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A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1007/11732990_17openalex-snapshot
New Methods for Detecting Lineage-Specific Selection
inferredcites →https://doi.org/10.1007/s10539-014-9441-3openalex-snapshot
Junk or functional DNA? ENCODE and the function controversy
inferredcites →https://doi.org/10.1016/j.bbrc.2012.12.074openalex-snapshot
Can ENCODE tell us how much junk DNA we carry in our genome?
inferredcites →https://doi.org/10.1016/j.cell.2006.02.041openalex-snapshot
A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells
inferredcites →https://doi.org/10.1016/j.cell.2010.09.009openalex-snapshot
Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells
inferredcites →https://doi.org/10.1016/j.cub.2012.10.002openalex-snapshot
The C-value paradox, junk DNA and ENCODE
inferredcites →https://doi.org/10.1016/j.cub.2013.03.023openalex-snapshot
The ENCODE project: Missteps overshadowing a success
inferredcites →https://doi.org/10.1016/j.molcel.2012.08.019openalex-snapshot
Janus-Faced PIDD: A Sensor for DNA Damage-Induced Cell Death or Survival?
inferredcites →https://doi.org/10.1016/j.tibs.2010.02.009openalex-snapshot
Polycomb group protein-mediated repression of transcription
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/nature13415openalex-snapshot
Comparative analysis of metazoan chromatin organization
inferredcites →https://doi.org/10.1038/nature14248openalex-snapshot
Integrative analysis of 111 reference human epigenomes
inferredcites →https://doi.org/10.1038/nbt.1662openalex-snapshot
Discovery and characterization of chromatin states for systematic annotation of the human genome
inferredcites →https://doi.org/10.1038/nbt.3157openalex-snapshot
Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues
inferredcites →https://doi.org/10.1038/ng.2892openalex-snapshot
A general framework for estimating the relative pathogenicity of human genetic variants
inferredcites →https://doi.org/10.1038/ng.3477openalex-snapshot
A spectral approach integrating functional genomic annotations for coding and noncoding variants
inferredcites →https://doi.org/10.1038/nmeth.1937openalex-snapshot
Unsupervised pattern discovery in human chromatin structure through genomic segmentation
inferredcites →https://doi.org/10.1073/pnas.1318948111openalex-snapshot
Defining functional DNA elements in the human genome
inferredcites →https://doi.org/10.1093/bioinformatics/btg1036openalex-snapshot
Using hidden Markov models to analyze gene expression time course data
inferredcites →https://doi.org/10.1093/bioinformatics/btm096openalex-snapshot
Unsupervised segmentation of continuous genomic data
inferredcites →https://doi.org/10.1093/bioinformatics/btn335openalex-snapshot
Automated mapping of large-scale chromatin structure in ENCODE
inferredcites →https://doi.org/10.1093/bioinformatics/btv117openalex-snapshot
hiHMM: Bayesian non-parametric joint inference of chromatin state maps
inferredcites →https://doi.org/10.1093/bioinformatics/btx603openalex-snapshot
Segway 2.0: Gaussian mixture models and minibatch training
inferredcites →https://doi.org/10.1093/biomet/36.1-2.149openalex-snapshot
SYSTEMS OF FREQUENCY CURVES GENERATED BY METHODS OF TRANSLATION
inferredcites →https://doi.org/10.1093/nar/gks1284openalex-snapshot
Integrative annotation of chromatin elements from ENCODE data
inferredcites →https://doi.org/10.1093/nar/gkt1229openalex-snapshot
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
inferredcites →https://doi.org/10.1093/nar/gkw278openalex-snapshot
Jointly characterizing epigenetic dynamics across multiple human cell types
inferredcites →https://doi.org/10.1093/nar/gkx659openalex-snapshot
Accurate and reproducible functional maps in 127 human cell types via 2D genome segmentation
inferredcites →https://doi.org/10.1101/gr.080861.108openalex-snapshot
H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome
inferredcites →https://doi.org/10.1101/gr.152140.112openalex-snapshot
Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions
inferredcites →https://doi.org/10.1101/gr.173518.114openalex-snapshot
High-throughput functional testing of ENCODE segmentation predictions
inferredcites →https://doi.org/10.1101/gr.184341.114openalex-snapshot
Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression
inferredcites →https://doi.org/10.1101/gr.3577405openalex-snapshot
Distribution and intensity of constraint in mammalian genomic sequence
inferredcites →https://doi.org/10.1101/gr.6081407openalex-snapshot
Identification of higher-order functional domains in the human ENCODE regions
inferredcites →https://doi.org/10.1109/tpds.2007.70712openalex-snapshot
An Efficient Parallel Implementation of the Hidden Markov Methods for Genomic Sequence-Search on a Massively Parallel System
inferredcites →https://doi.org/10.1126/science.1225057openalex-snapshot
Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions
inferredcites →https://doi.org/10.1126/science.1233195openalex-snapshot
Comment on “Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions”
inferredcites →https://doi.org/10.1126/science.1233366openalex-snapshot
Response to Comment on “Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions”
inferredcites →https://doi.org/10.1186/1471-2105-14-s2-s4openalex-snapshot
An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs
inferredcites →https://doi.org/10.1186/1471-2105-14-s5-s4openalex-snapshot
Discovering and mapping chromatin states using a tree hidden Markov model
inferredcites →https://doi.org/10.1186/1877-6566-7-2openalex-snapshot
The extent of functionality in the human genome
inferredcites →https://doi.org/10.1186/gb-2006-7-s1-s4openalex-snapshot
GENCODE: producing a reference annotation for ENCODE
inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot
Model-based Analysis of ChIP-Seq (MACS)
inferredcites →https://doi.org/10.1186/s13059-014-0572-2openalex-snapshot
De novo assembly of bacterial transcriptomes from RNA-seq data
inferredcites →https://doi.org/10.1186/s13059-015-0621-5openalex-snapshot
The Ensembl Regulatory Build
inferredcites →https://doi.org/10.1186/s13059-015-0708-zopenalex-snapshot
Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome
inferredcites →https://doi.org/10.1198/106186002402openalex-snapshot
Exact Computation of the Observed Information Matrix for Hidden Markov Models
inferredcites →https://doi.org/10.1242/jcs.00493openalex-snapshot
An epigenetic road map for histone lysine methylation
inferredcites →https://doi.org/10.1371/journal.pgen.0020168openalex-snapshot
Forces Shaping the Fastest Evolving Regions in the Human Genome
inferredcites →https://doi.org/10.1371/journal.pone.0098122openalex-snapshot
A Bayesian Method to Incorporate Hundreds of Functional Characteristics with Association Evidence to Improve Variant Prioritization
inferredcites →https://doi.org/10.1371/journal.pone.0169249openalex-snapshot
Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN
inferredcites →https://doi.org/10.48550/arxiv.1201.0490openalex-snapshot
Scikit-learn: Machine Learning in Python
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.ajhg.2018.03.026openalex-snapshot
FUN-LDA: A Latent Dirichlet Allocation Model for Predicting Tissue-Specific Functional Effects of Noncoding Variation: Methods and Applications
inferred← citeshttps://doi.org/10.1016/j.inffus.2018.09.012openalex-snapshot
Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities
inferred← citeshttps://doi.org/10.1016/j.molcel.2018.06.044openalex-snapshot
Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty957openalex-snapshot
RT States: systematic annotation of the human genome using cell type-specific replication timing programs
inferred← citeshttps://doi.org/10.1101/069229openalex-snapshot
FUN-LDA: A LATENT DIRICHLET ALLOCATION MODEL FOR PREDICTING TISSUE-SPECIFIC FUNCTIONAL EFFECTS OF NONCODING VARIATION
inferred← citeshttps://doi.org/10.1101/155473openalex-snapshot
Chromatin accessibility dynamics of myogenesis at single cell resolution
inferred← citeshttps://doi.org/10.1101/2025.06.18.660301openalex-snapshot
Epilogos: information-theoretic navigation of multi-tissue functional genomic annotations
inferred← citeshttps://doi.org/10.1101/473017openalex-snapshot
Continuous chromatin state feature annotation of the human epigenome
inferred← citeshttps://doi.org/10.1101/gr.278343.123openalex-snapshot
Robust chromatin state annotation
inferred← citeshttps://doi.org/10.1186/s13059-020-01977-6openalex-snapshot
Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome
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