancers and predicts developmental state
inferredcites →https://doi.org/10.1093/nar/5.9.3157openalex-snapshot
DNAase footprinting a simple method for the detection of protein-DNA binding specificity
inferredcites →https://doi.org/10.1101/gad.1165104openalex-snapshot
p63 is the molecular switch for initiation of an epithelial stratification program
inferredcites →https://doi.org/10.1101/gr.100479.109openalex-snapshot
A CTCF-independent role for cohesin in tissue-specific transcription
inferredcites →https://doi.org/10.1101/gr.121541.111openalex-snapshot
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
inferredcites →https://doi.org/10.1101/gr.122382.111openalex-snapshot
Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions
inferredcites →https://doi.org/10.1126/science.1222794openalex-snapshot
Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
inferredcites →https://doi.org/10.1126/science.1246426openalex-snapshot
Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution
inferredcites →https://doi.org/10.1146/annurev.bi.57.070188.001111openalex-snapshot
NUCLEASE HYPERSENSITIVE SITES IN CHROMATIN
inferredcites →https://doi.org/10.1161/hypertensionaha.111.183939openalex-snapshot
Effects of Reduced Gcm1 Expression on Trophoblast Morphology, Fetoplacental Vascularity, and Pregnancy Outcomes in Mice
inferredcites →https://doi.org/10.1182/blood-2002-04-1104openalex-snapshot
Locus control regions
inferredcites →https://doi.org/10.1186/gb-2012-13-9-r51openalex-snapshot
The GENCODE pseudogene resource
inferredcites →https://doi.org/10.1186/s13059-020-02038-8openalex-snapshot
Personalized and graph genomes reveal missing signal in epigenomic data
inferredcites →https://doi.org/10.1371/journal.pgen.1002789openalex-snapshot
Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection
inferredcites →https://doi.org/10.1371/journal.pgen.1003504openalex-snapshot
The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements
inferredcites →https://doi.org/10.3390/jcdd3030026openalex-snapshot
The Function of the MEF2 Family of Transcription Factors in Cardiac Development, Cardiogenomics, and Direct Reprogramming
inferredcites →https://doi.org/10.4161/onci.22475openalex-snapshot
The IRF family of transcription factors

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.cell.2020.06.002openalex-snapshot
A Chromatin Accessibility Atlas of the Developing Human Telencephalon
inferred← citeshttps://doi.org/10.1038/s41586-020-2528-xopenalex-snapshot
Global reference mapping of human transcription factor footprints
inferred← citeshttps://doi.org/10.1038/s41588-024-01913-5openalex-snapshot
Population-specific putative causal variants shape quantitative traits
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab148openalex-snapshot
S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types
inferred← citeshttps://doi.org/10.1093/nar/gkaa349openalex-snapshot
Matrix factorization and transfer learning uncover regulatory biology across multiple single-cell ATAC-seq data sets
inferred← citeshttps://doi.org/10.1101/2020.06.26.172718openalex-snapshot
Atlas and developmental dynamics of mouse DNase I hypersensitive sites
inferred← citeshttps://doi.org/10.1101/2020.07.01.183004openalex-snapshot
Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
inferred← citeshttps://doi.org/10.1101/2022.06.29.498092openalex-snapshot
Dimensionality reduction and statistical modeling of scGET-seq data
inferred← citeshttps://doi.org/10.12688/f1000research.22731.1openalex-snapshot
Fast analysis of scATAC-seq data using a predefined set of genomic regions
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1008050openalex-snapshot
Cross-species regulatory sequence activity prediction
inferred← citeshttps://doi.org/10.1371/journal.pone.0231824openalex-snapshot
Investigating the effect of dependence between conditions with Bayesian Linear Mixed Models for motif activity analysis
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