Idan Gabdank

The paper describes a collaborative submission model for building high-quality single-cell genomics data resources, emphasizing partnership between contributors and curators to improve metadata quality and resource scalability.

The paper develops a scalable workflow to reclassify variants of uncertain significance using experimental and predictive evidence, resolving 75% of VUS in 40 genes.

Long-read sequencing of 81 human and mouse samples yields 200,000 full-length transcripts plus a triplet framework that separates promoter choice, splicing and 3' end use across tissues.

ENCODE's containerised Workflow Description Language pipelines for ChIP-seq, ATAC-seq, DNase-seq, RNA-seq variants, Hi-C and bisulfite sequencing run on cloud or local clusters, with documented compute costs and provenance.

The paper introduces the EN-TEx resource, which provides personal epigenomes and variant-impact models across multiple tissues, revealing allele-specific loci and their associations with GWAS loci.

The paper reports 109 non-coding CRISPR screens analyzing 13.3Mb of the genome, identifies CRE-gene links, and provides guidelines and tools for screening non-coding regulatory elements.

The paper identifies and characterizes endogenous circular DNA (eccDNA) in C. elegans and human cells using unbiased methods, showing eccDNA originates from both coding and noncoding regions.

The paper introduces SnoVault, a metadata storage system, and encodeD, a tool for genomic data storage, both designed for the ENCODE project's data management needs.