An integrated encyclopedia of DNA elements in the human genome.

By ENCODEConsortium. 2012

1,034 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/003588890c332a4428744059acae88702a7f9cf2

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Citations in the corpus

Genome-wide analysis identifies 12 loci influencing human reproductive behavior (2016, unknown): “RegulomeDB integrates results from the Roadmap Epigenomics 26 and ENCODE 86 projects.”
Functional mapping and annotation of genetic associations with FUMA (2017, unknown): “9; see Supplementary Note 5 and Supplementary Fig.”
deepTools2: a next generation web server for deep-sequencing data analysis (2016, unknown): “Since deepTools employ a high level of parallelization for the computationally most expensive tasks, they are well suited to work with a large number of samples emerging from large-scale data production centers (12,13) or single-cell sequencing (14).”
Piercing the dark matter: bioinformatics of long-range sequencing and mapping (2018, background): “These second-generation technologies have enabled the sequencing of many new genomes and widespread resequencing efforts to analyse genomic diversity 2 and pathogenic variants 3 , as well as extensive studies of transcription, gene regulation and epigenetics in many species 4,5 .”
Comprehensive analysis of single cell ATAC-seq data with SnapATAC (2021, unknown): “…out unique functions. tightly Each cell lineage is established during development as a result of regulated spatiotemporal gene expression programs 1 , which are driven in part by sequence-speci ﬁ c transcription factors that interact with cis -regulatory sequences in a cell-type speci ﬁ c manner…”
Predicting variant deleteriousness in non-human species: applying the CADD approach in mouse (2018, unknown): “Histone modifications, transcription factor binding sites, DNAase Seq peaks and RNAseq expression measurements were downloaded from ENCODE [16].”
WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation (2013, background): “Although recent published data from the ENCODE Consortium [8] enabled to assign a bio-chemical function to the 80% of non-coding regions, the non-synonymous variations in the coding regions still represent the largest component of genetic variants annotated as “ pathogenic ” in the dbSNP database.”
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers (2014, unknown): “These are both “Tier 1” cell lines in the ENCODE project, allowing us to take advantage of abundant publicly available functional genomic data 24 .”
Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants (2013, unknown): “Our 10 cell type chromatin state maps replicated previous disease- and trait-associated SNP enrichment in cell-specific enhancer states (2, 7), including rheumatoid arthritis in GM12878 and colorectal cancer in HepG2 (Fig.”