ENCODE project cohort
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Related entities (11)
| Subject | Relation | Object | p-value | Evidence |
|---|---|---|---|---|
| ENCODE project | associated_with | associated SNPs | — | 1 |
| ENCODE project | targets | common variants | — | 1 |
| ENCODE project | associated_with | complex traits | — | 1 |
| ENCODE project | associated_with | Gm12878 | — | 1 |
| ENCODE project | associated_with | GWAS | — | 1 |
| ENCODE project | interacts_with | HapMap | — | 2 |
| EP300 | associated_with | ENCODE project | — | 1 |
| Gm12878 | associated_with | ENCODE project | — | 1 |
| H3K27ac | associated_with | ENCODE project | — | 1 |
| H3K4me1 | associated_with | ENCODE project | — | 1 |
| H3K4me2 | associated_with | ENCODE project | — | 1 |
Mentioned in (70)
Papers in which this entity is mentioned.
- Multi-omic quantitative trait loci link tandem repeat size variation to gene regulation in human brain. (2025)
- Functional analysis of cancer-associated germline risk variants. (2025)
- Three-dimensional genome landscape of primary human cancers. (2025)
- Tracing the evolution of single-cell 3D genomes in Kras-driven cancers. (2025)
- Synchronized long-read genome, methylome, epigenome and transcriptome profiling resolve a Mendelian condition. (2025)
- Nucleotide Transformer: building and evaluating robust foundation models for human genomics. (2025)
- Transcription start sites experience a high influx of heritable variants fueled by early development. (2025)
- Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy. (2024)
- BioPipeline Creator-a user-friendly Java-based GUI for managing and customizing biological data pipelines. (2024)
- Machine-guided design of cell-type-targeting cis-regulatory elements. (2024)
- SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms. (2024)
- BioPipeline Creator-a user-friendly Java-based GUI for managing and customizing biological data pipelines. (2024)
- A DNA methylation atlas of normal human cell types. (2023)
- DNA methylation and general psychopathology in childhood: an epigenome-wide meta-analysis from the PACE consortium. (2023)
- Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA. (2022)
- At the dawn: cell-free DNA fragmentomics and gene regulation. (2022)
- DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers. (2020)
- Reciprocal monoallelic expression of ASAR lncRNA genes controls replication timing of human chromosome 6. (2020)
- Defining the Genetic, Genomic, Cellular, and Diagnostic Architectures of Psychiatric Disorders. (2019)
- CommonMind Consortium provides transcriptomic and epigenomic data for Schizophrenia and Bipolar Disorder. (2019)
- The ENCODE Blacklist: Identification of Problematic Regions of the Genome. (2019)
- Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma. (2019)
- Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types. (2018)
- Sequence, Structure, and Context Preferences of Human RNA Binding Proteins. (2018)
- A compendium of conserved cleavage and polyadenylation events in mammalian genes. (2018)
- Watchdog - a workflow management system for the distributed analysis of large-scale experimental data. (2018)
- Accurate Recycling of Parental Histones Reproduces the Histone Modification Landscape during DNA Replication. (2018)
- Patterns and mechanisms of structural variations in human cancer. (2018)
- Nanopore Sequencing Reveals High-Resolution Structural Variation in the Cancer Genome (2017)
- Statistical algorithms improve accuracy of gene fusion detection. (2017)
- Ensembl 2017. (2017)
- Network analysis identifies chromosome intermingling regions as regulatory hotspots for transcription. (2017)
- PGBD5 promotes site-specific oncogenic mutations in human tumors. (2017)
- Fast and Accurate Genomic Analyses using Genome Graphs (2017)
- Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. (2016)
- Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin. (2016)
- The PsychENCODE project. (2015)
- Tools and best practices for data processing in allelic expression analysis. (2015)
- Recurrent somatic mutations in regulatory regions of human cancer genomes. (2015)
- A gene-based association method for mapping traits using reference transcriptome data. (2015)
- Genomic influences on alcohol problems in a population-based sample of young adults. (2015)
- Profiling tissue-resident T cell repertoires by RNA sequencing. (2015)
- Interindividual methylomic variation across blood, cortex, and cerebellum: implications for epigenetic studies of neurological and neuropsychiatric phenotypes. (2015)
- Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser. (2015)
- The landscape of long noncoding RNAs in the human transcriptome. (2015)
- Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data. (2015)
- An atlas of active enhancers across human cell types and tissues. (2014)
- Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain. (2014)
- Genome-wide analysis of noncoding regulatory mutations in cancer. (2014)
- A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. (2014)
- SRF regulates craniofacial development through selective recruitment of MRTF cofactors by PDGF signaling. (2014)
- Common DNA methylation alterations in multiple brain regions in autism. (2014)
- Normalization of RNA-seq data using factor analysis of control genes or samples. (2014)
- EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma. (2014)
- DNA methylation contributes to natural human variation. (2013)
- Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. (2013)
- The Growing Importance of CNVs: New Insights for Detection and Clinical Interpretation. (2013)
- ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. (2012)
- Landscape of transcription in human cells. (2012)
- Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. (2012)
- Annotation of functional variation in personal genomes using RegulomeDB. (2012)
- GENCODE: the reference human genome annotation for The ENCODE Project. (2012)
- An integrated encyclopedia of DNA elements in the human genome. (2012)
- Differential expression in RNA-seq: a matter of depth. (2011)
- An integrated ChIP-seq analysis platform with customizable workflows. (2011)
- Genetics of psychiatric disorders methods: molecular approaches. (2010)
- A groupwise association test for rare mutations using a weighted sum statistic. (2009)
- Marker selection for genetic case-control association studies. (2009)
Merged raw entities (2)
All extracted name/type variants the normalize job merged into this entity. Use this to spot wrong merges, or aliases that should be split off.
| Raw name | Type | Papers | Mentions |
|---|---|---|---|
| encode | cohort | 53 | 93 |
| encode project | cohort | 24 | 27 |