ENCODE project cohort

Aliases

ENCODE, ENCODE project

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Mentioned in (45)

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)
• 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)
• Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma. (2019)
• 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)
• 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)
• PGBD5 promotes site-specific oncogenic mutations in human tumors. (2017)
• Fast and Accurate Genomic Analyses using Genome Graphs (2017)
• 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)
• Profiling tissue-resident T cell repertoires by RNA sequencing. (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)
• 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)
• 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)
• Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. (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)
• 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)

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